Starting phenix.real_space_refine on Wed Sep 25 14:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xor_38538/09_2024/8xor_38538.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xor_38538/09_2024/8xor_38538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xor_38538/09_2024/8xor_38538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xor_38538/09_2024/8xor_38538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xor_38538/09_2024/8xor_38538.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xor_38538/09_2024/8xor_38538.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1900 atoms to isotropic. 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 58 5.16 5 C 5801 2.51 5 N 1478 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2481 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1848 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1729 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2400 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain breaks: 1 Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.62, per 1000 atoms: 0.63 Number of scatterers: 8979 At special positions: 0 Unit cell: (116.739, 116.739, 103.887, 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 58 16.00 O 1642 8.00 N 1478 7.00 C 5801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 175 " - pdb=" SG CYS R 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 40.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.708A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 26 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.212A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.222A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.458A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.544A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.807A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 89 through 98 Processing helix chain 'R' and resid 98 through 127 removed outlier: 5.016A pdb=" N VAL R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Proline residue: R 106 - end of helix Proline residue: R 118 - end of helix Processing helix chain 'R' and resid 135 through 164 removed outlier: 3.699A pdb=" N VAL R 139 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU R 155 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 170 through 206 removed outlier: 4.360A pdb=" N LEU R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 214 removed outlier: 3.689A pdb=" N LEU R 211 " --> pdb=" O PRO R 207 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP R 213 " --> pdb=" O GLN R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 240 Proline residue: R 236 - end of helix Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 265 through 279 Processing helix chain 'R' and resid 279 through 299 Processing helix chain 'R' and resid 299 through 306 removed outlier: 4.055A pdb=" N SER R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 339 Proline residue: R 328 - end of helix removed outlier: 3.757A pdb=" N PHE R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 361 removed outlier: 4.143A pdb=" N GLU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 375 through 380 removed outlier: 4.274A pdb=" N ARG R 380 " --> pdb=" O SER R 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.560A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.601A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.937A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.674A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.962A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.763A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.617A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.125A pdb=" N TRP E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ARG E 98 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN E 113 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N CYS E 96 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 148 removed outlier: 5.896A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 87 through 88 removed outlier: 6.133A pdb=" N PHE R 43 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 243 through 245 453 hydrogen bonds defined for protein. 