Starting phenix.real_space_refine on Wed Feb 14 17:28:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4h_31452/02_2024/7f4h_31452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4h_31452/02_2024/7f4h_31452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4h_31452/02_2024/7f4h_31452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4h_31452/02_2024/7f4h_31452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4h_31452/02_2024/7f4h_31452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4h_31452/02_2024/7f4h_31452_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 65 5.16 5 C 6249 2.51 5 N 1708 2.21 5 O 1826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9849 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "A" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1942 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "N" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 963 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2590 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2054 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Classifications: {'peptide': 12} Modifications used: {'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1, 'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9849 At special positions: 0 Unit cell: (117.04, 97.185, 129.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 65 16.00 O 1826 8.00 N 1708 7.00 C 6249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 267 " - pdb=" SG CYS R 273 " distance=2.04 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: 4.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN F 7 " Number of C-beta restraints generated: 2362 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 33.2% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'A' and resid 14 through 39 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 253 through 278 removed outlier: 3.906A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 349 removed outlier: 4.006A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'R' and resid 42 through 65 Processing helix chain 'R' and resid 67 through 69 No H-bonds generated for 'chain 'R' and resid 67 through 69' Processing helix chain 'R' and resid 72 through 102 Processing helix chain 'R' and resid 110 through 147 removed outlier: 3.612A pdb=" N LEU R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 155 removed outlier: 5.102A pdb=" N HIS R 153 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 181 Processing helix chain 'R' and resid 186 through 225 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix removed outlier: 3.656A pdb=" N VAL R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 298 removed outlier: 3.640A pdb=" N ILE R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN R 279 " --> pdb=" O CYS R 275 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE R 280 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 303 through 310 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.009A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= C, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.659A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.622A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.783A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.841A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.585A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.795A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.554A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.917A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.359A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 155 through 160 479 hydrogen bonds defined for protein. 