Starting phenix.real_space_refine on Tue Feb 13 19:42:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy9_20222/02_2024/6oy9_20222_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy9_20222/02_2024/6oy9_20222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy9_20222/02_2024/6oy9_20222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy9_20222/02_2024/6oy9_20222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy9_20222/02_2024/6oy9_20222_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oy9_20222/02_2024/6oy9_20222_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.436 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 63 5.16 5 C 4810 2.51 5 N 1249 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A ASP 55": "OD1" <-> "OD2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "R PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 249": "OE1" <-> "OE2" Residue "R TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7519 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1809 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "R" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2609 Unusual residues: {'RET': 1} Classifications: {'peptide': 326, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 307, None: 1} Not linked: pdbres="ASN R 326 " pdbres="RET R 401 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.21, per 1000 atoms: 0.69 Number of scatterers: 7519 At special positions: 0 Unit cell: (73.1, 124.7, 122.12, 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 63 16.00 O 1397 8.00 N 1249 7.00 C 4810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 8 sheets defined 36.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 26 Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.943A pdb=" N MET A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.005A pdb=" N SER A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 removed outlier: 4.642A pdb=" N LYS A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.409A pdb=" N ASN A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 removed outlier: 3.887A pdb=" N ASP A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 removed outlier: 3.930A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 22 removed outlier: 3.890A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 11 through 27 removed outlier: 4.316A pdb=" N LEU G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 50 removed outlier: 3.957A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 64 Proline residue: R 53 - end of helix Processing helix chain 'R' and resid 74 through 88 removed outlier: 3.687A pdb=" N ASP R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 99 Processing helix chain 'R' and resid 107 through 140 removed outlier: 4.139A pdb=" N PHE R 115 " --> pdb=" O ASN R 111 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY R 120 " --> pdb=" O PHE R 116 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 166 Processing helix chain 'R' and resid 196 through 198 No H-bonds generated for 'chain 'R' and resid 196 through 198' Processing helix chain 'R' and resid 200 through 210 Processing helix chain 'R' and resid 213 through 234 Processing helix chain 'R' and resid 241 through 265 removed outlier: 4.156A pdb=" N LYS R 248 " --> pdb=" O GLN R 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE R 255 " --> pdb=" O THR R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 277 Processing helix chain 'R' and resid 287 through 299 removed outlier: 3.734A pdb=" N ILE R 290 " --> pdb=" O PHE R 287 " (cutoff:3.500A) Proline residue: R 291 - end of helix removed outlier: 4.488A pdb=" N THR R 297 " --> pdb=" O PHE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 306 No H-bonds generated for 'chain 'R' and resid 303 through 306' Processing helix chain 'R' and resid 314 through 317 No H-bonds generated for 'chain 'R' and resid 314 through 317' Processing sheet