1272 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: 2.55 Time building geometry restraints manager: 2.89 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: 2811 1.34 - 1.46: 1740 1.46 - 1.58: 4561 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9192 Sorted by residual: bond pdb=" CD2 HIS E 232 " pdb=" NE2 HIS E 232 " ideal model delta sigma weight residual 1.374 1.397 -0.023 1.10e-02 8.26e+03 4.54e+00 bond pdb=" ND1 HIS E 35 " pdb=" CE1 HIS E 35 " ideal model delta sigma weight residual 1.321 1.342 -0.021 1.00e-02 1.00e+04 4.49e+00 bond pdb=" C13 CLR R1405 " pdb=" C17 CLR R1405 " ideal model delta sigma weight residual 1.550 1.508 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C13 CLR R1403 " pdb=" C17 CLR R1403 " ideal model delta sigma weight residual 1.550 1.509 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C13 CLR R1402 " pdb=" C17 CLR R1402 " ideal model delta sigma weight residual 1.550 1.509 0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 9187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 11885 1.78 - 3.56: 544 3.56 - 5.34: 86 5.34 - 7.13: 18 7.13 - 8.91: 11 Bond angle restraints: 12544 Sorted by residual: angle pdb=" OE1 GLN E 231 " pdb=" CD GLN E 231 " pdb=" NE2 GLN E 231 " ideal model delta sigma weight residual 122.60 117.91 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" CB HIS E 35 " pdb=" CG HIS E 35 " pdb=" CD2 HIS E 35 " ideal model delta sigma weight residual 131.20 125.34 5.86 1.30e+00 5.92e-01 2.03e+01 angle pdb=" N PRO E 236 " pdb=" CA PRO E 236 " pdb=" C PRO E 236 " ideal model delta sigma weight residual 113.81 107.34 6.47 1.45e+00 4.76e-01 1.99e+01 angle pdb=" CA ASP E 137 " pdb=" CB ASP E 137 " pdb=" CG ASP E 137 " ideal model delta sigma weight residual 112.60 117.00 -4.40 1.00e+00 1.00e+00 1.93e+01 angle pdb=" CB HIS E 167 " pdb=" CG HIS E 167 " pdb=" CD2 HIS E 167 " ideal model delta sigma weight residual 131.20 125.78 5.42 1.30e+00 5.92e-01 1.74e+01 ... (remaining 12539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 5346 21.31 - 42.61: 255 42.61 - 63.92: 56 63.92 - 85.23: 13 85.23 - 106.53: 6 Dihedral angle restraints: 5676 sinusoidal: 2289 harmonic: 3387 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU R 44 " pdb=" C LEU R 44 " pdb=" N LEU R 45 " pdb=" CA LEU R 45 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1222 0.070 - 0.139: 217 0.139 - 0.209: 14 0.209 - 0.278: 8 0.278 - 0.348: 7 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C13 CLR R1405 " pdb=" C12 CLR R1405 " pdb=" C14 CLR R1405 " pdb=" C17 CLR R1405 " both_signs ideal model delta sigma weight residual False -2.93 -2.58 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C13 CLR R1402 " pdb=" C12 CLR R1402 " pdb=" C14 CLR R1402 " pdb=" C17 CLR R1402 " both_signs ideal model delta sigma weight residual False -2.93 -2.60 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C13 CLR R1401 " pdb=" C12 CLR R1401 " pdb=" C14 CLR R1401 " pdb=" C17 CLR R1401 " both_signs ideal model delta sigma weight residual False -2.93 -2.60 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1465 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 101 " -0.087 2.00e-02 2.50e+03 5.04e-02 5.08e+01 pdb=" CG TYR E 101 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR E 101 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR E 101 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR E 101 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR E 101 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR E 101 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR E 101 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 