Starting phenix.real_space_refine on Wed Feb 14 10:43:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p02_13141/02_2024/7p02_13141_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p02_13141/02_2024/7p02_13141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p02_13141/02_2024/7p02_13141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p02_13141/02_2024/7p02_13141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p02_13141/02_2024/7p02_13141_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p02_13141/02_2024/7p02_13141_updated.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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 63 5.16 5 C 5805 2.51 5 N 1542 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9062 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1870 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2347 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 77 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.36, per 1000 atoms: 0.59 Number of scatterers: 9062 At special positions: 0 Unit cell: (88.536, 123.69, 130.2, 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 1652 8.00 N 1542 7.00 C 5805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 176 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 14 sheets defined 35.2% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 79 through 81 No H-bonds generated for 'chain 'H' and resid 79 through 81' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 105 through 107 No H-bonds generated for 'chain 'H' and resid 105 through 107' Processing helix chain 'B' and resid 9 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.995A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'G' and resid 13 through 24 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 247 through 261 removed outlier: 4.527A pdb=" N GLU A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 315 through 334 Processing helix chain 'A' and resid 353 through 373 Processing helix chain 'R' and resid 29 through 59 Processing helix chain 'R' and resid 67 through 83 removed outlier: 4.424A pdb=" N LEU R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 4.272A pdb=" N HIS R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 108 Processing helix chain 'R' and resid 111 through 135 Processing helix chain 'R' and resid 144 through 167 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 191 through 204 removed outlier: 3.536A pdb=" N HIS R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 224 Processing helix chain 'R' and resid 238 through 273 Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 275 through 278 No H-bonds generated for 'chain 'R' and resid 275 through 278' Processing helix chain 'R' and resid 281 through 308 removed outlier: 3.507A pdb=" N MET R 295 " --> pdb=" O TRP R 292 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN R 301 " --> pdb=" O THR R 298 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.748A pdb=" N LEU R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 318 Processing sheet with id= A, first strand: chain 'H' and resid 20 through 24 Processing sheet with id= B, first strand: chain 'H' and resid 27 through 29 removed outlier: 6.290A pdb=" N ARG H 55 " --> pdb=" O TRP H 64 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TRP H 64 " --> pdb=" O ARG H 55 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA H 57 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU H 62 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 163 through 165 removed outlier: 6.355A pdb=" N LYS H 261 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU H 195 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU H 204 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 172 through 177 Processing sheet with id= E, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.679A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.069A 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: 3.639A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.792A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.792A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.948A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.584A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.671A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.269A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 34 through 37 Processing sheet with id= M, first strand: chain 'A' and resid 239 through 242 removed outlier: 3.530A pdb=" N VAL A 241 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 169 through 173 410 hydrogen bonds defined for protein. 