1335 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: 3.19 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 2962 1.34 - 1.47: 2757 1.47 - 1.61: 4239 1.61 - 1.74: 0 1.74 - 1.88: 91 Bond restraints: 10049 Sorted by residual: bond pdb=" N GLY B 341 " pdb=" CA GLY B 341 " ideal model delta sigma weight residual 1.449 1.496 -0.047 1.45e-02 4.76e+03 1.04e+01 bond pdb=" CB THR S 78 " pdb=" OG1 THR S 78 " ideal model delta sigma weight residual 1.433 1.398 0.035 1.60e-02 3.91e+03 4.90e+00 bond pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " ideal model delta sigma weight residual 1.808 1.880 -0.072 3.30e-02 9.18e+02 4.78e+00 bond pdb=" CB LYS R 310 " pdb=" CG LYS R 310 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.81e+00 bond pdb=" N PHE A 345 " pdb=" CA PHE A 345 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.26e-02 6.30e+03 3.79e+00 ... (remaining 10044 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.42: 208 106.42 - 113.52: 5493 113.52 - 120.62: 4092 120.62 - 127.72: 3726 127.72 - 134.81: 98 Bond angle restraints: 13617 Sorted by residual: angle pdb=" O ASN B 340 " pdb=" C ASN B 340 " pdb=" N GLY B 341 " ideal model delta sigma weight residual 122.72 115.74 6.98 1.33e+00 5.65e-01 2.75e+01 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C THR N 28 " pdb=" N PHE N 29 " pdb=" CA PHE N 29 " ideal model delta sigma weight residual 120.82 126.35 -5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 121.54 -8.36 2.37e+00 1.78e-01 1.24e+01 angle pdb=" CA ASP B 76 " pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " ideal model delta sigma weight residual 112.60 115.89 -3.29 1.00e+00 1.00e+00 1.08e+01 ... (remaining 13612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5560 17.79 - 35.58: 344 35.58 - 53.37: 43 53.37 - 71.16: 14 71.16 - 88.95: 11 Dihedral angle restraints: 5972 sinusoidal: 2307 harmonic: 3665 Sorted by residual: dihedral pdb=" CA THR S 172 " pdb=" C THR S 172 " pdb=" N TYR S 173 " pdb=" CA TYR S 173 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1018 0.056 - 0.112: 389 0.112 - 0.168: 124 0.168 - 0.224: 16 0.224 - 0.281: 3 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA TYR S 173 " pdb=" N TYR S 173 " pdb=" C TYR S 173 " pdb=" CB TYR S 173 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA MET S 192 " pdb=" N MET S 192 " pdb=" C MET S 192 " pdb=" CB MET S 192 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1547 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 340 " -0.046 2.00e-02 2.50e+03 8.94e-02 8.00e+01 pdb=" C ASN B 340 " 0.155 2.00e-02 2.50e+03 pdb=" O ASN B 340 " -0.058 2.00e-02 2.50e+03 pdb=" N GLY B 341 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 72 " -0.341 9.50e-02 1.11e+02 1.53e-01 1.55e+01 pdb=" NE ARG N 72 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG N 72 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG N 72 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG N 72 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 173 " -0.017 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR S 173 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR S 173 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR S 173 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR S 173 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR S 173 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR S 173 " 0.030 2.00e-02 2.50e+03 pdb=" OH TYR S 173 " -0.048 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1801 2.78 - 3.31: 10025 3.31 - 3.84: 17772 3.84 - 4.37: 21674 4.37 - 4.90: 36054 Nonbonded interactions: 87326 Sorted by model distance: nonbonded pdb=" O DPN F 7 " pdb="CA CA R 501 " model vdw 2.253 2.510 nonbonded pdb=" OD1 ASP R 121 " pdb="CA CA R 501 " model vdw 2.255 2.510 nonbonded pdb=" OE2 GLU A 314 " pdb=" NZ LYS N 65 " model vdw 2.265 2.520 nonbonded pdb=" OD2 ASP R 121 " pdb="CA CA R 501 " model vdw 2.298 2.510 nonbonded pdb=" OE2 GLU A 344 " pdb=" NH1 ARG A 347 " model vdw 2.303 2.520 ... (remaining 87321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.280 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.060 Find NCS groups from input model: 0.310 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:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.010 0.072 10049 Z= 0.637 Angle : 1.042 8.359 13617 Z= 0.626 Chirality : 0.064 0.281 1550 Planarity : 0.011 0.153 1730 