50 " 0.087 2.00e-02 2.50e+03 4.99e-02 4.99e+01 pdb=" CG TYR E 50 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR E 50 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR E 50 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR E 50 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR E 50 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR E 50 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR E 50 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 276 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ALA R 276 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA R 276 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL R 277 " 0.022 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1655 2.77 - 3.31: 9047 3.31 - 3.84: 15053 3.84 - 4.37: 18390 4.37 - 4.90: 31188 Nonbonded interactions: 75333 Sorted by model distance: nonbonded pdb=" OH TYR R 161 " pdb=" OD2 ASP R 256 " model vdw 2.242 3.040 nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 2.353 3.040 nonbonded pdb=" CE1 HIS R 143 " pdb=" C19 CLR R1405 " model vdw 2.363 3.680 nonbonded pdb=" OD2 ASP A 9 " pdb=" ND2 ASN E 169 " model vdw 2.400 3.120 nonbonded pdb=" OH TYR A 327 " pdb=" OD2 ASP A 348 " model vdw 2.401 3.040 ... (remaining 75328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.005 0.042 9192 Z= 0.324 Angle : 0.901 8.907 12544 Z= 0.511 Chirality : 0.058 0.348 1468 Planarity : 0.007 0.056 1546 Dihedral : 14.200 106.534 3489 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.33 % Allowed : 4.67 % Favored : 95.01 % 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: -0.55 (0.23), residues: 1144 helix: -0.42 (0.23), residues: 407 sheet: 0.27 (0.30), residues: 276 loop : -0.52 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP E 47 HIS 0.011 0.002 HIS E 232 PHE 0.030 0.002 PHE E 177 TYR 0.087 0.007 TYR E 101 ARG 0.043 0.008 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8333 (pt0) cc_final: 0.8028 (pp30) REVERT: B 259 GLN cc_start: 0.7626 (pt0) cc_final: 0.7411 (pt0) REVERT: B 275 SER cc_start: 0.8846 (t) cc_final: 0.8361 (m) REVERT: B 280 LYS cc_start: 0.9250 (tttt) cc_final: 0.9034 (tttm) REVERT: A 25 LYS cc_start: 0.7565 (tptt) cc_final: 0.6934 (tmmm) REVERT: A 27 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7568 (mmtt) REVERT: A 281 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8810 (mp0) REVERT: E 3 GLN cc_start: 0.8677 (tt0) cc_final: 0.8342 (tt0) REVERT: E 73 ASP cc_start: 0.7823 (t0) cc_final: 0.7278 (t0) REVERT: E 186 GLN cc_start: 0.8566 (tt0) cc_final: 0.8330 (tt0) REVERT: R 91 ASP cc_start: 0.8560 (p0) cc_final: 0.8269 (p0) REVERT: R 240 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7898 (mmtm) REVERT: R 245 GLN cc_start: 0.8573 (tp40) cc_final: 0.8339 (mm-40) REVERT: R 304 ASN cc_start: 0.9201 (m-40) cc_final: 0.8919 (m110) REVERT: R 347 GLU cc_start: 0.9067 (mp0) cc_final: 0.8678 (mp0) REVERT: R 377 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8117 (tp30) outliers start: 3 outliers final: 0 residues processed: 165 average time/residue: 1.4419 time to fit residues: 251.2942 Evaluate side-chains 116 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.0170 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 62 HIS B 75 GLN B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN A 216 ASN E 194 ASN R 47 ASN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9192 Z= 0.230 Angle : 0.664 7.788 12544 Z= 0.347 Chirality : 0.046 0.263 1468 Planarity : 0.005 0.047 1546 Dihedral : 9.044 56.817 1644 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.74 % Allowed : 10.21 % Favored : 88.06 % 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: 0.62 (0.25), residues: 1144 helix: 1.22 (0.27), residues: 410 sheet: 0.42 (0.30), residues: 261 loop : -0.21 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 211 HIS 0.003 0.001 HIS R 336 PHE 0.015 0.002 PHE B 253 TYR 0.024 0.002 