with id= A, first strand: chain 'A' and resid 30 through 33 removed outlier: 3.570A pdb=" N ARG A 193 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 61 through 63 removed outlier: 4.053A pdb=" N HIS B 62 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.012A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.989A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.181A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.900A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 7.117A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 702 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: 1.86 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2300 1.34 - 1.45: 1462 1.45 - 1.57: 3827 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7683 Sorted by residual: bond pdb=" C7 RET R 401 " pdb=" C8 RET R 401 " ideal model delta sigma weight residual 1.349 1.298 0.051 2.00e-02 2.50e+03 6.44e+00 bond pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " ideal model delta sigma weight residual 1.525 1.492 0.033 1.47e-02 4.63e+03 5.06e+00 bond pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sigma weight residual 1.502 1.451 0.051 2.30e-02 1.89e+03 4.95e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.61e+00 bond pdb=" C PHE B 199 " pdb=" N VAL B 200 " ideal model delta sigma weight residual 1.327 1.269 0.058 2.97e-02 1.13e+03 3.84e+00 ... (remaining 7678 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.97: 144 105.97 - 113.65: 4258 113.65 - 121.32: 4160 121.32 - 128.99: 1771 128.99 - 136.67: 62 Bond angle restraints: 10395 Sorted by residual: angle pdb=" CA LEU G 32 " pdb=" CB LEU G 32 " pdb=" CG LEU G 32 " ideal model delta sigma weight residual 116.30 133.75 -17.45 3.50e+00 8.16e-02 2.48e+01 angle pdb=" C VAL R 300 " pdb=" N TYR R 301 " pdb=" CA TYR R 301 " ideal model delta sigma weight residual 122.38 114.17 8.21 1.81e+00 3.05e-01 2.06e+01 angle pdb=" C GLU R 25 " pdb=" N ALA R 26 " pdb=" CA ALA R 26 " ideal model delta sigma weight residual 121.80 132.53 -10.73 2.44e+00 1.68e-01 1.93e+01 angle pdb=" CA PRO R 291 " pdb=" N PRO R 291 " pdb=" CD PRO R 291 " ideal model delta sigma weight residual 112.00 106.52 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" C CYS R 322 " pdb=" N CYS R 323 " pdb=" CA CYS R 323 " ideal model delta sigma weight residual 122.08 127.41 -5.33 1.47e+00 4.63e-01 1.31e+01 ... (remaining 10390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3915 16.99 - 33.98: 526 33.98 - 50.98: 95 50.98 - 67.97: 13 67.97 - 84.96: 5 Dihedral angle restraints: 4554 sinusoidal: 1805 harmonic: 2749 Sorted by residual: dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -139.86 53.86 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LYS A 275 " pdb=" C LYS A 275 " pdb=" N LYS A 276 " pdb=" CA LYS A 276 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 4551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1050 0.112 - 0.224: 105 0.224 - 0.336: 1 0.336 - 0.448: 0 0.448 - 0.561: 1 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE R 214 " pdb=" CA ILE R 214 " pdb=" CG1 ILE R 214 " pdb=" CG2 ILE R 214 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" CB VAL B 320 " pdb=" CA VAL B 320 " pdb=" CG1 VAL B 320 " pdb=" CG2 VAL B 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1154 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 70 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO R 71 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 170 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO R 171 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.021 2.00e-02 2.50e+03 2.05e-02 1.06e+01 pdb=" CG TRP B 82 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2150 2.80 - 3.32: 6921 3.32 - 3.85: 11939 3.85 - 4.37: 12527 4.37 - 4.90: 21434 Nonbonded interactions: 54971 Sorted by model distance: nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.269 