Dihedral : 12.812 88.946 3595 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.58 (0.22), residues: 1240 helix: 0.04 (0.22), residues: 404 sheet: -0.43 (0.29), residues: 285 loop : -0.52 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.010 TRP A 281 HIS 0.020 0.006 HIS R 209 PHE 0.035 0.008 PHE N 68 TYR 0.048 0.009 TYR S 173 ARG 0.027 0.005 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 33 LYS cc_start: 0.8573 (ttmt) cc_final: 0.7917 (tttt) REVERT: N 39 GLN cc_start: 0.8754 (tt0) cc_final: 0.8296 (tt0) REVERT: N 53 GLN cc_start: 0.8504 (pm20) cc_final: 0.8091 (pm20) REVERT: B 6 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8888 (tm-30) REVERT: B 259 GLN cc_start: 0.7109 (mt0) cc_final: 0.6874 (mt0) REVERT: B 292 PHE cc_start: 0.8777 (m-10) cc_final: 0.8463 (m-10) REVERT: B 325 MET cc_start: 0.8337 (mmt) cc_final: 0.7789 (mmm) REVERT: R 68 ASN cc_start: 0.7906 (m-40) cc_final: 0.7630 (m-40) REVERT: R 262 THR cc_start: 0.8466 (m) cc_final: 0.8192 (p) REVERT: S 223 ASP cc_start: 0.8515 (m-30) cc_final: 0.8280 (m-30) REVERT: S 244 LYS cc_start: 0.9083 (tttm) cc_final: 0.8811 (ttmm) outliers start: 0 outliers final: 1 residues processed: 287 average time/residue: 1.3929 time to fit residues: 423.9385 Evaluate side-chains 178 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN A 292 ASN A 294 GLN N 74 ASN N 123 GLN B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN S 13 GLN S 39 GLN S 179 GLN S 183 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10049 Z= 0.206 Angle : 0.640 7.192 13617 Z= 0.342 Chirality : 0.043 0.264 1550 Planarity : 0.004 0.043 1730 Dihedral : 5.693 30.486 1384 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.35 % Allowed : 12.70 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.70 (0.24), residues: 1240 helix: 1.74 (0.24), residues: 407 sheet: -0.44 (0.27), residues: 309 loop : 0.18 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.022 0.002 PHE R 45 TYR 0.014 0.002 TYR N 32 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 22 GLU cc_start: 0.7986 (tt0) cc_final: 0.7758 (mt-10) REVERT: G 38 MET cc_start: 0.7854 (ptp) cc_final: 0.7467 (ttm) REVERT: G 42 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 27 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7503 (mt-10) REVERT: N 33 LYS cc_start: 0.8546 (ttmt) cc_final: 0.7874 (tttt) REVERT: N 39 GLN cc_start: 0.8818 (tt0) cc_final: 0.8465 (tt0) REVERT: N 53 GLN cc_start: 0.8340 (pm20) cc_final: 0.7908 (pm20) REVERT: N 73 ASP cc_start: 0.7949 (t0) cc_final: 0.7304 (t0) REVERT: N 76 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8403 (mtmm) REVERT: B 10 GLU cc_start: 0.8573 (tp30) cc_final: 0.8028 (tp30) REVERT: B 243 THR cc_start: 0.8451 (p) cc_final: 0.8144 (p) REVERT: B 325 MET cc_start: 0.8166 (mmt) cc_final: 0.7929 (mmm) REVERT: R 114 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7464 (tm-30) REVERT: R 226 LYS cc_start: 0.7263 (mmmt) cc_final: 0.7047 (mmmt) REVERT: S 73 ASP cc_start: 0.7769 (t0) cc_final: 0.7398 (t0) REVERT: S 179 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: S 186 GLN cc_start: 0.8249 (pt0) cc_final: 0.8000 (pt0) REVERT: S 218 ARG cc_start: 0.8018 (ptp-110) cc_final: 0.7469 (mtm110) REVERT: S 223 ASP cc_start: 0.8358 (m-30) cc_final: 0.7768 (m-30) outliers start: 25 outliers final: 8 residues processed: 207 average time/residue: 1.3580 time to fit residues: 299.3017 Evaluate side-chains 180 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.0010 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 118 ASN S 39 GLN S 77 ASN S 179 GLN S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10049 Z= 0.219 Angle : 0.576 7.182 13617 Z= 0.306 Chirality : 0.042 0.250 1550 Planarity : 0.004 0.035 1730 Dihedral : 5.107 26.358 1382 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.63 % Allowed : 13.64 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.94 (0.24), residues: 1240 helix: 1.95 (0.25), residues: 412 sheet: -0.37 (0.28), residues: 309 loop : 0.34 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.002 