TYR R 109 ARG 0.010 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9509 (tppp) cc_final: 0.9258 (mppt) REVERT: B 175 GLN cc_start: 0.8475 (pt0) cc_final: 0.8168 (pp30) REVERT: B 228 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7879 (p0) REVERT: B 259 GLN cc_start: 0.7634 (pt0) cc_final: 0.7283 (pt0) REVERT: B 275 SER cc_start: 0.8830 (t) cc_final: 0.8388 (m) REVERT: B 280 LYS cc_start: 0.9157 (tttt) cc_final: 0.8912 (tttm) REVERT: A 25 LYS cc_start: 0.7531 (tptt) cc_final: 0.7009 (tmmm) REVERT: A 27 LYS cc_start: 0.7951 (tmtt) cc_final: 0.7435 (mmtm) REVERT: A 52 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8672 (pp30) REVERT: A 281 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8831 (mp0) REVERT: E 3 GLN cc_start: 0.8706 (tt0) cc_final: 0.8425 (tt0) REVERT: E 13 GLN cc_start: 0.9265 (tp40) cc_final: 0.8696 (pp30) REVERT: E 73 ASP cc_start: 0.7770 (t0) cc_final: 0.7321 (t0) REVERT: E 74 ASP cc_start: 0.8436 (m-30) cc_final: 0.8179 (m-30) REVERT: E 186 GLN cc_start: 0.8754 (tt0) cc_final: 0.8524 (tt0) REVERT: E 223 ASP cc_start: 0.8529 (m-30) cc_final: 0.8172 (m-30) REVERT: E 230 MET cc_start: 0.9153 (ttp) cc_final: 0.8922 (ttt) REVERT: R 91 ASP cc_start: 0.8592 (p0) cc_final: 0.8352 (p0) REVERT: R 132 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8611 (mmmm) REVERT: R 264 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8332 (mt-10) REVERT: R 347 GLU cc_start: 0.9129 (mp0) cc_final: 0.8460 (mp0) REVERT: R 362 ILE cc_start: 0.9237 (tt) cc_final: 0.9022 (pp) outliers start: 16 outliers final: 4 residues processed: 136 average time/residue: 1.3858 time to fit residues: 199.5612 Evaluate side-chains 114 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 112 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9192 Z= 0.238 Angle : 0.614 8.061 12544 Z= 0.323 Chirality : 0.045 0.240 1468 Planarity : 0.004 0.051 1546 Dihedral : 8.065 59.302 1644 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.41 % Allowed : 12.60 % Favored : 85.99 % 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: 0.87 (0.25), residues: 1144 helix: 1.51 (0.27), residues: 410 sheet: 0.44 (0.30), residues: 262 loop : -0.07 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.002 0.001 HIS A 329 PHE 0.013 0.001 PHE B 199 TYR 0.017 0.002 TYR R 109 ARG 0.007 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7997 (mpt-90) cc_final: 0.7794 (mpt-90) REVERT: B 23 LYS cc_start: 0.9494 (tppp) cc_final: 0.9259 (mppt) REVERT: B 175 GLN cc_start: 0.8530 (pt0) cc_final: 0.8178 (pp30) REVERT: B 228 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7855 (p0) REVERT: B 275 SER cc_start: 0.8842 (t) cc_final: 0.8447 (m) REVERT: B 280 LYS cc_start: 0.9071 (tttt) cc_final: 0.8831 (tttm) REVERT: C 29 LYS cc_start: 0.8909 (mttm) cc_final: 0.8665 (mmpt) REVERT: A 25 LYS cc_start: 0.7494 (tptt) cc_final: 0.7136 (tmmm) REVERT: A 27 LYS cc_start: 0.7950 (tmtt) cc_final: 0.7419 (mmtm) REVERT: A 52 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8621 (pp30) REVERT: E 3 GLN cc_start: 0.8723 (tt0) cc_final: 0.8397 (tt0) REVERT: E 13 GLN cc_start: 0.9290 (tp40) cc_final: 0.8828 (pp30) REVERT: E 73 ASP cc_start: 0.7872 (t0) cc_final: 0.7383 (t0) REVERT: E 74 ASP cc_start: 0.8609 (m-30) cc_final: 0.8352 (m-30) REVERT: E 183 GLN cc_start: 0.8391 (mp10) cc_final: 0.8064 (mm-40) REVERT: E 186 GLN cc_start: 0.8743 (tt0) cc_final: 0.8520 (tt0) REVERT: E 223 ASP cc_start: 0.8656 (m-30) cc_final: 0.8209 (m-30) REVERT: E 230 MET cc_start: 0.9145 (ttp) cc_final: 0.8744 (ttp) REVERT: R 134 LYS cc_start: 0.9257 (mtpt) cc_final: 0.9049 (mtpp) REVERT: R 245 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8203 (tp-100) REVERT: R 264 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8221 (mt-10) REVERT: R 347 GLU cc_start: 0.9098 (mp0) cc_final: 0.8311 (mp0) outliers start: 13 outliers final: 7 residues processed: 129 average time/residue: 1.3563 time to