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.291 2.440 nonbonded pdb=" OG SER R 22 " pdb=" OE1 GLU R 25 " model vdw 2.302 2.440 nonbonded pdb=" O SER R 298 " pdb=" OG SER R 298 " model vdw 2.304 2.440 ... (remaining 54966 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.000 Extract box with map and model: 3.490 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 23.930 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.009 0.089 7683 Z= 0.602 Angle : 1.097 17.446 10395 Z= 0.589 Chirality : 0.065 0.561 1157 Planarity : 0.008 0.108 1326 Dihedral : 15.304 84.962 2777 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.24 % Allowed : 17.56 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.69 (0.21), residues: 938 helix: -2.38 (0.22), residues: 348 sheet: -3.07 (0.36), residues: 135 loop : -3.78 (0.21), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP B 82 HIS 0.009 0.002 HIS B 54 PHE 0.022 0.003 PHE B 241 TYR 0.038 0.004 TYR R 96 ARG 0.005 0.000 ARG G 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8397 (ptp90) REVERT: A 49 MET cc_start: 0.8944 (tpp) cc_final: 0.8415 (mmm) REVERT: A 193 ARG cc_start: 0.8934 (ttm110) cc_final: 0.8649 (mtp85) REVERT: A 238 ARG cc_start: 0.8755 (ttm170) cc_final: 0.8474 (ttp-170) REVERT: A 306 LEU cc_start: 0.9248 (tp) cc_final: 0.8920 (tp) REVERT: B 215 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7994 (mm-30) REVERT: B 260 GLU cc_start: 0.8122 (mp0) cc_final: 0.7888 (mp0) REVERT: B 271 CYS cc_start: 0.7359 (p) cc_final: 0.6616 (p) REVERT: B 290 ASP cc_start: 0.7761 (m-30) cc_final: 0.7186 (m-30) REVERT: B 325 MET cc_start: 0.8172 (mmt) cc_final: 0.7877 (mmm) REVERT: G 12 LYS cc_start: 0.7789 (mttt) cc_final: 0.7407 (mmmt) REVERT: R 44 MET cc_start: 0.8920 (tpp) cc_final: 0.8666 (tpp) REVERT: R 69 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7844 (ttm-80) REVERT: R 179 ILE cc_start: 0.8710 (mt) cc_final: 0.8494 (tp) REVERT: R 190 ASP cc_start: 0.7536 (p0) cc_final: 0.7011 (p0) REVERT: R 200 ASN cc_start: 0.7987 (t0) cc_final: 0.6630 (t0) REVERT: R 231 LYS cc_start: 0.8897 (tppt) cc_final: 0.8596 (tmtt) outliers start: 2 outliers final: 2 residues processed: 154 average time/residue: 0.2244 time to fit residues: 44.4631 Evaluate side-chains 116 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 198 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 183 HIS B 293 ASN B 311 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS R 238 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7683 Z= 0.233 Angle : 0.663 15.211 10395 Z= 0.340 Chirality : 0.043 0.241 1157 Planarity : 0.005 0.084 1326 Dihedral : 6.223 45.430 1027 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.41 % Allowed : 22.07 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.17 (0.25), residues: 938 helix: -0.43 (0.28), residues: 336 sheet: -2.56 (0.39), residues: 137 loop : -3.35 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 35 HIS 0.003 0.001 HIS B 311 PHE 0.022 0.001 PHE B 235 TYR 0.014 0.002 TYR R 301 ARG 0.002 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8642 (ptp-170) cc_final: 0.8380 (ptp90) REVERT: A 49 MET cc_start: 0.8906 (tpp) cc_final: 0.8327 (mmm) REVERT: A 238 ARG cc_start: 0.8634 (ttm170) cc_final: 0.8346 (ttm110) REVERT: A 239 MET cc_start: 0.7975 (tmm) cc_final: 0.7690 (tmm) REVERT: A 306 LEU cc_start: 0.9146 (tp) cc_final: 0.8491 (tt) REVERT: B 215 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8025 (mm-30) REVERT: B 271 CYS cc_start: 0.7105 (p) cc_final: 0.6297 (p) REVERT: B 290 ASP cc_start: 0.7406 (m-30) cc_final: 0.6854 (m-30) REVERT: G 12 LYS cc_start: 0.7720 (mttt) cc_final: 0.7327 (mmmt) REVERT: R 28 GLN cc_start: 0.8233 (mt0) cc_final: 0.7980 (tm-30) REVERT: R 44 MET cc_start: 0.8886 (tpp) cc_final: 0.8671 (tpp) REVERT: R 64 GLN cc_start: 0.8565 (tt0) cc_final: 0.8198 (tt0) REVERT: R 69 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7791 (ttm-80) REVERT: R 179 ILE cc_start: 0.8790 (mt) cc_final: 0.8528 (tp) REVERT: R 190 ASP cc_start: 0.7274 (p0) cc_final: 0.7047 (p0) REVERT: R 200 ASN cc_start: 0.7275 (t0) cc_final: 0.6985 (t0) REVERT: R 231 LYS cc_start: 0.8889 (tppt) cc_final: 0.8629 (tmtt) outliers start: 28 outliers final: 12 residues processed: 162 average time/residue: 0.2143 time to fit residues: 45.5641 Evaluate side-chains 133 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7683 Z= 0.219 Angle : 0.639 12.467 10395 Z= 0.325 Chirality : 0.043 0.249 1157 Planarity : 0.005 0.079 1326 Dihedral : 5.631 36.101 1026 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.17 % Allowed : 26.10 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.26), residues: 938 helix: 0.31 (0.29), residues: 339 sheet: -2.32 (0.41), residues: 137 loop : -3.27 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.007 0.001 HIS B 311 PHE 0.020 0.001 PHE B 235 TYR 0.014 0.002 TYR R 206 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8609 (ptp-170) cc_final: 0.8330 (ptp90) REVERT: A 49 MET cc_start: 0.8913 (tpp) cc_final: 0.8303 (mmm) REVERT: A 228 MET cc_start: 0.8227 (tpt) cc_final: 0.7828 (tpt) REVERT: A 238 ARG cc_start: 0.8741 (ttm170) cc_final: 0.8140 (ttp-110) REVERT: A 306 LEU cc_start: 0.9117 (tp) cc_final: 0.8492 (tt) REVERT: B 170 ASP cc_start: 0.7775 (t0) cc_final: 0.7352 (t0) REVERT: B 215 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8060 (mm-30) REVERT: G 12 LYS cc_start: 0.7701 (mttt) cc_final: 0.7323 (mmmt) REVERT: R 44 MET cc_start: 0.8917 (tpp) cc_final: 0.8697 (tpp) REVERT: R 69 ARG cc_start: 0.8168 (ttp-170) cc_final: 0.7678 (ttm-80) REVERT: R 179 ILE cc_start: 0.8799 (mt) cc_final: 0.8529 (tp) REVERT: R 183 MET cc_start: 0.8734 (mmt) cc_final: 0.8495 (mmt) REVERT: R 190 ASP cc_start: 0.7090 (p0) cc_final: 0.6854 (p0) REVERT: R 200 ASN cc_start: 0.7379 (t0) cc_final: 0.7020 (t0) REVERT: R 231 LYS cc_start: 0.8890 (tppt) cc_final: 0.8641 (tmtt) outliers start: 26 outliers final: 17 residues processed: 151 average time/residue: 0.2150 time to fit residues: 43.1097 Evaluate side-chains 142 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7683 Z= 0.347 Angle : 0.698 12.023 10395 Z= 0.359 Chirality : 0.045 0.252 1157 Planarity : 0.005 0.074 1326 Dihedral : 5.638 36.000 1025 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 4.88 % Allowed : 26.59 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.48 (0.27), residues: 938 helix: 0.47 (0.29), residues: 340 sheet: -2.38 (0.44), residues: 133 loop : -3.19 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 35 HIS 0.007 0.001 HIS B 311 PHE 0.019 0.002 PHE B 235 TYR 0.018 0.002 TYR R 206 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.245 Fit side-chains REVERT: A 28 ARG cc_start: 0.8645 (ptp-170) cc_final: 0.8423 (ptp90) REVERT: A 238 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8555 (ttp-170) REVERT: A 342 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 215 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8095 (mm-30) REVERT: G 12 LYS cc_start: 0.7719 (mttt) cc_final: 0.7320 (mmmt) REVERT: R 44 MET cc_start: 0.8955 (tpp) cc_final: 0.8750 (tpp) REVERT: R 69 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7837 (ttm-80) REVERT: R 122 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: R 183 MET cc_start: 0.8882 (mmt) cc_final: 0.8243 (mmp) REVERT: R 200 ASN cc_start: 0.7819 (t0) cc_final: 0.6475 (t0) REVERT: R 231 LYS cc_start: 0.8914 (tppt) cc_final: 0.8658 (tmtt) REVERT: R 311 LYS cc_start: 0.8970 (tppp) cc_final: 0.8745 (tppp) outliers start: 40 outliers final: 28 residues processed: 155 average time/residue: 0.2230 time to fit residues: 46.6055 Evaluate side-chains 145 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 0.0020 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7683 Z= 0.261 Angle : 0.666 12.682 10395 Z= 0.336 Chirality : 0.043 0.244 1157 