PHE R 45 TYR 0.013 0.001 TYR N 32 ARG 0.012 0.001 ARG S 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7916 (ptp-110) REVERT: G 26 ASP cc_start: 0.8197 (p0) cc_final: 0.7867 (p0) REVERT: G 38 MET cc_start: 0.7764 (ptp) cc_final: 0.7429 (ttm) REVERT: N 33 LYS cc_start: 0.8614 (ttmt) cc_final: 0.7941 (tttt) REVERT: N 39 GLN cc_start: 0.8842 (tt0) cc_final: 0.8537 (tt0) REVERT: N 53 GLN cc_start: 0.8406 (pm20) cc_final: 0.7997 (pm20) REVERT: N 73 ASP cc_start: 0.7963 (t0) cc_final: 0.7483 (t0) REVERT: B 10 GLU cc_start: 0.8784 (tp30) cc_final: 0.8088 (tp30) REVERT: B 59 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: B 61 MET cc_start: 0.7936 (ptm) cc_final: 0.7715 (ppp) REVERT: B 78 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8551 (ttmm) REVERT: B 243 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8266 (p) REVERT: B 258 ASP cc_start: 0.8046 (t0) cc_final: 0.7405 (t0) REVERT: B 325 MET cc_start: 0.8336 (mmt) cc_final: 0.8135 (mmm) REVERT: R 114 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7416 (tm-30) REVERT: R 278 LYS cc_start: 0.9207 (mmpt) cc_final: 0.8562 (mtmt) REVERT: R 307 ARG cc_start: 0.7292 (tpp-160) cc_final: 0.6738 (tpm170) REVERT: S 73 ASP cc_start: 0.7786 (t0) cc_final: 0.7527 (t0) REVERT: S 77 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8369 (m110) REVERT: S 218 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7649 (ptp-110) outliers start: 28 outliers final: 6 residues processed: 201 average time/residue: 1.3504 time to fit residues: 289.0531 Evaluate side-chains 186 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 218 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 292 ASN N 84 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 ASN S 39 GLN S 179 GLN S 183 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10049 Z= 0.232 Angle : 0.566 6.880 13617 Z= 0.299 Chirality : 0.042 0.251 1550 Planarity : 0.004 0.036 1730 Dihedral : 4.883 23.148 1382 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.63 % Allowed : 16.46 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.99 (0.24), residues: 1240 helix: 1.98 (0.25), residues: 410 sheet: -0.44 (0.27), residues: 324 loop : 0.49 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.002 PHE R 45 TYR 0.012 0.001 TYR N 32 ARG 0.006 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 ASP cc_start: 0.8183 (p0) cc_final: 0.7645 (p0) REVERT: G 42 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7613 (mm-30) REVERT: A 356 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7651 (mtm110) REVERT: N 33 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8010 (tttt) REVERT: N 39 GLN cc_start: 0.8942 (tt0) cc_final: 0.8633 (tt0) REVERT: N 46 GLU cc_start: 0.7549 (tt0) cc_final: 0.7329 (tt0) REVERT: N 53 GLN cc_start: 0.8454 (pm20) cc_final: 0.8071 (pm20) REVERT: N 73 ASP cc_start: 0.7949 (t0) cc_final: 0.7634 (t0) REVERT: B 10 GLU cc_start: 0.8812 (tp30) cc_final: 0.8067 (tp30) REVERT: B 13 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8050 (pp30) REVERT: B 59 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 61 MET cc_start: 0.8123 (ptm) cc_final: 0.7851 (ppp) REVERT: B 217 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7938 (pmm) REVERT: B 243 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8417 (p) REVERT: B 258 ASP cc_start: 0.8160 (t0) cc_final: 0.7475 (t0) REVERT: B 325 MET cc_start: 0.8284 (mmt) cc_final: 0.8069 (mmm) REVERT: R 114 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7413 (tm-30) REVERT: R 185 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7777 (m-70) REVERT: S 73 ASP cc_start: 0.7745 (t0) cc_final: 0.7514 (t0) REVERT: S 179 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: S 186 GLN cc_start: 0.8376 (pt0) cc_final: 0.8136 (pt0) outliers start: 28 outliers final: 13 residues processed: 203 average time/residue: 1.3980 time to fit residues: 301.9866 Evaluate side-chains 191 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN N 84 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10049 