1059 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: 2.53 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1689 1.32 - 1.45: 2403 1.45 - 1.57: 5094 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9280 Sorted by residual: bond pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 1.332 1.439 -0.107 1.36e-02 5.41e+03 6.14e+01 bond pdb=" CG ASN R 96 " pdb=" OD1 ASN R 96 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.35e+01 bond pdb=" N PHE R 111 " pdb=" CA PHE R 111 " ideal model delta sigma weight residual 1.463 1.497 -0.033 6.90e-03 2.10e+04 2.34e+01 bond pdb=" CG ASN R 96 " pdb=" ND2 ASN R 96 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.24e+01 bond pdb=" C CYS B 103 " pdb=" N ALA B 104 " ideal model delta sigma weight residual 1.330 1.268 0.061 1.41e-02 5.03e+03 1.90e+01 ... (remaining 9275 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.38: 260 106.38 - 113.37: 4901 113.37 - 120.36: 4303 120.36 - 127.35: 3031 127.35 - 134.34: 103 Bond angle restraints: 12598 Sorted by residual: angle pdb=" CA VAL B 187 " pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 116.33 125.15 -8.82 1.03e+00 9.43e-01 7.33e+01 angle pdb=" N ASP B 154 " pdb=" CA ASP B 154 " pdb=" C ASP B 154 " ideal model delta sigma weight residual 113.02 103.88 9.14 1.20e+00 6.94e-01 5.81e+01 angle pdb=" C HIS B 311 " pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta sigma weight residual 122.60 112.54 10.06 1.56e+00 4.11e-01 4.16e+01 angle pdb=" O VAL B 187 " pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 122.66 116.62 6.04 1.07e+00 8.73e-01 3.19e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 112.68 105.34 7.34 1.33e+00 5.65e-01 3.04e+01 ... (remaining 12593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 5129 16.70 - 33.39: 309 33.39 - 50.09: 64 50.09 - 66.79: 21 66.79 - 83.48: 3 Dihedral angle restraints: 5526 sinusoidal: 2202 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS H 39 " pdb=" SG CYS H 39 " pdb=" SG CYS H 113 " pdb=" CB CYS H 113 " ideal model delta sinusoidal sigma weight residual 93.00 60.66 32.34 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" C PHE B 151 " pdb=" N PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta harmonic sigma weight residual -122.60 -113.69 -8.91 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" CA TYR H 252 " pdb=" C TYR H 252 " pdb=" N PRO H 253 " pdb=" CA PRO H 253 " ideal model delta harmonic sigma weight residual 0.00 17.10 -17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 459 0.053 - 0.106: 451 0.106 - 0.158: 334 0.158 - 0.211: 136 0.211 - 0.264: 27 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CB VAL R 126 " pdb=" CA VAL R 126 " pdb=" CG1 VAL R 126 " pdb=" CG2 VAL R 126 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1404 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C CYS B 103 " -0.063 2.00e-02 2.50e+03 pdb=" O CYS B 103 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 104 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 245 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ASP A 245 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP A 245 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR B 196 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 196 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 197 " 0.010 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 53 2.65 - 3.21: 8589 3.21 - 3.77: 14571 3.77 - 4.34: 21411 4.34 - 4.90: 33262 Nonbonded interactions: 77886 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.086 2.440 nonbonded pdb=" CD2 PHE R 70 " pdb=" OD2 ASP R 129 " model vdw 2.209 3.340 nonbonded pdb=" N ASP B 154 " pdb=" N ASN B 155 " model vdw 2.506 2.560 nonbonded pdb=" O THR H 161 " pdb=" OG1 THR H 260 " model vdw 2.520 2.440 nonbonded pdb=" N CYS B 166 " pdb=" O CYS B 166 " model