Starting phenix.real_space_refine on Thu Mar 14 08:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6v_25729/03_2024/7t6v_25729_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6v_25729/03_2024/7t6v_25729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6v_25729/03_2024/7t6v_25729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6v_25729/03_2024/7t6v_25729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6v_25729/03_2024/7t6v_25729_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6v_25729/03_2024/7t6v_25729_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.048 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 5734 2.51 5 N 1506 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 89": "OE1" <-> "OE2" Residue "R ASP 106": "OD1" <-> "OD2" Residue "R PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 201": "NH1" <-> "NH2" Residue "R TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8949 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2346 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} 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: "C" 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: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.39, per 1000 atoms: 0.60 Number of scatterers: 8949 At special positions: 0 Unit cell: (106.029, 106.029, 132.804, 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 1645 8.00 N 1506 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.08 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 3.61 Conformation dependent library (CDL) restraints added in 1.9 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 13 sheets defined 35.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'R' and resid 23 through 52 Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 59 through 86 Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 95 through 128 removed outlier: 3.584A pdb=" N ASP R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 139 through 163 removed outlier: 4.020A pdb=" N VAL R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix removed outlier: 3.504A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 187 through 207 removed outlier: 3.535A pdb=" N THR R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 238 through 266 removed outlier: 3.855A pdb=" N LEU R 243 " --> pdb=" O PRO R 239 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR R 244 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 274 Processing helix chain 'R' and resid 278 through 302 removed outlier: 3.525A pdb=" N VAL R 284 " --> pdb=" O ASP R 281 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN R 285 " --> pdb=" O ILE R 282 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.523A pdb=" N LEU R 290 " --> pdb=" O THR R 287 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN R 298 " --> pdb=" O SER R 295 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 3.564A pdb=" N TYR R 302 " --> pdb=" O PRO R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 316 Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.001A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 6 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' 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: 6.473A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.946A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.003A 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: 6.748A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.020A 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: 6.890A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.052A 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: 6.770A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A 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: 6.645A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.442A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.549A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.972A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.786A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 143 through 147 407 hydrogen bonds defined for protein. 