Z= 0.187 Angle : 0.548 6.971 13617 Z= 0.290 Chirality : 0.041 0.251 1550 Planarity : 0.004 0.037 1730 Dihedral : 4.711 21.197 1382 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.45 % Allowed : 17.40 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1240 helix: 2.00 (0.25), residues: 410 sheet: -0.44 (0.27), residues: 323 loop : 0.56 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.002 PHE R 45 TYR 0.011 0.001 TYR A 360 ARG 0.010 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7744 (ptp-110) REVERT: G 22 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7710 (mt-10) REVERT: G 26 ASP cc_start: 0.8214 (p0) cc_final: 0.7754 (p0) REVERT: A 356 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7665 (mtm110) REVERT: N 33 LYS cc_start: 0.8523 (ttmt) cc_final: 0.7978 (tttt) REVERT: N 39 GLN cc_start: 0.8873 (tt0) cc_final: 0.8673 (tt0) REVERT: N 45 LEU cc_start: 0.8509 (tp) cc_final: 0.8082 (tt) REVERT: N 46 GLU cc_start: 0.7528 (tt0) cc_final: 0.7250 (tt0) REVERT: N 53 GLN cc_start: 0.8429 (pm20) cc_final: 0.7996 (pm20) REVERT: B 10 GLU cc_start: 0.8828 (tp30) cc_final: 0.8124 (tp30) REVERT: B 13 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8007 (pp30) REVERT: B 59 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: B 172 GLU cc_start: 0.7453 (pm20) cc_final: 0.7089 (pm20) REVERT: B 188 MET cc_start: 0.8319 (mmm) cc_final: 0.8025 (mmm) REVERT: B 217 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8032 (pmm) REVERT: B 243 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8351 (p) REVERT: B 258 ASP cc_start: 0.8080 (t0) cc_final: 0.7475 (t0) REVERT: R 42 ASP cc_start: 0.8327 (m-30) cc_final: 0.7907 (m-30) REVERT: R 66 ASN cc_start: 0.7518 (t0) cc_final: 0.7185 (t0) REVERT: R 114 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7335 (tm-30) REVERT: R 278 LYS cc_start: 0.9171 (mmpt) cc_final: 0.8112 (mtmt) REVERT: S 73 ASP cc_start: 0.7734 (t0) cc_final: 0.7514 (t0) REVERT: S 93 MET cc_start: 0.8338 (ttm) cc_final: 0.8131 (ttm) REVERT: S 186 GLN cc_start: 0.8411 (pt0) cc_final: 0.8193 (pt0) REVERT: F 6 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6345 (t-90) outliers start: 26 outliers final: 12 residues processed: 203 average time/residue: 1.3944 time to fit residues: 301.1310 Evaluate side-chains 187 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain F residue 6 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 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 279 ASN N 1 GLN N 84 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10049 Z= 0.200 Angle : 0.559 7.277 13617 Z= 0.293 Chirality : 0.041 0.224 1550 Planarity : 0.004 0.037 1730 Dihedral : 4.634 20.306 1382 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.63 % Allowed : 17.78 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1240 helix: 2.00 (0.24), residues: 411 sheet: -0.50 (0.26), residues: 335 loop : 0.66 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 45 TYR 0.012 0.001 TYR N 32 ARG 0.009 0.001 ARG S 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7736 (mtt-85) REVERT: G 22 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7663 (mt-10) REVERT: G 26 ASP cc_start: 0.8247 (p0) cc_final: 0.7792 (p0) REVERT: A 356 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7671 (mtm110) REVERT: N 31 ASN cc_start: 0.8902 (m-40) cc_final: 0.8566 (m110) REVERT: N 33 LYS cc_start: 0.8511 (ttmt) cc_final: 0.7966 (tttt) REVERT: N 46 GLU cc_start: 0.7506 (tt0) cc_final: 0.7247 (tt0) REVERT: N 53 GLN cc_start: 0.8433 (pm20) cc_final: 0.8012 (pm20) REVERT: B 10 GLU cc_start: 0.8849 (tp30) cc_final: 0.8171 (tp30) REVERT: B 13 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8048 (pp30) REVERT: B 59 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: B 61 MET cc_start: 0.8212 (ppp) cc_final: 0.7977 (ppp) REVERT: B 76 ASP cc_start: 0.8543 (p0) cc_final: 0.8307 (p0) REVERT: B 188 MET cc_start: 0.8245 (mmm) cc_final: 0.8024 (mmm) REVERT: B 217 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8060 (pmm) REVERT: B 243 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8365 (p) REVERT: B 258 ASP cc_start: 0.8120 (t0) cc_final: 0.7508 (t0) REVERT: R 42 ASP cc_start: 0.8347 (m-30) cc_final: 0.7886 (m-30) REVERT: R 66 ASN cc_start: 0.7610 (t0) cc_final: 0.7311 (t0) REVERT: R 114 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7414 (tm-30) REVERT: S 73 ASP cc_start: 0.7656 (t0) cc_final: 0.7419 (t0) REVERT: S 186 GLN cc_start: 0.8448 (pt0) cc_final: 0.8213 (pt0) REVERT: F 6 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6457 (t-90) outliers start: 28 outliers final: 15 residues processed: 196 average time/residue: 1.3935 time to fit residues: 290.7477 Evaluate side-chains 192 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain F residue 6 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 279 ASN N 1 GLN N 84 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10049 Z= 0.230 Angle : 0.567 7.899 13617 Z= 0.296 Chirality : 0.041 0.228 1550 Planarity : 0.003 0.037 1730 Dihedral : 4.594 20.276 1382 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.54 % Allowed : 18.63 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1240 helix: 2.07 (0.24), residues: 411 sheet: -0.51 (0.27), residues: 329 loop : 0.63 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.002 PHE R 147 TYR 0.011 0.001 TYR N 32 ARG 0.007 0.001 ARG S 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7702 (mtt-85) REVERT: G 22 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7593 (mt-10) REVERT: G 26 ASP cc_start: 0.8267 (p0) cc_final: 0.7812 (p0) REVERT: A 317 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: A 356 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7687 (mtm110) REVERT: N 31 ASN cc_start: 0.8879 (m-40) cc_final: 0.8561 (m110) REVERT: N 33 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8030 (tttt) REVERT: N 45 LEU cc_start: 0.8924 (mt) cc_final: 0.8614 (tt) REVERT: N 46 GLU cc_start: 0.7478 (tt0) cc_final: 0.7232 (tt0) REVERT: N 53 GLN cc_start: 0.8455 (pm20) cc_final: 0.8037 (pm20) REVERT: B 8 ARG cc_start: 0.8420 (mtt90) cc_final: 0.8187 (mmt90) REVERT: B 10 GLU cc_start: 0.8898 (tp30) cc_final: 0.8285 (tp30) REVERT: B 13 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8037 (pp30) REVERT: B 59 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: B 188 MET cc_start: 0.8247 (mmm) cc_final: 0.8024 (mmm) REVERT: B 217 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8008 (pmm) REVERT: B 243 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8422 (p) REVERT: B 258 ASP cc_start: 0.8171 (t0) cc_final: 0.7517 (t0) REVERT: R 55 GLU cc_start: 0.8700 (tt0) cc_final: 0.8402 (tt0) REVERT: R 66 ASN cc_start: 0.7662 (t0) cc_final: 0.7387 (t0) REVERT: R 114 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7454 (tm-30) REVERT: R 226 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7413 (mmmt) REVERT: S 73 ASP cc_start: 0.7670 (t0) cc_final: 0.7432 (t0) REVERT: S 83 MET cc_start: 0.8612 (mtm) cc_final: 0.8379 (ptm) REVERT: F 6 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.6477 (t-90) outliers start: 27 outliers final: 15 residues processed: 198 average time/residue: 1.3643 time to fit residues: 287.6565 Evaluate side-chains 192 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain F residue 6 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 1 GLN N 84 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 171 ASN S 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10049 Z= 0.190 Angle : 0.554 8.397 13617 Z= 0.289 Chirality : 0.041 0.217 1550 Planarity : 0.004 0.039 1730 Dihedral : 4.498 20.066 1382 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.73 % Allowed : 19.10 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1240 helix: 2.21 (0.24), residues: 409 sheet: -0.49 (0.27), residues: 328 loop : 0.57 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE R 45 TYR 0.011 0.001 TYR A 360 ARG 0.008 0.001 ARG R 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7593 (mtt-85) REVERT: G 22 