vdw 2.561 2.496 ... (remaining 77881 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: 3.250 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: 15.080 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.012 0.107 9280 Z= 0.817 Angle : 1.511 10.057 12598 Z= 1.178 Chirality : 0.103 0.264 1407 Planarity : 0.004 0.036 1588 Dihedral : 11.726 83.483 3373 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.12 % Allowed : 7.05 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.72 (0.23), residues: 1120 helix: -0.91 (0.24), residues: 378 sheet: -0.86 (0.31), residues: 236 loop : -1.34 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.009 0.002 HIS B 311 PHE 0.021 0.002 PHE B 151 TYR 0.023 0.002 TYR H 207 ARG 0.006 0.001 ARG R 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 256 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 GLU cc_start: 0.7576 (tt0) cc_final: 0.7325 (tm-30) REVERT: B 155 ASN cc_start: 0.7592 (t0) cc_final: 0.7196 (t0) REVERT: B 263 THR cc_start: 0.8886 (t) cc_final: 0.8659 (m) REVERT: A 6 SER cc_start: 0.8271 (p) cc_final: 0.7890 (p) REVERT: A 8 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7688 (mm-30) REVERT: A 9 ASP cc_start: 0.7798 (m-30) cc_final: 0.7434 (m-30) REVERT: A 17 LYS cc_start: 0.7843 (mmtp) cc_final: 0.7326 (mtpt) REVERT: A 263 ARG cc_start: 0.7061 (ptm160) cc_final: 0.6829 (ptm160) REVERT: A 368 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6937 (mtt-85) REVERT: A 372 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6756 (tpt-90) REVERT: R 51 VAL cc_start: 0.7563 (t) cc_final: 0.7154 (p) REVERT: R 63 MET cc_start: 0.6860 (mmm) cc_final: 0.6296 (mtt) REVERT: R 109 ASN cc_start: 0.6708 (m-40) cc_final: 0.6060 (m-40) REVERT: R 161 LEU cc_start: 0.7349 (tp) cc_final: 0.7079 (tt) REVERT: R 163 PHE cc_start: 0.6569 (t80) cc_final: 0.6198 (t80) REVERT: R 182 ILE cc_start: 0.7803 (mt) cc_final: 0.7453 (mp) REVERT: P 8 PHE cc_start: 0.8219 (m-80) cc_final: 0.7845 (m-10) outliers start: 11 outliers final: 2 residues processed: 266 average time/residue: 1.1684 time to fit residues: 332.5745 Evaluate side-chains 176 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain A residue 368 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 266 HIS A 206 GLN A 211 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN R 68 ASN R 73 ASN R 109 ASN R 274 ASN R 301 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9280 Z= 0.228 Angle : 0.586 7.488 12598 Z= 0.313 Chirality : 0.043 0.153 1407 Planarity : 0.005 0.046 1588 Dihedral : 4.413 45.065 1317 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.47 % Allowed : 15.22 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1120 helix: 1.12 (0.25), residues: 389 sheet: -0.81 (0.28), residues: 263 loop : -0.62 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.027 0.002 PHE H 85 TYR 0.019 0.002 TYR B 105 ARG 0.006 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 ASP cc_start: 0.6930 (p0) cc_final: 0.6596 (p0) REVERT: B 247 ASP cc_start: 0.6925 (t0) cc_final: 0.6682 (t0) REVERT: G 18 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7301 (tp40) REVERT: A 17 LYS cc_start: 0.7962 (mmtp) cc_final: 0.7420 (mtpt) REVERT: A 21 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7506 (mtmm) REVERT: A 372 ARG cc_start: 0.7235 (mtt90) cc_final: 0.6714 (tpp-160) REVERT: R 63 MET cc_start: 0.6881 (mmm) cc_final: 0.6397 (mtt) REVERT: R 73 ASN cc_start: 0.7153 (t0) cc_final: 0.6844 (t0) REVERT: R 161 LEU cc_start: 0.7246 (tp) cc_final: 0.6962 (tt) REVERT: R 163 PHE cc_start: 0.6630 (t80) cc_final: 0.6238 (t80) REVERT: R 300 TYR cc_start: 0.6881 (m-80) cc_final: 0.6681 (m-80) REVERT: P 8 PHE cc_start: 0.8325 (m-80) cc_final: 0.7942 (m-10) outliers start: 34 outliers final: 17 residues processed: 221 average time/residue: 1.1549 time to fit residues: 273.4904 Evaluate side-chains 179 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN A 206 GLN A 261 ASN A 277 GLN R 136 HIS R 301 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9280 Z= 0.178 Angle : 0.539 7.592 12598 Z= 0.286 Chirality : 0.042 0.171 1407 Planarity : 0.004 0.042 1588 Dihedral : 4.011 23.071 1312 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.47 % Allowed : 