Planarity : 0.004 0.072 1326 Dihedral : 5.356 33.506 1025 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 5.98 % Allowed : 26.71 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.27), residues: 938 helix: 0.74 (0.29), residues: 334 sheet: -2.31 (0.44), residues: 133 loop : -2.92 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 35 HIS 0.005 0.001 HIS B 311 PHE 0.017 0.001 PHE B 235 TYR 0.014 0.002 TYR R 206 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 132 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8647 (ptp-170) cc_final: 0.8392 (ptp90) REVERT: A 342 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 82 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.8574 (p90) REVERT: B 215 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 278 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7494 (m-10) REVERT: G 12 LYS cc_start: 0.7675 (mttt) cc_final: 0.7424 (mmmt) REVERT: G 36 CYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7339 (p) REVERT: R 44 MET cc_start: 0.8919 (tpp) cc_final: 0.8711 (tpp) REVERT: R 69 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7736 (ttm-80) REVERT: R 76 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8628 (tt) REVERT: R 122 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: R 183 MET cc_start: 0.8888 (mmt) cc_final: 0.8221 (mmp) REVERT: R 201 GLU cc_start: 0.7869 (tp30) cc_final: 0.7487 (tp30) REVERT: R 231 LYS cc_start: 0.8881 (tppt) cc_final: 0.8621 (tmtt) outliers start: 49 outliers final: 31 residues processed: 171 average time/residue: 0.1906 time to fit residues: 43.9002 Evaluate side-chains 158 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7683 Z= 0.230 Angle : 0.667 13.947 10395 Z= 0.330 Chirality : 0.042 0.231 1157 Planarity : 0.004 0.072 1326 Dihedral : 5.186 35.082 1025 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 5.37 % Allowed : 28.78 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.01 (0.28), residues: 938 helix: 0.88 (0.30), residues: 334 sheet: -2.21 (0.46), residues: 129 loop : -2.85 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 35 HIS 0.004 0.001 HIS B 311 PHE 0.022 0.001 PHE B 235 TYR 0.012 0.001 TYR R 206 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8633 (ptp-170) cc_final: 0.8320 (ptp90) REVERT: A 238 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8400 (ttp-170) REVERT: A 342 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8029 (tm-30) REVERT: B 82 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8557 (p90) REVERT: B 215 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 278 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: G 12 LYS cc_start: 0.7618 (mttt) cc_final: 0.7371 (mmmt) REVERT: G 36 CYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7308 (p) REVERT: R 44 MET cc_start: 0.8918 (tpp) cc_final: 0.8699 (tpp) REVERT: R 69 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7735 (ttm-80) REVERT: R 76 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8565 (tt) REVERT: R 122 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: R 145 ASN cc_start: 0.8350 (t0) cc_final: 0.8130 (t0) REVERT: R 183 MET cc_start: 0.8912 (mmt) cc_final: 0.8233 (mmp) REVERT: R 201 GLU cc_start: 0.7736 (tp30) cc_final: 0.7352 (tp30) REVERT: R 231 LYS cc_start: 0.8877 (tppt) cc_final: 0.8618 (tmtt) outliers start: 44 outliers final: 35 residues processed: 166 average time/residue: 0.2050 time to fit residues: 46.0915 Evaluate side-chains 167 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7683 Z= 0.180 Angle : 0.636 12.882 10395 Z= 0.314 Chirality : 0.041 0.224 1157 Planarity : 0.004 0.073 1326 Dihedral : 4.979 34.282 1025 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.51 % Allowed : 31.34 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.28), residues: 938 helix: 1.05 (0.30), residues: 334 sheet: -1.84 (0.48), residues: 125 loop : -2.84 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 