fit residues: 185.7718 Evaluate side-chains 119 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 104 optimal weight: 0.1980 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN B 176 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9192 Z= 0.224 Angle : 0.592 7.943 12544 Z= 0.312 Chirality : 0.043 0.229 1468 Planarity : 0.004 0.051 1546 Dihedral : 7.662 58.873 1644 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.85 % Allowed : 13.68 % Favored : 84.47 % 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: 0.98 (0.25), residues: 1144 helix: 1.63 (0.27), residues: 409 sheet: 0.43 (0.30), residues: 267 loop : 0.02 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.002 0.001 HIS A 329 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR E 235 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.9510 (tppp) cc_final: 0.9280 (mppt) REVERT: B 175 GLN cc_start: 0.8552 (pt0) cc_final: 0.8229 (pp30) REVERT: B 275 SER cc_start: 0.8821 (t) cc_final: 0.8459 (m) REVERT: B 280 LYS cc_start: 0.9006 (tttt) cc_final: 0.8786 (tttm) REVERT: C 29 LYS cc_start: 0.8859 (mttm) cc_final: 0.8534 (mmtt) REVERT: C 31 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8341 (m) REVERT: A 27 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7323 (mmtm) REVERT: A 52 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8572 (pp30) REVERT: E 3 GLN cc_start: 0.8769 (tt0) cc_final: 0.8430 (tt0) REVERT: E 13 GLN cc_start: 0.9311 (tp40) cc_final: 0.8823 (pp30) REVERT: E 73 ASP cc_start: 0.7961 (t0) cc_final: 0.7515 (t0) REVERT: E 74 ASP cc_start: 0.8714 (m-30) cc_final: 0.8463 (m-30) REVERT: E 183 GLN cc_start: 0.8428 (mp10) cc_final: 0.8195 (mm-40) REVERT: E 186 GLN cc_start: 0.8749 (tt0) cc_final: 0.8506 (tt0) REVERT: E 223 ASP cc_start: 0.8656 (m-30) cc_final: 0.8145 (m-30) REVERT: E 230 MET cc_start: 0.9125 (ttp) cc_final: 0.8724 (ttp) REVERT: R 245 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8246 (tp-100) REVERT: R 264 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8271 (mt-10) REVERT: R 347 GLU cc_start: 0.9108 (mp0) cc_final: 0.8830 (mm-30) outliers start: 17 outliers final: 7 residues processed: 129 average time/residue: 1.3048 time to fit residues: 179.0949 Evaluate side-chains 116 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN B 230 ASN B 259 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9192 Z= 0.340 Angle : 0.629 8.473 12544 Z= 0.332 Chirality : 0.045 0.254 1468 Planarity : 0.004 0.053 1546 Dihedral : 7.571 59.548 1644 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.50 % Allowed : 14.12 % Favored : 83.39 % 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: 0.95 (0.25), residues: 1144 helix: 1.65 (0.27), residues: 409 sheet: 0.31 (0.31), residues: 267 loop : 0.02 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 211 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.002 PHE B 253 TYR 0.020 0.002 TYR E 235 ARG 0.009 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8575 (pt0) cc_final: 0.8221 (pp30) REVERT: B 275 SER cc_start: 0.8856 (t) cc_final: 0.8450 (m) REVERT: C 31 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8410 (m) REVERT: A 18 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8199 (mtm) REVERT: A 27 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7417 (mmtm) REVERT: A 52 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8620 (pp30) REVERT: A 180 LYS cc_start: 0.8390 (mmpt) cc_final: 0.7899 (mptt) REVERT: E 3 GLN cc_start: 0.8775 (tt0) cc_final: 0.8472 (tt0) REVERT: E 13 GLN cc_start: 0.9367 (tp40) cc_final: 0.8920 (pp30) REVERT: E 73 ASP cc_start: 0.8062 (t0) cc_final: 0.7593 (t0) REVERT: E 186 GLN cc_start: 0.8792 (tt0) cc_final: 0.8474 (tt0) REVERT: E 223 ASP cc_start: 0.8662 (m-30) cc_final: 0.8084 (m-30) REVERT: E 230 MET cc_start: 0.9189 (ttp) cc_final: 0.8773 (ttp) REVERT: R 141 MET cc_start: 0.8457 (mtp) cc_final: 0.8231 (mtm) REVERT: R 264 