17.77 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1120 helix: 1.45 (0.26), residues: 382 sheet: -0.69 (0.27), residues: 274 loop : -0.34 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 213 PHE 0.031 0.002 PHE H 85 TYR 0.015 0.001 TYR R 121 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 226 GLU cc_start: 0.7995 (mp0) cc_final: 0.7482 (mp0) REVERT: B 247 ASP cc_start: 0.6899 (t0) cc_final: 0.6588 (t0) REVERT: G 18 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7391 (tp40) REVERT: A 17 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7423 (mtpt) REVERT: A 21 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7530 (mtmm) REVERT: A 372 ARG cc_start: 0.7256 (mtt90) cc_final: 0.6895 (tpt170) REVERT: R 63 MET cc_start: 0.6860 (mmm) cc_final: 0.6406 (mtt) REVERT: R 73 ASN cc_start: 0.7216 (t0) cc_final: 0.6900 (t0) REVERT: R 161 LEU cc_start: 0.7281 (tp) cc_final: 0.7007 (tt) REVERT: R 163 PHE cc_start: 0.6611 (t80) cc_final: 0.6236 (t80) REVERT: R 205 TYR cc_start: 0.7808 (t80) cc_final: 0.7053 (t80) REVERT: P 8 PHE cc_start: 0.8314 (m-80) cc_final: 0.8018 (m-80) outliers start: 34 outliers final: 17 residues processed: 192 average time/residue: 1.1705 time to fit residues: 240.3439 Evaluate side-chains 174 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 259 GLN A 206 GLN A 261 ASN A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9280 Z= 0.368 Angle : 0.615 9.833 12598 Z= 0.326 Chirality : 0.045 0.153 1407 Planarity : 0.005 0.040 1588 Dihedral : 4.434 23.441 1312 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.60 % Allowed : 17.47 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1120 helix: 1.17 (0.25), residues: 383 sheet: -0.50 (0.28), residues: 272 loop : -0.35 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.010 0.002 HIS A 213 PHE 0.037 0.002 PHE H 85 TYR 0.019 0.002 TYR A 246 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: H 208 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7074 (mtp180) REVERT: B 52 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7809 (mtt90) REVERT: B 217 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6804 (pmt) REVERT: B 226 GLU cc_start: 0.8082 (mp0) cc_final: 0.7824 (mp0) REVERT: B 247 ASP cc_start: 0.7187 (t0) cc_final: 0.6947 (t0) REVERT: B 258 ASP cc_start: 0.8002 (t0) cc_final: 0.7617 (t70) REVERT: A 17 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7578 (mtpt) REVERT: A 21 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7614 (mtmm) REVERT: A 26 ASP cc_start: 0.7525 (m-30) cc_final: 0.7205 (m-30) REVERT: A 290 LYS cc_start: 0.8421 (mppt) cc_final: 0.8183 (mptp) REVERT: A 372 ARG cc_start: 0.7275 (mtt90) cc_final: 0.6792 (tpt170) REVERT: R 63 MET cc_start: 0.6882 (mmm) cc_final: 0.6480 (mtt) REVERT: R 81 MET cc_start: 0.7326 (ttm) cc_final: 0.7119 (ptp) REVERT: R 161 LEU cc_start: 0.7249 (tp) cc_final: 0.6916 (tt) REVERT: R 163 PHE cc_start: 0.6699 (t80) cc_final: 0.6344 (t80) REVERT: R 205 TYR cc_start: 0.7885 (t80) cc_final: 0.7031 (t80) REVERT: R 262 LEU cc_start: 0.8023 (tp) cc_final: 0.7661 (tp) REVERT: P 8 PHE cc_start: 0.8378 (m-80) cc_final: 0.8013 (m-80) outliers start: 45 outliers final: 19 residues processed: 195 average time/residue: 1.1705 time to fit residues: 244.0243 Evaluate side-chains 172 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.0470 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 88 ASN B 259 GLN G 18 GLN A 206 GLN A 213 HIS A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9280 Z= 0.182 Angle : 0.533 8.035 12598 Z= 0.283 Chirality : 0.042 0.140 1407 Planarity : 0.004 0.039 1588 Dihedral : 4.179 24.678 1312 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.19 % Allowed : 19.41 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1120 helix: 1.17 (0.25), residues: 387 sheet: -0.47 (0.28), residues: 277 loop : -0.23 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS H 52 PHE 0.022 0.001 PHE H 85 TYR 0.023 0.001 TYR R 305 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: H 180 LYS cc_start: 0.8718 (ptmm) cc_final: 0.8419 (ptmt) REVERT: H 208 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.6910 (mtp180) REVERT: B 52 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7790 (mtt90) REVERT: B 247 ASP cc_start: 0.7051 (t0) cc_final: 0.6833 (t0) REVERT: B 258 ASP cc_start: 0.7825 (t0) cc_final: 0.7423 (t70) REVERT: G 18 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7433 (tp-100) REVERT: G 19 LEU cc_start: 0.8089 (mm) cc_final: 0.7870 (mm) REVERT: A 17 LYS cc_start: 0.7957 (mmtp) cc_final: 0.7500 (mtpt) REVERT: A 21 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7571 (mtmm) REVERT: A 290 LYS cc_start: 0.8381 (mppt) cc_final: 0.8146 (mptp) REVERT: A 326 ASP cc_start: 0.7109 (t0) cc_final: 0.6767 (t70) REVERT: R 63 MET cc_start: 0.6847 (mmm) cc_final: 0.6524 (mtt) REVERT: R 161 LEU cc_start: 0.7265 (tp) cc_final: 0.7053 (tp) REVERT: R 163 PHE cc_start: 0.6671 (t80) cc_final: 0.6323 (t80) REVERT: R 205 TYR cc_start: 0.7860 (t80) cc_final: 0.7033 (t80) REVERT: R 262 LEU cc_start: 0.7933 (tp) cc_final: 0.7524 (tp) REVERT: P 8 PHE cc_start: 0.8388 (m-80) cc_final: 0.8008 (m-80) outliers start: 41 outliers final: 18 residues processed: 189 average time/residue: 1.1801 time to fit residues: 238.3331 Evaluate side-chains 174 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 310 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 88 ASN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9280 Z= 0.255 Angle : 0.566 10.486 12598 Z= 0.299 Chirality : 0.043 0.151 1407 Planarity : 0.004 0.037 1588 Dihedral : 4.198 21.762 1311 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.78 % Allowed : 20.63 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1120 helix: 1.05 (0.25), residues: 384 sheet: -0.43 (0.28), residues: 283 loop : -0.20 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS A 213 PHE 0.035 0.002 PHE H 85 TYR 0.022 0.002 TYR R 305 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 63 GLU cc_start: 0.7629 (tt0) cc_final: 0.7407 (tm-30) REVERT: H 180 LYS cc_start: 0.8731 (ptmm) cc_final: 0.8507 (ptmt) REVERT: H 208 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.6974 (mtp180) REVERT: B 52 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7842 (mtt90) REVERT: B 217 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6660 (pmt) REVERT: B 247 ASP cc_start: 0.7189 (t0) cc_final: 0.6970 (t0) REVERT: B 258 ASP cc_start: 0.7882 (t0) cc_final: 0.7530 (t70) REVERT: A 17 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7553 (mtpt) REVERT: A 21 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7575 (mtmm) REVERT: A 290 LYS cc_start: 0.8445 (mppt) cc_final: 0.8217 (mptp) REVERT: R 63 MET cc_start: 0.6855 (mmm) cc_final: 0.6553 (mtt) REVERT: R 161 LEU cc_start: 0.7258 (tp) cc_final: 0.7049 (tp) REVERT: R 163 PHE cc_start: 0.6709 (t80) cc_final: 0.6336 (t80) REVERT: R 205 TYR cc_start: 0.7909 (t80) cc_final: 0.7044 (t80) REVERT: R 262 LEU cc_start: 0.7966 (tp) cc_final: 0.7563 (tp) REVERT: R 300 TYR cc_start: 0.7196 (m-10) cc_final: 0.6745 (m-10) REVERT: P 8 PHE cc_start: 0.8399 (m-80) cc_final: 0.8000 (m-80) outliers start: 37 outliers final: 22 residues processed: 189 average time/residue: 1.1641 time to fit residues: 235.1806 Evaluate side-chains 182 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 310 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.0000 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN A 206 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9280 Z= 0.224 Angle : 0.570 11.044 12598 Z= 0.296 Chirality : 0.043 0.217 1407 Planarity : 0.004 0.036 1588 Dihedral : 4.159 21.339 1311 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.47 % Allowed : 21.35 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1120 helix: 0.95 (0.26), residues: 383 sheet: -0.32 (0.29), residues: 280 loop : -0.16 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 213 PHE 0.028 0.002 PHE H 85 TYR 0.021 0.001 TYR R 305 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 63 GLU cc_start: 0.7616 (tt0) cc_final: 0.7400 (tm-30) REVERT: H 208 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.6944 (mtp180) REVERT: B 52 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7824 (mtt90) REVERT: B 217 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6623 (pmt) REVERT: B 258 ASP cc_start: 0.7874 (t0) cc_final: 0.7531 (t70) REVERT: B 266 HIS cc_start: 0.7047 (t70) cc_final: 