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7560 (mt-10) REVERT: G 26 ASP cc_start: 0.8256 (p0) cc_final: 0.7814 (p0) REVERT: A 356 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7659 (mtm110) REVERT: N 31 ASN cc_start: 0.8824 (m-40) cc_final: 0.8530 (m110) REVERT: N 33 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8005 (tttt) REVERT: N 45 LEU cc_start: 0.8965 (mt) cc_final: 0.8685 (tt) REVERT: N 46 GLU cc_start: 0.7487 (tt0) cc_final: 0.7213 (tt0) REVERT: N 53 GLN cc_start: 0.8436 (pm20) cc_final: 0.8051 (pm20) REVERT: B 10 GLU cc_start: 0.8933 (tp30) cc_final: 0.8388 (tp30) REVERT: B 13 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8085 (pp30) REVERT: B 44 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: B 59 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: B 188 MET cc_start: 0.8175 (mmm) cc_final: 0.7974 (mmm) REVERT: B 217 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8039 (pmm) REVERT: B 243 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8389 (p) REVERT: B 258 ASP cc_start: 0.8202 (t0) cc_final: 0.7541 (t0) REVERT: R 42 ASP cc_start: 0.8420 (m-30) cc_final: 0.8106 (m-30) REVERT: R 55 GLU cc_start: 0.8650 (tt0) cc_final: 0.8339 (tt0) REVERT: R 66 ASN cc_start: 0.7661 (t0) cc_final: 0.7394 (t0) REVERT: R 114 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7424 (tm-30) REVERT: R 278 LYS cc_start: 0.9254 (mmpt) cc_final: 0.8525 (mtmt) REVERT: S 11 LEU cc_start: 0.9281 (mm) cc_final: 0.8980 (tm) REVERT: S 73 ASP cc_start: 0.7635 (t0) cc_final: 0.7400 (t0) REVERT: S 83 MET cc_start: 0.8695 (mtm) cc_final: 0.8433 (ptm) REVERT: F 6 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6544 (t-90) outliers start: 29 outliers final: 18 residues processed: 197 average time/residue: 1.3105 time to fit residues: 275.5180 Evaluate side-chains 196 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain F residue 6 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 1 GLN N 84 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10049 Z= 0.186 Angle : 0.555 9.029 13617 Z= 0.288 Chirality : 0.041 0.233 1550 Planarity : 0.003 0.037 1730 Dihedral : 4.427 19.921 1382 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.63 % Allowed : 19.47 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1240 helix: 2.37 (0.24), residues: 404 sheet: -0.45 (0.27), residues: 328 loop : 0.50 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE R 45 TYR 0.011 0.001 TYR A 360 ARG 0.007 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 22 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7490 (mt-10) REVERT: G 26 ASP cc_start: 0.8245 (p0) cc_final: 0.7805 (p0) REVERT: A 356 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7657 (mtm110) REVERT: N 31 ASN cc_start: 0.8776 (m-40) cc_final: 0.8492 (m110) REVERT: N 33 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8026 (tttt) REVERT: N 45 LEU cc_start: 0.8974 (mt) cc_final: 0.8698 (tt) REVERT: N 46 GLU cc_start: 0.7461 (tt0) cc_final: 0.7174 (tt0) REVERT: N 53 GLN cc_start: 0.8429 (pm20) cc_final: 0.8047 (pm20) REVERT: N 87 LYS cc_start: 0.9186 (ptpp) cc_final: 0.8976 (ptpp) REVERT: N 120 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7521 (tp-100) REVERT: B 10 GLU cc_start: 0.8953 (tp30) cc_final: 0.8405 (tp30) REVERT: B 13 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8136 (pp30) REVERT: B 44 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: B 59 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 217 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8040 (pmm) REVERT: B 243 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8379 (p) REVERT: B 258 ASP cc_start: 0.8215 (t0) cc_final: 0.7535 (t0) REVERT: R 42 ASP cc_start: 0.8412 (m-30) cc_final: 0.8098 (m-30) REVERT: R 55 GLU cc_start: 0.8640 (tt0) cc_final: 0.8335 (tt0) REVERT: R 114 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7490 (tm-30) REVERT: R 278 LYS cc_start: 0.9310 (mmpt) cc_final: 0.8575 (mtmt) REVERT: R 304 GLU cc_start: 0.7756 (tp30) cc_final: 0.6971 (tp30) REVERT: S 11 LEU cc_start: 