1134 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: 2.77 Time building geometry restraints manager: 3.96 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: 1578 1.32 - 1.45: 2386 1.45 - 1.57: 5081 1.57 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 9139 Sorted by residual: bond pdb=" CA SER R 84 " pdb=" CB SER R 84 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.56e-02 4.11e+03 1.40e+01 bond pdb=" CA SER R 112 " pdb=" CB SER R 112 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.55e-02 4.16e+03 1.32e+01 bond pdb=" CA SER R 73 " pdb=" CB SER R 73 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.21e+01 bond pdb=" N ILE R 195 " pdb=" CA ILE R 195 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" CA SER R 211 " pdb=" CB SER R 211 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.58e-02 4.01e+03 1.19e+01 ... (remaining 9134 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.16: 203 106.16 - 113.23: 4905 113.23 - 120.30: 4398 120.30 - 127.37: 2788 127.37 - 134.44: 79 Bond angle restraints: 12373 Sorted by residual: angle pdb=" C PRO R 92 " pdb=" CA PRO R 92 " pdb=" CB PRO R 92 " ideal model delta sigma weight residual 112.64 100.70 11.94 1.43e+00 4.89e-01 6.97e+01 angle pdb=" CA PHE B 235 " pdb=" CB PHE B 235 " pdb=" CG PHE B 235 " ideal model delta sigma weight residual 113.80 120.19 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" C PHE R 161 " pdb=" CA PHE R 161 " pdb=" CB PHE R 161 " ideal model delta sigma weight residual 110.88 101.62 9.26 1.57e+00 4.06e-01 3.48e+01 angle pdb=" C LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta sigma weight residual 110.85 120.76 -9.91 1.70e+00 3.46e-01 3.40e+01 angle pdb=" C TYR R 302 " pdb=" N VAL R 303 " pdb=" CA VAL R 303 " ideal model delta sigma weight residual 122.77 116.71 6.06 1.05e+00 9.07e-01 3.33e+01 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 4918 16.49 - 32.99: 396 32.99 - 49.48: 67 49.48 - 65.97: 10 65.97 - 82.46: 8 Dihedral angle restraints: 5399 sinusoidal: 2108 harmonic: 3291 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -163.28 77.28 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 163.97 -70.97 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" C LYS R 99 " pdb=" N LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta harmonic sigma weight residual -122.60 -138.12 15.52 0 2.50e+00 1.60e-01 3.86e+01 ... (remaining 5396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1078 0.102 - 0.205: 303 0.205 - 0.307: 26 0.307 - 0.409: 4 0.409 - 0.512: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LYS R 99 " pdb=" N LYS R 99 " pdb=" C LYS R 99 " pdb=" CB LYS R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA ASP R 106 " pdb=" N ASP R 106 " pdb=" C ASP R 106 " pdb=" CB ASP R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN R 135 " pdb=" N ASN R 135 " pdb=" C ASN R 135 " pdb=" CB ASN R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1409 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 205 " -0.020 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C ARG R 205 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG R 205 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE R 206 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 299 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C PRO R 299 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO R 299 " -0.023 2.00e-02 2.50e+03 pdb=" N MET R 300 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 183 " 0.027 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP R 183 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP R 183 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 183 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 183 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP R 183 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 183 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 183 " 0.000 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 87 2.62 - 3.19: 7913 3.19 - 3.76: 13198 3.76 - 4.33: 18979 4.33 - 4.90: 31141 Nonbonded interactions: 71318 Sorted by model distance: nonbonded pdb=" O ILE L 4 " pdb=" OXT ILE L 5 " model vdw 2.047 3.040 nonbonded pdb=" O THR A 262 " pdb=" NZ LYS A 317 " model vdw 2.268 