0.6646 (OUTLIER) REVERT: A 17 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7543 (mtpt) REVERT: A 21 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7639 (mtmm) REVERT: A 213 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6653 (t-170) REVERT: A 290 LYS cc_start: 0.8469 (mppt) cc_final: 0.8245 (mptp) REVERT: R 63 MET cc_start: 0.6822 (mmm) cc_final: 0.6544 (mtt) REVERT: R 161 LEU cc_start: 0.7263 (tp) cc_final: 0.7061 (tp) REVERT: R 163 PHE cc_start: 0.6716 (t80) cc_final: 0.6353 (t80) REVERT: R 174 MET cc_start: 0.5652 (ppp) cc_final: 0.5387 (ppp) REVERT: R 205 TYR cc_start: 0.7907 (t80) cc_final: 0.7087 (t80) REVERT: R 262 LEU cc_start: 0.7908 (tp) cc_final: 0.7545 (tp) REVERT: R 300 TYR cc_start: 0.7159 (m-10) cc_final: 0.6758 (m-10) REVERT: R 314 LEU cc_start: 0.5829 (pp) cc_final: 0.5502 (mp) REVERT: P 8 PHE cc_start: 0.8424 (m-80) cc_final: 0.8019 (m-80) outliers start: 34 outliers final: 26 residues processed: 182 average time/residue: 1.1964 time to fit residues: 232.3036 Evaluate side-chains 178 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 310 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 88 ASN B 259 GLN B 266 HIS G 18 GLN A 206 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9280 Z= 0.182 Angle : 0.548 11.683 12598 Z= 0.284 Chirality : 0.042 0.192 1407 Planarity : 0.004 0.036 1588 Dihedral : 4.034 19.830 1311 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.68 % Allowed : 21.35 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1120 helix: 0.94 (0.26), residues: 380 sheet: -0.24 (0.29), residues: 279 loop : -0.01 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 213 PHE 0.026 0.001 PHE H 85 TYR 0.018 0.001 TYR R 305 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: H 208 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.6924 (mtp180) REVERT: B 52 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (mtt90) REVERT: B 215 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6968 (mt-10) REVERT: B 217 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6603 (pmt) REVERT: B 226 GLU cc_start: 0.7783 (mp0) cc_final: 0.7460 (mp0) REVERT: B 258 ASP cc_start: 0.7798 (t0) cc_final: 0.7420 (t70) REVERT: A 17 LYS cc_start: 0.7954 (mmtp) cc_final: 0.7527 (mtpt) REVERT: A 21 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7607 (mtmm) REVERT: A 213 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.6644 (t-170) REVERT: A 290 LYS cc_start: 0.8498 (mppt) cc_final: 0.8262 (mptp) REVERT: R 63 MET cc_start: 0.6772 (mmm) cc_final: 0.6503 (mtt) REVERT: R 163 PHE cc_start: 0.6706 (t80) cc_final: 0.6351 (t80) REVERT: R 205 TYR cc_start: 0.7904 (t80) cc_final: 0.7068 (t80) REVERT: R 262 LEU cc_start: 0.7856 (tp) cc_final: 0.7477 (tp) REVERT: R 300 TYR cc_start: 0.7245 (m-80) cc_final: 0.6823 (m-10) REVERT: R 314 LEU cc_start: 0.5827 (pp) cc_final: 0.5460 (mp) REVERT: P 8 PHE cc_start: 0.8416 (m-80) cc_final: 0.8003 (m-80) outliers start: 36 outliers final: 23 residues processed: 187 average time/residue: 1.2307 time to fit residues: 245.6257 Evaluate side-chains 180 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 299 MET Chi-restraints excluded: chain R residue 310 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN A 28 GLN A 206 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9280 Z= 0.203 Angle : 0.583 12.410 12598 Z= 0.297 Chirality : 0.043 0.187 1407 Planarity : 0.004 0.039 1588 Dihedral : 4.102 22.181 1311 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.27 % Allowed : 21.65 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1120 helix: 0.98 (0.26), residues: 373 sheet: -0.19 (0.29), residues: 280 loop : 0.05 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 213 PHE 0.023 0.001 PHE H 85 TYR 0.022 0.001 TYR R 272 ARG 0.011 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: H 208 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.6890 (mtp180) REVERT: B 52 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7727 (mtt90) REVERT: B 215 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 217 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6615 (pmt) REVERT: B 226 GLU cc_start: 0.7694 (mp0) cc_final: 0.7386 (mp0) REVERT: B 258 ASP cc_start: 0.7834 (t0) cc_final: 0.7534 (t70) REVERT: A 17 LYS cc_start: 0.7989 (mmtp) cc_final: 0.7569 (mtpt) REVERT: A 21 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7525 (mtmm) REVERT: A 213 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6644 (t-170) REVERT: A 290 LYS cc_start: 0.8518 (mppt) cc_final: 0.8281 (mptp) REVERT: R 63 MET cc_start: 0.6743 (mmm) cc_final: 0.6529 (mtt) REVERT: R 163 PHE cc_start: 0.6736 (t80) cc_final: 0.6366 (t80) REVERT: R 174 MET cc_start: 0.5756 (ppp) cc_final: 0.5504 (ppp) REVERT: R 205 TYR cc_start: 0.7898 (t80) cc_final: 0.7027 (t80) REVERT: R 262 LEU cc_start: 0.7856 (tp) cc_final: 0.7448 (tp) REVERT: R 300 TYR cc_start: 0.7200 (m-80) cc_final: 0.6795 (m-10) REVERT: R 314 LEU cc_start: 0.5830 (pp) cc_final: 0.5487 (mp) REVERT: P 8 PHE cc_start: 0.8424 (m-80) cc_final: 0.8072 (m-80) outliers start: 32 outliers final: 22 residues processed: 182 average time/residue: 1.2433 time to fit residues: 241.4563 Evaluate side-chains 175 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 299 MET Chi-restraints excluded: chain R residue 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS A 206 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9280 Z= 0.257 Angle : 0.628 12.981 12598 Z= 0.318 Chirality : 0.044 0.226 1407 Planarity : 0.004 0.039 1588 Dihedral : 4.225 21.692 1311 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.06 % Allowed : 22.47 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1120 helix: 0.86 (0.26), residues: 371 sheet: -0.30 (0.29), residues: 285 loop : 0.01 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.007 0.001 HIS A 213 PHE 0.031 0.002 PHE H 85 TYR 0.056 0.002 TYR R 272 ARG 0.013 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: H 63 GLU cc_start: 0.7609 (tt0) cc_final: 0.7337 (tm-30) REVERT: H 208 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.6982 (mtp180) REVERT: B 52 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (mtt90) REVERT: B 215 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6993 (mt-10) REVERT: B 217 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6612 (pmt) REVERT: B 226 GLU cc_start: 0.7726 (mp0) cc_final: 0.7524 (mp0) REVERT: B 258 ASP cc_start: 0.7889 (t0) cc_final: 0.7673 (t0) REVERT: A 17 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7584 (mtpt) REVERT: A 21 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7623 (mtmm) REVERT: A 213 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6666 (t-170) REVERT: A 290 LYS cc_start: 0.8582 (mppt) cc_final: 0.8364 (mptp) REVERT: R 63 MET cc_start: 0.6749 (mmm) cc_final: 0.6510 (mtt) REVERT: R 163 PHE cc_start: 0.6751 (t80) cc_final: 0.6362 (t80) REVERT: R 205 TYR cc_start: 0.7922 (t80) cc_final: 0.7057 (t80) REVERT: R 262 LEU cc_start: 0.7896 (tp) cc_final: 0.7497 (tp) REVERT: R 299 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7098 (mtm) REVERT: R 300 TYR cc_start: 0.7198 (m-80) cc_final: 0.6776 (m-10) REVERT: R 314 LEU cc_start: 0.5867 (pp) cc_final: 0.5491 (mp) REVERT: P 8 PHE cc_start: 0.8410 (m-80) cc_final: 0.8075 (m-80) outliers start: 30 outliers final: 22 residues processed: 177 average time/residue: 1.2134 time to fit residues: 229.1543 Evaluate side-chains 173 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 299 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS G 18 GLN A 206 GLN A 277 GLN ** R 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.183695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126149 restraints weight = 9965.878| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.14 r_work: 0.3216 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9280 Z= 0.190 Angle : 0.605 12.837 12598 Z= 0.304 Chirality : 0.043 0.220 1407 Planarity : 0.004 0.039 1588 Dihedral : 4.118 22.553 1311 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.76 % Allowed : 22.68 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1120 helix: 0.92 (0.26), residues: 371 sheet: -0.13 (0.29), residues: 284 loop : 0.02 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 213 PHE 0.033 0.001 PHE R 282 TYR 0.018 0.001 TYR R 278 ARG 0.013 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.23 seconds wall clock time: 80 minutes 59.69 seconds (4859.69 seconds total)