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8293 (mt-10) REVERT: R 347 GLU cc_start: 0.9157 (mp0) cc_final: 0.8875 (mm-30) outliers start: 23 outliers final: 9 residues processed: 120 average time/residue: 1.2807 time to fit residues: 163.8087 Evaluate side-chains 119 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN B 259 GLN A 352 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9192 Z= 0.201 Angle : 0.582 7.667 12544 Z= 0.307 Chirality : 0.042 0.210 1468 Planarity : 0.004 0.050 1546 Dihedral : 7.234 59.590 1644 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 15.42 % Favored : 82.41 % 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: 1.11 (0.25), residues: 1144 helix: 1.78 (0.27), residues: 405 sheet: 0.40 (0.31), residues: 273 loop : 0.13 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE R 279 TYR 0.015 0.001 TYR E 235 ARG 0.010 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8560 (pt0) cc_final: 0.8264 (pp30) REVERT: B 220 GLN cc_start: 0.9030 (mt0) cc_final: 0.8741 (mt0) REVERT: B 275 SER cc_start: 0.8836 (t) cc_final: 0.8502 (m) REVERT: C 29 LYS cc_start: 0.8801 (mttm) cc_final: 0.8476 (mmpt) REVERT: C 31 SER cc_start: 0.8923 (t) cc_final: 0.8472 (m) REVERT: C 32 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8278 (ptpp) REVERT: C 41 CYS cc_start: 0.8995 (m) cc_final: 0.8772 (m) REVERT: C 48 ASP cc_start: 0.8713 (t0) cc_final: 0.8489 (t0) REVERT: C 52 THR cc_start: 0.8525 (m) cc_final: 0.7919 (p) REVERT: A 18 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8180 (mtm) REVERT: A 27 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7357 (mmtm) REVERT: E 3 GLN cc_start: 0.8755 (tt0) cc_final: 0.8452 (tt0) REVERT: E 73 ASP cc_start: 0.8021 (t0) cc_final: 0.7600 (t0) REVERT: E 186 GLN cc_start: 0.8803 (tt0) cc_final: 0.8506 (tt0) REVERT: E 223 ASP cc_start: 0.8662 (m-30) cc_final: 0.8146 (m-30) REVERT: E 230 MET cc_start: 0.9145 (ttp) cc_final: 0.8751 (ttp) REVERT: R 242 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8443 (mm-40) REVERT: R 264 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8281 (mt-10) REVERT: R 347 GLU cc_start: 0.9117 (mp0) cc_final: 0.8875 (mm-30) outliers start: 20 outliers final: 11 residues processed: 133 average time/residue: 1.3488 time to fit residues: 191.4759 Evaluate side-chains 125 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 B 259 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN R 169 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9192 Z= 0.203 Angle : 0.593 7.883 12544 Z= 0.312 Chirality : 0.042 0.217 1468 Planarity : 0.004 0.049 1546 Dihedral : 6.970 58.739 1644 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.39 % Allowed : 16.50 % Favored : 81.11 % 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: 1.15 (0.26), residues: 1144 helix: 1.87 (0.27), residues: 404 sheet: 0.42 (0.32), residues: 252 loop : 0.11 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE R 279 TYR 0.018 0.001 TYR A 230 ARG 0.011 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 LEU cc_start: 0.8598 (mp) cc_final: 0.8384 (mp) REVERT: B 17 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8541 (pp30) REVERT: B 175 GLN cc_start: 0.8574 (pt0) cc_final: 0.8278 (pp30) REVERT: B 275 SER cc_start: 0.8829 (t) cc_final: 0.8512 (m) REVERT: B 301 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7598 (mtpp) REVERT: C 29 LYS cc_start: 0.8773 (mttm) cc_final: 0.8452 (mmpt) REVERT: C 31 SER cc_start: 0.8986 (t) cc_final: 0.8561 (m) REVERT: C 32 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8362 (ptpp) REVERT: C 41 CYS cc_start: 0.8979 (m) cc_final: 0.8671 (m) REVERT: C 42 GLU cc_start: 0.8237 (pp20) cc_final: 0.8021 (pp20) REVERT: C 48 ASP cc_start: 0.8698 (t0) cc_final: 0.8486 (t0) REVERT: C 52 THR cc_start: 0.8582 (m) cc_final: 0.7982 (p) REVERT: A 18 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: A 22 GLN cc_start: 0.7916 (tp40) cc_final: 