35 HIS 0.002 0.001 HIS B 311 PHE 0.018 0.001 PHE B 235 TYR 0.012 0.001 TYR A 286 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8624 (ptp-170) cc_final: 0.8381 (ptp90) REVERT: A 228 MET cc_start: 0.8175 (tpp) cc_final: 0.7715 (tpp) REVERT: A 239 MET cc_start: 0.8084 (tmm) cc_final: 0.7658 (tmm) REVERT: A 342 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 82 TRP cc_start: 0.8844 (OUTLIER) cc_final: 0.8573 (p90) REVERT: B 120 ILE cc_start: 0.8811 (mt) cc_final: 0.8454 (mm) REVERT: B 278 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: G 12 LYS cc_start: 0.7532 (mttt) cc_final: 0.7320 (mmmt) REVERT: G 20 ASP cc_start: 0.8230 (m-30) cc_final: 0.7440 (p0) REVERT: G 36 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7284 (p) REVERT: R 44 MET cc_start: 0.8863 (tpp) cc_final: 0.8428 (mmm) REVERT: R 69 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7718 (ttm-80) REVERT: R 122 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: R 183 MET cc_start: 0.8898 (mmt) cc_final: 0.8213 (mmp) REVERT: R 201 GLU cc_start: 0.7633 (tp30) cc_final: 0.7232 (tp30) REVERT: R 231 LYS cc_start: 0.8880 (tppt) cc_final: 0.8629 (tmtt) outliers start: 37 outliers final: 25 residues processed: 163 average time/residue: 0.1906 time to fit residues: 41.6037 Evaluate side-chains 155 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7683 Z= 0.251 Angle : 0.684 12.140 10395 Z= 0.339 Chirality : 0.043 0.225 1157 Planarity : 0.004 0.071 1326 Dihedral : 5.043 35.058 1025 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.76 % Allowed : 32.07 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.28), residues: 938 helix: 1.07 (0.30), residues: 334 sheet: -1.89 (0.47), residues: 125 loop : -2.84 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 35 HIS 0.004 0.001 HIS B 311 PHE 0.020 0.001 PHE B 235 TYR 0.022 0.002 TYR B 111 ARG 0.005 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.081 Fit side-chains REVERT: A 28 ARG cc_start: 0.8590 (ptp-170) cc_final: 0.8312 (ptp90) REVERT: A 342 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 82 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8580 (p90) REVERT: B 278 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7705 (m-10) REVERT: G 20 ASP cc_start: 0.8267 (m-30) cc_final: 0.7466 (p0) REVERT: G 36 CYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7292 (p) REVERT: R 44 MET cc_start: 0.8916 (tpp) cc_final: 0.8494 (mmm) REVERT: R 69 ARG cc_start: 0.8006 (ttp-170) cc_final: 0.7740 (ttm-80) REVERT: R 122 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7128 (tp30) REVERT: R 183 MET cc_start: 0.8935 (mmt) cc_final: 0.8263 (mmp) REVERT: R 201 GLU cc_start: 0.7672 (tp30) cc_final: 0.7289 (tp30) REVERT: R 231 LYS cc_start: 0.8884 (tppt) cc_final: 0.8625 (tmtt) outliers start: 39 outliers final: 30 residues processed: 157 average time/residue: 0.1932 time to fit residues: 40.8295 Evaluate side-chains 157 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 50.0000 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7683 Z= 0.216 Angle : 0.675 11.904 10395 Z= 0.331 Chirality : 0.042 0.227 1157 Planarity : 0.004 0.072 1326 Dihedral : 4.943 31.956 1025 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.63 % Allowed : 32.44 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.74 (0.28), residues: 938 helix: 1.14 (0.30), residues: 334 sheet: -1.79 (0.48), residues: 125 loop : -2.80 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 35 HIS 0.003 0.001 HIS B 311 PHE 0.018 0.001 PHE B 235 TYR 0.022 0.002 TYR B 111 ARG 0.005 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 0.889 Fit side-chains REVERT: A 28 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8308 (ptp90) REVERT: A 342 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 82 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.8567 (p90) REVERT: B 246 ASP cc_start: 0.8586 (p0) cc_final: 