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.319 2.440 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.319 2.520 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.325 2.440 ... (remaining 71313 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: 0.360 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: 2.200 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.670 Find NCS groups from input model: 0.270 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.011 0.058 9139 Z= 0.697 Angle : 1.265 11.936 12373 Z= 0.933 Chirality : 0.089 0.512 1412 Planarity : 0.006 0.054 1553 Dihedral : 12.331 82.461 3271 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 2.94 % 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: 1123 helix: 2.04 (0.24), residues: 402 sheet: 0.60 (0.30), residues: 278 loop : -0.19 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP R 183 HIS 0.012 0.002 HIS R 136 PHE 0.033 0.002 PHE B 235 TYR 0.022 0.002 TYR R 302 ARG 0.008 0.001 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: R 77 THR cc_start: 0.8744 (t) cc_final: 0.8414 (p) REVERT: R 103 ILE cc_start: 0.8263 (mm) cc_final: 0.8023 (mt) REVERT: R 161 PHE cc_start: 0.8002 (m-80) cc_final: 0.7785 (m-80) REVERT: R 229 HIS cc_start: 0.7711 (t-90) cc_final: 0.7482 (t-170) REVERT: R 278 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8611 (mmmt) REVERT: R 281 ASP cc_start: 0.7515 (m-30) cc_final: 0.7149 (m-30) REVERT: A 209 LYS cc_start: 0.8085 (mttt) cc_final: 0.7885 (mttt) REVERT: A 271 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7851 (ttpp) REVERT: A 275 GLU cc_start: 0.8400 (tp30) cc_final: 0.8074 (tp30) REVERT: A 309 ASP cc_start: 0.8277 (t70) cc_final: 0.7985 (t70) REVERT: B 45 MET cc_start: 0.8520 (mtt) cc_final: 0.8295 (mtt) REVERT: B 215 GLU cc_start: 0.7986 (mp0) cc_final: 0.7173 (mp0) REVERT: B 233 CYS cc_start: 0.7807 (t) cc_final: 0.7568 (t) REVERT: B 258 ASP cc_start: 0.7777 (t0) cc_final: 0.7333 (t0) REVERT: B 259 GLN cc_start: 0.7507 (tt0) cc_final: 0.7294 (tt0) outliers start: 1 outliers final: 1 residues processed: 270 average time/residue: 0.2696 time to fit residues: 92.5278 Evaluate side-chains 239 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9139 Z= 0.190 Angle : 0.549 8.792 12373 Z= 0.287 Chirality : 0.043 0.173 1412 Planarity : 0.005 0.045 1553 Dihedral : 4.661 52.608 1245 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.74 % Allowed : 10.46 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.15 (0.24), residues: 1123 helix: 2.04 (0.25), residues: 404 sheet: 0.47 (0.30), residues: 274 loop : -0.17 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 95 HIS 0.005 0.001 HIS A 188 PHE 0.014 0.001 PHE B 235 TYR 0.018 0.001 TYR R 175 ARG 0.004 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 258 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8515 (t) cc_final: 0.8222 (m) REVERT: R 164 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7764 (tt) REVERT: R 189 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7611 (tm-30) REVERT: R 211 SER cc_start: 0.7999 (m) cc_final: 0.7555 (p) REVERT: R 276 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8719 (ttmm) REVERT: R 278 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8375 (mmmt) REVERT: R 281 ASP cc_start: 0.7533 (m-30) cc_final: 0.7107 (m-30) REVERT: R 282 ILE cc_start: 0.8649 (tp) cc_final: 0.8435 (tp) REVERT: A 209 LYS cc_start: 0.8151 (mttt) cc_final: 0.7929 (mttt) REVERT: A 275 GLU cc_start: 0.8327 (tp30) cc_final: 0.8120 (tp30) REVERT: A 309 ASP cc_start: 0.8227 (t70) cc_final: 0.7813 (t70) REVERT: B 13 GLN cc_start: 0.8415 (tt0) cc_final: 0.7842 (tt0) REVERT: B 45 MET cc_start: 0.8469 (mtt) cc_final: 0.8239 (mtt) REVERT: B 188 MET cc_start: 0.8308 (mmm) cc_final: 0.7991 (mmt) REVERT: B 212 ASP cc_start: 0.7744 (t0) cc_final: 0.6452 (t0) REVERT: B 215 GLU cc_start: 0.7966 (mp0) cc_final: 0.7380 (mp0) REVERT: B 233 CYS cc_start: 0.7860 (t) cc_final: 0.7592 (t) REVERT: B 258 ASP cc_start: 0.7823 (t0) cc_final: 0.7382 (t0) outliers start: 17 outliers final: 8 residues processed: 264 average time/residue: 0.2927 time to fit residues: 98.1303 Evaluate side-chains 253 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 