0.9267 (mm) cc_final: 0.8980 (tm) REVERT: S 218 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7639 (ptp-110) REVERT: F 6 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6584 (t-90) outliers start: 28 outliers final: 18 residues processed: 195 average time/residue: 1.3499 time to fit residues: 280.5255 Evaluate side-chains 197 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 218 ARG Chi-restraints excluded: chain F residue 6 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN A 279 ASN N 1 GLN N 82 GLN N 84 ASN B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10049 Z= 0.259 Angle : 0.602 9.308 13617 Z= 0.311 Chirality : 0.042 0.217 1550 Planarity : 0.004 0.046 1730 Dihedral : 4.562 20.424 1382 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.82 % Allowed : 19.85 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1240 helix: 2.38 (0.24), residues: 404 sheet: -0.42 (0.27), residues: 327 loop : 0.49 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 147 TYR 0.013 0.001 TYR R 74 ARG 0.014 0.001 ARG G 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8034 (mtt-85) REVERT: G 22 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7526 (mt-10) REVERT: G 26 ASP cc_start: 0.8269 (p0) cc_final: 0.7821 (p0) REVERT: A 356 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7725 (mtm110) REVERT: N 31 ASN cc_start: 0.8846 (m-40) cc_final: 0.8545 (m110) REVERT: N 33 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8043 (tttt) REVERT: N 45 LEU cc_start: 0.9015 (mt) cc_final: 0.8748 (tt) REVERT: N 46 GLU cc_start: 0.7538 (tt0) cc_final: 0.7217 (tt0) REVERT: N 53 GLN cc_start: 0.8481 (pm20) cc_final: 0.8082 (pm20) REVERT: B 10 GLU cc_start: 0.8958 (tp30) cc_final: 0.8338 (tp30) REVERT: B 13 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8051 (pp30) REVERT: B 44 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: B 59 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: B 217 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8080 (pmm) REVERT: B 243 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8463 (p) REVERT: B 258 ASP cc_start: 0.8240 (t0) cc_final: 0.7547 (t0) REVERT: R 42 ASP cc_start: 0.8458 (m-30) cc_final: 0.8096 (m-30) REVERT: R 55 GLU cc_start: 0.8655 (tt0) cc_final: 0.8357 (tt0) REVERT: R 114 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7512 (tm-30) REVERT: R 278 LYS cc_start: 0.9256 (mmpt) cc_final: 0.8544 (mtmt) REVERT: R 303 GLN cc_start: 0.7449 (mm-40) cc_final: 0.7188 (mp-120) REVERT: S 11 LEU cc_start: 0.9279 (mm) cc_final: 0.8993 (tm) REVERT: S 83 MET cc_start: 0.8619 (mtm) cc_final: 0.8368 (ptm) REVERT: S 163 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8497 (ttpp) REVERT: S 218 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7549 (ptp-110) REVERT: F 6 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6640 (t-90) outliers start: 30 outliers final: 19 residues processed: 192 average time/residue: 1.3426 time to fit residues: 274.6128 Evaluate side-chains 195 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 308 THR Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 218 ARG Chi-restraints excluded: chain F residue 6 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 1 GLN N 84 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068594 restraints weight = 17685.862| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.72 r_work: 0.2842 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10049 Z= 0.226 Angle : 0.595 10.063 13617 Z= 0.305 Chirality : 0.042 0.239 1550 Planarity : 0.004 0.054 1730 Dihedral : 4.537 20.478 1382 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.45 % Allowed : 20.41 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1240 helix: 2.44 (0.24), residues: 403 sheet: -0.44 (0.27), residues: 327 loop : 0.44 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE R 147 TYR 0.013 0.001 TYR A 311 ARG 0.014 0.001 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4943.29 seconds wall clock time: 88 minutes 4.59 seconds (5284.59 seconds total)