0.8318 (p0) REVERT: B 262 MET cc_start: 0.8279 (tpt) cc_final: 0.7714 (tpp) REVERT: B 278 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: G 12 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7319 (mmtp) REVERT: G 20 ASP cc_start: 0.8270 (m-30) cc_final: 0.7500 (p0) REVERT: G 32 LEU cc_start: 0.8286 (pt) cc_final: 0.7923 (pp) REVERT: G 36 CYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7153 (p) REVERT: R 44 MET cc_start: 0.8890 (tpp) cc_final: 0.8466 (mmm) REVERT: R 69 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7713 (ttm-80) REVERT: R 122 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7059 (tp30) REVERT: R 183 MET cc_start: 0.8941 (mmt) cc_final: 0.8265 (mmp) REVERT: R 201 GLU cc_start: 0.7659 (tp30) cc_final: 0.7275 (tp30) REVERT: R 231 LYS cc_start: 0.8886 (tppt) cc_final: 0.8628 (tmtt) outliers start: 38 outliers final: 30 residues processed: 159 average time/residue: 0.1980 time to fit residues: 42.0834 Evaluate side-chains 159 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7683 Z= 0.221 Angle : 0.679 11.721 10395 Z= 0.335 Chirality : 0.042 0.225 1157 Planarity : 0.004 0.072 1326 Dihedral : 4.944 32.940 1025 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.63 % Allowed : 32.68 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.28), residues: 938 helix: 1.16 (0.30), residues: 334 sheet: -1.70 (0.48), residues: 125 loop : -2.79 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 35 HIS 0.003 0.001 HIS B 311 PHE 0.016 0.001 PHE B 235 TYR 0.022 0.002 TYR B 111 ARG 0.005 0.000 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8589 (ptp-170) cc_final: 0.8341 (ptp90) REVERT: A 342 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 82 TRP cc_start: 0.8848 (OUTLIER) cc_final: 0.8573 (p90) REVERT: B 246 ASP cc_start: 0.8531 (p0) cc_final: 0.8217 (p0) REVERT: B 264 TYR cc_start: 0.8328 (m-80) cc_final: 0.7929 (m-80) REVERT: B 278 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7624 (m-10) REVERT: G 12 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7209 (mmtp) REVERT: G 32 LEU cc_start: 0.8374 (pt) cc_final: 0.8047 (pp) REVERT: G 36 CYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7163 (p) REVERT: R 44 MET cc_start: 0.8893 (tpp) cc_final: 0.8474 (mmm) REVERT: R 69 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7711 (ttm-80) REVERT: R 122 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: R 183 MET cc_start: 0.8962 (mmt) cc_final: 0.8287 (mmp) REVERT: R 201 GLU cc_start: 0.7643 (tp30) cc_final: 0.7265 (tp30) REVERT: R 231 LYS cc_start: 0.8893 (tppt) cc_final: 0.8636 (tmtt) outliers start: 38 outliers final: 31 residues processed: 162 average time/residue: 0.1940 time to fit residues: 42.1486 Evaluate side-chains 161 residues out of total 821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 122 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 309 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.0670 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101746 restraints weight = 14766.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104811 restraints weight = 8259.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106877 restraints weight = 5714.441| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7683 Z= 0.154 Angle : 0.676 11.947 10395 Z= 0.325 Chirality : 0.041 0.214 1157 Planarity : 0.004 0.074 1326 Dihedral : 4.612 34.293 1025 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.17 % Allowed : 34.27 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.49 (0.28), residues: 938 helix: 1.28 (0.30), residues: 334 sheet: -1.39 (0.49), residues: 126 loop : -2.69 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 35 HIS 0.002 0.000 HIS B 91 PHE 0.014 0.001 PHE B 235 TYR 0.020 0.001 TYR B 111 ARG 0.005 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1682.09 seconds wall clock time: 31 minutes 30.72 seconds (1890.72 seconds total)