76 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9139 Z= 0.187 Angle : 0.517 10.022 12373 Z= 0.266 Chirality : 0.041 0.172 1412 Planarity : 0.004 0.040 1553 Dihedral : 4.466 50.664 1243 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.33 % Allowed : 14.67 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.06 (0.25), residues: 1123 helix: 1.89 (0.26), residues: 404 sheet: 0.62 (0.30), residues: 261 loop : -0.26 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 91 HIS 0.007 0.001 HIS R 102 PHE 0.029 0.001 PHE R 180 TYR 0.016 0.001 TYR R 175 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 ASP cc_start: 0.7771 (t0) cc_final: 0.7554 (t0) REVERT: R 177 THR cc_start: 0.7676 (OUTLIER) cc_final: 0.7198 (p) REVERT: R 189 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7568 (tm-30) REVERT: R 276 LYS cc_start: 0.9024 (ttmm) cc_final: 0.8803 (ttmm) REVERT: R 278 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8375 (mmmt) REVERT: R 281 ASP cc_start: 0.7524 (m-30) cc_final: 0.7167 (m-30) REVERT: R 282 ILE cc_start: 0.8676 (tp) cc_final: 0.8465 (tp) REVERT: A 197 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7650 (mtpp) REVERT: A 209 LYS cc_start: 0.8179 (mttt) cc_final: 0.7970 (mttt) REVERT: A 275 GLU cc_start: 0.8406 (tp30) cc_final: 0.8066 (tp30) REVERT: A 309 ASP cc_start: 0.8196 (t70) cc_final: 0.7777 (t0) REVERT: B 13 GLN cc_start: 0.8379 (tt0) cc_final: 0.7910 (tt0) REVERT: B 45 MET cc_start: 0.8393 (mtt) cc_final: 0.8154 (mtt) REVERT: B 191 SER cc_start: 0.8447 (t) cc_final: 0.8079 (t) REVERT: B 212 ASP cc_start: 0.7768 (t0) cc_final: 0.6778 (t0) REVERT: B 215 GLU cc_start: 0.7965 (mp0) cc_final: 0.7286 (mp0) REVERT: B 233 CYS cc_start: 0.7923 (t) cc_final: 0.7621 (t) REVERT: B 258 ASP cc_start: 0.7868 (t0) cc_final: 0.7487 (t0) REVERT: B 294 CYS cc_start: 0.7335 (t) cc_final: 0.7034 (t) REVERT: E 76 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8560 (mtpt) outliers start: 13 outliers final: 9 residues processed: 254 average time/residue: 0.2775 time to fit residues: 89.9120 Evaluate side-chains 238 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 228 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 315 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.0270 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9139 Z= 0.197 Angle : 0.517 8.987 12373 Z= 0.264 Chirality : 0.041 0.178 1412 Planarity : 0.004 0.041 1553 Dihedral : 4.412 50.390 1243 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.46 % Allowed : 14.67 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.00 (0.25), residues: 1123 helix: 1.81 (0.26), residues: 404 sheet: 0.54 (0.30), residues: 267 loop : -0.25 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 91 HIS 0.004 0.001 HIS R 102 PHE 0.021 0.001 PHE R 180 TYR 0.023 0.001 TYR A 296 ARG 0.009 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 255 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 106 ASP cc_start: 0.7838 (t0) cc_final: 0.7589 (t0) REVERT: R 189 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7506 (tm-30) REVERT: R 203 ILE cc_start: 0.8673 (tt) cc_final: 0.8312 (mm) REVERT: R 276 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8809 (ttmm) REVERT: R 278 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8336 (mmmt) REVERT: R 281 ASP cc_start: 0.7483 (m-30) cc_final: 0.7074 (m-30) REVERT: R 282 ILE cc_start: 0.8700 (tp) cc_final: 0.8475 (tp) REVERT: A 189 PHE cc_start: 0.8704 (p90) cc_final: 0.8318 (p90) REVERT: A 197 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7659 (mtpp) REVERT: A 209 LYS cc_start: 0.8234 (mttt) cc_final: 0.8019 (mttt) REVERT: A 275 GLU cc_start: 0.8367 (tp30) cc_final: 0.8112 (tp30) REVERT: A 309 ASP cc_start: 0.8209 (t70) cc_final: 0.7689 (t0) REVERT: B 13 GLN cc_start: 0.8361 (tt0) cc_final: 0.7954 (tt0) REVERT: B 191 SER cc_start: 0.8390 (t) cc_final: 0.8060 (t) REVERT: B 212 ASP cc_start: 0.7819 (t0) cc_final: 0.6809 (t0) REVERT: B 215 GLU cc_start: 0.8012 (mp0) cc_final: 0.7303 (mp0) REVERT: B 228 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8000 (p0) REVERT: B 233 CYS cc_start: 0.7945 (t) cc_final: 0.7667 (t) REVERT: B 258 ASP cc_start: 0.7782 (t0) cc_final: 0.7412 (t0) REVERT: B 259 GLN cc_start: 0.7839 (tt0) cc_final: 0.7637 (mt0) REVERT: B 336 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7988 (mp) outliers start: 24 outliers final: 15 residues processed: 266 average time/residue: 0.2898 time to fit residues: 97.5101 Evaluate side-chains 260 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9139 Z= 0.198 Angle : 0.516 8.684 12373 Z= 0.264 Chirality : 0.041 0.179 1412 Planarity : 0.004 0.044 1553 Dihedral : 4.360 49.624 1243 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.36 % Allowed : 16.51 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.00 (0.25), residues: 1123 helix: 1.78 (0.26), residues: 405 sheet: 0.51 (0.30), residues: 268 loop : -0.20 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 PHE 0.027 0.001 PHE R 180 TYR 0.023 0.001 TYR A 296 ARG 0.010 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6725 (mmm160) REVERT: R 167 VAL cc_start: 0.8975 (t) cc_final: 0.8651 (m) REVERT: R 177 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7061 (p) REVERT: R 189 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7538 (tm-30) REVERT: R 203 ILE cc_start: 0.8673 (tt) cc_final: 0.8350 (mm) REVERT: R 276 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8819 (ttmm) REVERT: R 278 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8334 (mmmt) REVERT: R 281 ASP cc_start: 0.7470 (m-30) cc_final: 0.7064 (m-30) REVERT: R 282 ILE cc_start: 0.8722 (tp) cc_final: 0.8497 (tp) REVERT: R 310 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8226 (mtm110) REVERT: R 312 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7928 (tpp80) REVERT: A 189 PHE cc_start: 0.8710 (p90) cc_final: 0.8317 (p90) REVERT: A 197 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7638 (mtpp) REVERT: A 209 LYS cc_start: 0.8265 (mttt) cc_final: 0.8032 (mttt) REVERT: A 257 LYS cc_start: 0.8892 (pttp) cc_final: 0.8545 (pttp) REVERT: A 275 GLU cc_start: 0.8369 (tp30) cc_final: 0.8086 (tp30) REVERT: A 309 ASP cc_start: 0.8237 (t70) cc_final: 0.7784 (t70) REVERT: B 191 SER cc_start: 0.8410 (t) cc_final: 0.8091 (t) REVERT: B 212 ASP cc_start: 0.7838 (t0) cc_final: 0.6812 (t0) REVERT: B 215 GLU cc_start: 0.8019 (mp0) cc_final: 0.7275 (mp0) REVERT: B 228 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 233 CYS cc_start: 0.7914 (t) cc_final: 0.7630 (t) REVERT: B 254 ASP cc_start: 0.7068 (t0) cc_final: 0.6836 (t0) REVERT: B 258 ASP cc_start: 0.7858 (t0) cc_final: 0.7468 (t0) REVERT: B 336 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7979 (mp) outliers start: 23 outliers final: 17 residues processed: 270 average time/residue: 0.2823 time to fit residues: 96.7297 Evaluate side-chains 261 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 0.0040 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.4550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9139 Z= 0.151 Angle : 0.501 9.284 12373 Z= 0.254 Chirality : 0.040 0.184 1412 Planarity : 0.004 0.047 1553 Dihedral : 4.198 45.990 1243 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.15 % Allowed : 17.64 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.00 (0.25), residues: 1123 helix: 1.84 (0.27), residues: 402 sheet: 0.45 (0.30), residues: 278 loop : -0.21 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 PHE 0.029 0.001 PHE R 180 TYR 0.023 0.001 TYR A 296 ARG 0.012 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 250 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6770 (mmm160) REVERT: R 170 PRO cc_start: 0.7847 (Cg_endo) cc_final: 0.7635 (Cg_exo) REVERT: R 189 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7488 (tm-30) REVERT: R 203 ILE cc_start: 0.8662 (tt) cc_final: 0.8337 (mm) REVERT: R 231 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8403 (ptpp) REVERT: R 276 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8791 (ttmm) REVERT: R 278 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8256 (mmmt) REVERT: R 281 ASP cc_start: 0.7440 (m-30) cc_final: 0.7046 (m-30) REVERT: R 310 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8192 (mtm110) REVERT: R 312 ARG cc_start: 0.8361 (tpp80) cc_final: 0.8042 (tpp80) REVERT: A 8 GLU cc_start: 0.6990 (tt0) cc_final: 0.6659 (tt0) REVERT: A 189 PHE cc_start: 0.8627 (p90) cc_final: 0.8274 (p90) REVERT: A 197 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7557 (mttm) REVERT: A 209 LYS cc_start: 0.8273 (mttt) cc_final: 0.8035 (mttt) REVERT: A 275 GLU cc_start: 0.8353 (tp30) cc_final: 0.8068 (tp30) REVERT: A 309 ASP cc_start: 0.8206 (t70) cc_final: 0.7790 (t70) REVERT: B 191 SER cc_start: 0.8380 (t) cc_final: 0.7999 (t) REVERT: B 212 ASP cc_start: 0.7793 (t0) cc_final: 0.7420 (t0) REVERT: B 228 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8033 (p0) REVERT: B 233 CYS cc_start: 0.7907 (t) cc_final: 0.7630 (t) REVERT: B 254 ASP cc_start: 0.7044 (t0) cc_final: 0.6819 (t0) REVERT: B 258 ASP cc_start: 0.7860 (t0) cc_final: 0.7445 (t0) REVERT: B 259 GLN cc_start: 0.8042 (tt0) cc_final: 0.7818 (mt0) REVERT: B 336 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7978 (mp) outliers start: 21 outliers final: 16 residues processed: 264 average time/residue: 0.2556 time to fit residues: 86.8151 Evaluate side-chains 266 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 0.0570 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 119 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9139 Z= 0.145 Angle : 0.498 8.968 12373 Z= 0.253 Chirality : 0.040 0.185 1412 Planarity : 0.004 0.042 1553 Dihedral : 4.097 42.555 1243 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 17.85 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.10 (0.25), residues: 1123 helix: 1.90 (0.27), residues: 401 sheet: 0.49 (0.30), residues: 278 loop : -0.11 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 PHE 0.029 0.001 PHE R 180 TYR 0.024 0.001 TYR A 296 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 260 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 103 ILE cc_start: 0.8373 (mm) cc_final: 0.8151 (mt) REVERT: R 189 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7473 (tm-30) REVERT: R 203 ILE cc_start: 0.8686 (tt) cc_final: 0.8365 (mm) REVERT: R 231 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8436 (ptpp) REVERT: R 278 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8211 (mmmt) REVERT: R 281 ASP cc_start: 0.7461 (m-30) cc_final: 0.7028 (m-30) REVERT: R 310 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8203 (mtm110) REVERT: A 8 GLU cc_start: 0.6945 (tt0) cc_final: 0.6742 (tt0) REVERT: A 52 GLN cc_start: 0.8242 (mt0) cc_final: 0.8039 (mt0) REVERT: A 189 PHE cc_start: 0.8547 (p90) cc_final: 0.8236 (p90) REVERT: A 197 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7603 (mttm) REVERT: A 209 LYS cc_start: 0.8282 (mttt) cc_final: 0.8041 (mttt) REVERT: A 232 LEU cc_start: 0.8895 (mt) cc_final: 0.8668 (mp) REVERT: A 275 GLU cc_start: 0.8340 (tp30) cc_final: 0.8049 (tp30) REVERT: A 309 ASP cc_start: 0.8195 (t70) cc_final: 0.7789 (t70) REVERT: B 191 SER cc_start: 0.8366 (t) cc_final: 0.8020 (t) REVERT: B 195 ASP cc_start: 0.7890 (p0) cc_final: 0.7682 (p0) REVERT: B 212 ASP cc_start: 0.7767 (t0) cc_final: 0.6707 (t0) REVERT: B 215 GLU cc_start: 0.7989 (mp0) cc_final: 0.7201 (mp0) REVERT: B 228 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8001 (p0) REVERT: B 233 CYS cc_start: 0.7925 (t) cc_final: 0.7605 (t) REVERT: B 254 ASP cc_start: 0.7035 (t0) cc_final: 0.6788 (t0) REVERT: B 258 ASP cc_start: 0.7849 (t0) cc_final: 0.7436 (t0) REVERT: B 336 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8006 (mp) REVERT: E 76 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8617 (mtpt) REVERT: E 219 GLN cc_start: 0.8709 (pp30) cc_final: 0.8157 (pp30) outliers start: 22 outliers final: 17 residues processed: 275 average time/residue: 0.2615 time to fit residues: 92.8388 Evaluate side-chains 264 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 245 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9139 Z= 0.177 Angle : 0.517 9.408 12373 Z= 0.264 Chirality : 0.041 0.194 1412 Planarity : 0.004 0.042 1553 Dihedral : 4.105 38.949 1243 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.26 % Allowed : 19.49 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.10 (0.25), residues: 1123 helix: 1.89 (0.27), residues: 401 sheet: 0.53 (0.31), residues: 272 loop : -0.13 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 PHE 0.029 0.001 PHE R 180 TYR 0.024 0.001 TYR A 296 ARG 0.007 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 249 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 ARG cc_start: 0.7354 (mmm160) cc_final: 0.6850 (mmm160) REVERT: R 57 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8497 (tpp80) REVERT: R 103 ILE cc_start: 0.8367 (mm) cc_final: 0.8128 (mt) REVERT: R 177 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.6916 (p) REVERT: R 189 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7505 (tm-30) REVERT: R 203 ILE cc_start: 0.8694 (tt) cc_final: 0.8394 (mm) REVERT: R 231 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8429 (ptpp) REVERT: R 309 PHE cc_start: 0.8756 (t80) cc_final: 0.8476 (t80) REVERT: R 310 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8234 (mtm110) REVERT: A 8 GLU cc_start: 0.6967 (tt0) cc_final: 0.6715 (tt0) REVERT: A 189 PHE cc_start: 0.8562 (p90) cc_final: 0.8290 (p90) REVERT: A 197 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7586 (mttm) REVERT: A 209 LYS cc_start: 0.8303 (mttt) cc_final: 0.8059 (mttt) REVERT: A 232 LEU cc_start: 0.8885 (mt) cc_final: 0.8660 (mp) REVERT: A 251 ASP cc_start: 0.8137 (t0) cc_final: 0.7935 (t0) REVERT: A 275 GLU cc_start: 0.8364 (tp30) cc_final: 0.8075 (tp30) REVERT: A 309 ASP cc_start: 0.8191 (t70) cc_final: 0.7840 (t70) REVERT: B 195 ASP cc_start: 0.7930 (p0) cc_final: 0.7581 (p0) REVERT: B 197 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7615 (mmm160) REVERT: B 212 ASP cc_start: 0.7771 (t0) cc_final: 0.6754 (t0) REVERT: B 215 GLU cc_start: 0.8006 (mp0) cc_final: 0.7253 (mp0) REVERT: B 228 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7852 (p0) REVERT: B 233 CYS cc_start: 0.7971 (t) cc_final: 0.7697 (t) REVERT: B 254 ASP cc_start: 0.7082 (t0) cc_final: 0.6830 (t0) REVERT: B 258 ASP cc_start: 0.7848 (t0) cc_final: 0.7413 (t0) REVERT: B 259 GLN cc_start: 0.8024 (tt0) cc_final: 0.7607 (mt0) REVERT: B 298 ASP cc_start: 0.7917 (t0) cc_final: 0.7680 (t0) REVERT: B 336 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8011 (mp) REVERT: E 76 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8608 (mtpt) REVERT: E 219 GLN cc_start: 0.8741 (pp30) cc_final: 0.8226 (pp30) REVERT: E 234 GLU cc_start: 0.7212 (pm20) cc_final: 0.6282 (pm20) outliers start: 22 outliers final: 17 residues processed: 263 average time/residue: 0.2756 time to fit residues: 92.6147 Evaluate side-chains 264 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9139 Z= 0.227 Angle : 0.544 9.427 12373 Z= 0.278 Chirality : 0.041 0.199 1412 Planarity : 0.004 0.042 1553 Dihedral : 4.223 34.409 1243 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.15 % Allowed : 19.28 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1123 helix: 1.79 (0.27), residues: 401 sheet: 0.48 (0.31), residues: 277 loop : -0.10 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 PHE 0.030 0.002 PHE R 180 TYR 0.026 0.001 TYR A 296 ARG 0.007 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 ARG cc_start: 0.7383 (mmm160) cc_final: 0.6835 (mmm160) REVERT: R 161 PHE cc_start: 0.7907 (m-10) cc_final: 0.7667 (m-10) REVERT: R 177 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7078 (p) REVERT: R 189 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7509 (tm-30) REVERT: R 203 ILE cc_start: 0.8696 (tt) cc_final: 0.8452 (mm) REVERT: R 231 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8431 (ptpp) REVERT: R 309 PHE cc_start: 0.8782 (t80) cc_final: 0.8454 (t80) REVERT: R 310 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8186 (mtm110) REVERT: A 8 GLU cc_start: 0.6971 (tt0) cc_final: 0.6726 (tt0) REVERT: A 189 PHE cc_start: 0.8609 (p90) cc_final: 0.8293 (p90) REVERT: A 197 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7575 (mttm) REVERT: A 209 LYS cc_start: 0.8356 (mttt) cc_final: 0.8089 (mttt) REVERT: A 275 GLU cc_start: 0.8369 (tp30) cc_final: 0.8073 (tp30) REVERT: A 309 ASP cc_start: 0.8220 (t70) cc_final: 0.7882 (t0) REVERT: B 195 ASP cc_start: 0.7929 (p0) cc_final: 0.7710 (p0) REVERT: B 212 ASP cc_start: 0.7809 (t0) cc_final: 0.6813 (t0) REVERT: B 215 GLU cc_start: 0.8044 (mp0) cc_final: 0.7310 (mp0) REVERT: B 228 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.7997 (p0) REVERT: B 233 CYS cc_start: 0.7943 (t) cc_final: 0.7687 (t) REVERT: B 258 ASP cc_start: 0.7850 (t0) cc_final: 0.7413 (t0) REVERT: B 259 GLN cc_start: 0.8021 (tt0) cc_final: 0.7665 (mt0) REVERT: B 289 TYR cc_start: 0.8507 (m-80) cc_final: 0.8021 (m-80) REVERT: B 298 ASP cc_start: 0.7947 (t0) cc_final: 0.7716 (t0) REVERT: B 336 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8021 (mp) REVERT: E 219 GLN cc_start: 0.8757 (pp30) cc_final: 0.8248 (pp30) REVERT: E 234 GLU cc_start: 0.7195 (pm20) cc_final: 0.6289 (pm20) outliers start: 21 outliers final: 17 residues processed: 258 average time/residue: 0.2690 time to fit residues: 89.2842 Evaluate side-chains 261 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 0.0020 chunk 101 optimal weight: 0.0970 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9139 Z= 0.155 Angle : 0.531 9.424 12373 Z= 0.269 Chirality : 0.040 0.183 1412 Planarity : 0.004 0.059 1553 Dihedral : 4.023 33.729 1243 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.95 % Allowed : 19.59 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.07 (0.25), residues: 1123 helix: 1.84 (0.27), residues: 402 sheet: 0.53 (0.31), residues: 276 loop : -0.14 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 91 HIS 0.003 0.001 HIS A 188 PHE 0.024 0.001 PHE R 180 TYR 0.025 0.001 TYR A 296 ARG 0.015 0.001 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 ARG cc_start: 0.7352 (mmm160) cc_final: 0.6799 (mmm160) REVERT: R 57 ARG cc_start: 0.8736 (tpp80) cc_final: 0.8507 (tpp80) REVERT: R 189 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7451 (tm-30) REVERT: R 203 ILE cc_start: 0.8673 (tt) cc_final: 0.8410 (mm) REVERT: R 231 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8400 (ptpp) REVERT: R 310 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8252 (mtm110) REVERT: A 8 GLU cc_start: 0.6621 (tt0) cc_final: 0.6367 (tt0) REVERT: A 197 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7570 (mttm) REVERT: A 209 LYS cc_start: 0.8270 (mttt) cc_final: 0.7997 (mttt) REVERT: A 232 LEU cc_start: 0.8943 (mt) cc_final: 0.8702 (mp) REVERT: A 275 GLU cc_start: 0.8365 (tp30) cc_final: 0.8074 (tp30) REVERT: A 309 ASP cc_start: 0.8196 (t70) cc_final: 0.7867 (t70) REVERT: B 195 ASP cc_start: 0.7939 (p0) cc_final: 0.7731 (p0) REVERT: B 197 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7405 (ttm-80) REVERT: B 212 ASP cc_start: 0.7749 (t0) cc_final: 0.6721 (t0) REVERT: B 215 GLU cc_start: 0.7987 (mp0) cc_final: 0.7220 (mp0) REVERT: B 228 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7820 (p0) REVERT: B 233 CYS cc_start: 0.7943 (t) cc_final: 0.7677 (t) REVERT: B 258 ASP cc_start: 0.7867 (t0) cc_final: 0.7410 (t0) REVERT: B 259 GLN cc_start: 0.8063 (tt0) cc_final: 0.7676 (mt0) REVERT: B 336 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8012 (mp) REVERT: E 76 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8625 (mtpt) REVERT: E 219 GLN cc_start: 0.8748 (pp30) cc_final: 0.8353 (pp30) REVERT: E 234 GLU cc_start: 0.7270 (pm20) cc_final: 0.6350 (pm20) outliers start: 19 outliers final: 15 residues processed: 258 average time/residue: 0.2735 time to fit residues: 89.7008 Evaluate side-chains 259 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 63 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091607 restraints weight = 14562.513| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.43 r_work: 0.3165 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9139 Z= 0.164 Angle : 0.530 9.011 12373 Z= 0.271 Chirality : 0.040 0.188 1412 Planarity : 0.004 0.040 1553 Dihedral : 3.982 33.073 1243 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.15 % Allowed : 19.90 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1.09 (0.25), residues: 1123 helix: 1.88 (0.27), residues: 401 sheet: 0.52 (0.30), residues: 277 loop : -0.12 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 91 HIS 0.005 0.001 HIS A 188 PHE 0.026 0.001 PHE R 180 TYR 0.025 0.001 TYR A 296 ARG 0.008 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2577.18 seconds wall clock time: 353 minutes 20.78 seconds (21200.78 seconds total)