0.7488 (tp40) REVERT: A 27 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7444 (mmtm) REVERT: A 180 LYS cc_start: 0.8332 (mmpt) cc_final: 0.7853 (mptt) REVERT: A 251 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9160 (t) REVERT: A 325 ILE cc_start: 0.9026 (mt) cc_final: 0.8539 (tp) REVERT: E 3 GLN cc_start: 0.8714 (tt0) cc_final: 0.8404 (tt0) REVERT: E 73 ASP cc_start: 0.8031 (t0) cc_final: 0.7597 (t0) REVERT: E 186 GLN cc_start: 0.8805 (tt0) cc_final: 0.8507 (tt0) REVERT: E 223 ASP cc_start: 0.8709 (m-30) cc_final: 0.8137 (m-30) REVERT: E 230 MET cc_start: 0.9150 (ttp) cc_final: 0.8817 (ttp) REVERT: R 347 GLU cc_start: 0.9125 (mp0) cc_final: 0.8915 (mm-30) outliers start: 22 outliers final: 12 residues processed: 123 average time/residue: 1.3734 time to fit residues: 179.4917 Evaluate side-chains 121 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9192 Z= 0.319 Angle : 0.637 8.397 12544 Z= 0.335 Chirality : 0.044 0.240 1468 Planarity : 0.004 0.053 1546 Dihedral : 7.041 58.380 1644 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 17.26 % Favored : 80.46 % 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: 1.15 (0.25), residues: 1144 helix: 1.89 (0.27), residues: 403 sheet: 0.45 (0.33), residues: 250 loop : 0.07 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE B 199 TYR 0.021 0.002 TYR A 230 ARG 0.011 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8589 (pt0) cc_final: 0.8277 (pp30) REVERT: B 275 SER cc_start: 0.8852 (t) cc_final: 0.8504 (m) REVERT: C 29 LYS cc_start: 0.8846 (mttm) cc_final: 0.8527 (mmpt) REVERT: C 31 SER cc_start: 0.8991 (t) cc_final: 0.8601 (m) REVERT: C 52 THR cc_start: 0.8594 (m) cc_final: 0.7999 (p) REVERT: A 22 GLN cc_start: 0.7851 (tp40) cc_final: 0.7180 (tp-100) REVERT: A 25 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7991 (tmmm) REVERT: A 27 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7525 (mmtm) REVERT: A 180 LYS cc_start: 0.8358 (mmpt) cc_final: 0.7926 (mptt) REVERT: A 251 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9151 (t) REVERT: E 3 GLN cc_start: 0.8726 (tt0) cc_final: 0.8420 (tt0) REVERT: E 73 ASP cc_start: 0.8107 (t0) cc_final: 0.7640 (t0) REVERT: E 186 GLN cc_start: 0.8792 (tt0) cc_final: 0.8491 (tt0) REVERT: E 223 ASP cc_start: 0.8714 (m-30) cc_final: 0.8108 (m-30) REVERT: E 230 MET cc_start: 0.9169 (ttp) cc_final: 0.8766 (ttp) REVERT: R 91 ASP cc_start: 0.8792 (p0) cc_final: 0.8429 (p0) outliers start: 21 outliers final: 11 residues processed: 120 average time/residue: 1.2987 time to fit residues: 165.9515 Evaluate side-chains 119 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN A 28 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9192 Z= 0.196 Angle : 0.610 8.365 12544 Z= 0.320 Chirality : 0.042 0.200 1468 Planarity : 0.004 0.049 1546 Dihedral : 6.849 56.666 1644 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.74 % Allowed : 18.24 % Favored : 80.02 % 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: 1.17 (0.26), residues: 1144 helix: 1.89 (0.27), residues: 398 sheet: 0.49 (0.33), residues: 253 loop : 0.12 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE R 279 TYR 0.021 0.001 TYR E 235 ARG 0.013 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8575 (pt0) cc_final: 0.8277 (pp30) REVERT: B 275 SER cc_start: 0.8839 (t) cc_final: 0.8545 (m) REVERT: C 29 LYS cc_start: 0.8718 (mttm) cc_final: 0.8398 (mmpt) REVERT: C 31 SER cc_start: 0.9028 (t) cc_final: 0.8631 (m) REVERT: C 32 LYS cc_start: 0.8463 (mtmm) cc_final: 0.8194 (ptpp) REVERT: C 41 CYS cc_start: 0.9008 (m) cc_final: 0.8753 (m) REVERT: C 42 GLU cc_start: 0.8237 (pp20) cc_final: 0.8035 (pp20) REVERT: C 48 ASP cc_start: 0.8663 (t0) cc_final: 0.8428 (t0) REVERT: C 52 THR cc_start: 0.8568 (m) cc_final: 0.7977 (p) REVERT: A 22 GLN cc_start: 0.7861 (tp40) cc_final: 0.7347 (tp40) REVERT: A 25 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7932 (tmmm) REVERT: A 27 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7492 (mmtm) REVERT: A 180 LYS cc_start: 0.8441 (mmpt) cc_final: 0.8053 (mptt) REVERT: A 251 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9150 (t) REVERT: A 325 ILE cc_start: 0.9027 (mt) cc_final: 0.8545 (tp) REVERT: E 3 GLN cc_start: 0.8699 (tt0) cc_final: 0.8408 (tt0) REVERT: E 73 ASP cc_start: 0.8094 (t0) cc_final: 0.7646 (t0) REVERT: E 186 GLN cc_start: 0.8793 (tt0) cc_final: 0.8496 (tt0) REVERT: E 223 ASP cc_start: 0.8701 (m-30) cc_final: 0.8081 (m-30) REVERT: E 230 MET cc_start: 0.9128 (ttp) cc_final: 0.8770 (ttp) REVERT: R 173 GLU cc_start: 0.8368 (mp0) cc_final: 0.7524 (mm-30) REVERT: R 347 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8963 (mm-30) outliers start: 16 outliers final: 9 residues processed: 122 average time/residue: 1.2418 time to fit residues: 161.7096 Evaluate side-chains 117 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.0030 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0670 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 75 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9192 Z= 0.171 Angle : 0.605 8.402 12544 Z= 0.318 Chirality : 0.041 0.191 1468 Planarity : 0.004 0.056 1546 Dihedral : 6.558 54.403 1644 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.17 % Allowed : 18.13 % Favored : 79.70 % 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: 1.20 (0.26), residues: 1144 helix: 1.81 (0.27), residues: 405 sheet: 0.58 (0.33), residues: 252 loop : 0.15 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.000 HIS E 35 PHE 0.009 0.001 PHE R 279 TYR 0.016 0.001 TYR E 235 ARG 0.014 0.001 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8573 (pt0) cc_final: 0.8296 (pp30) REVERT: B 220 GLN cc_start: 0.8646 (mt0) cc_final: 0.8298 (mt0) REVERT: B 271 CYS cc_start: 0.7896 (m) cc_final: 0.7613 (p) REVERT: B 275 SER cc_start: 0.8836 (t) cc_final: 0.8623 (m) REVERT: B 301 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7831 (mtpp) REVERT: C 29 LYS cc_start: 0.8719 (mttm) cc_final: 0.8355 (mmtt) REVERT: C 31 SER cc_start: 0.9044 (t) cc_final: 0.8743 (m) REVERT: C 32 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8179 (ptpp) REVERT: C 41 CYS cc_start: 0.8993 (m) cc_final: 0.8391 (m) REVERT: C 42 GLU cc_start: 0.8226 (pp20) cc_final: 0.8008 (pp20) REVERT: C 52 THR cc_start: 0.8667 (m) cc_final: 0.8126 (p) REVERT: A 22 GLN cc_start: 0.7796 (tp40) cc_final: 0.7445 (tp-100) REVERT: A 25 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.8011 (tmmm) REVERT: A 27 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7483 (mptm) REVERT: A 180 LYS cc_start: 0.8389 (mmpt) cc_final: 0.8081 (mptt) REVERT: A 251 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9154 (t) REVERT: A 325 ILE cc_start: 0.9067 (mt) cc_final: 0.8635 (tp) REVERT: A 331 THR cc_start: 0.8212 (m) cc_final: 0.7683 (p) REVERT: E 3 GLN cc_start: 0.8642 (tt0) cc_final: 0.8367 (tt0) REVERT: E 13 GLN cc_start: 0.9395 (tp40) cc_final: 0.9000 (pp30) REVERT: E 73 ASP cc_start: 0.8089 (t0) cc_final: 0.7653 (t0) REVERT: E 186 GLN cc_start: 0.8740 (tt0) cc_final: 0.8455 (tt0) REVERT: E 223 ASP cc_start: 0.8696 (m-30) cc_final: 0.8086 (m-30) REVERT: E 230 MET cc_start: 0.9072 (ttp) cc_final: 0.8605 (ttm) REVERT: E 244 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8499 (tppp) REVERT: R 91 ASP cc_start: 0.8789 (p0) cc_final: 0.8491 (p0) REVERT: R 264 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8395 (pp20) outliers start: 20 outliers final: 9 residues processed: 133 average time/residue: 1.1539 time to fit residues: 165.4596 Evaluate side-chains 120 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 MET Chi-restraints excluded: chain R residue 358 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 0.0370 chunk 5 optimal weight: 0.0370 chunk 65 optimal weight: 0.7980 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 336 HIS ** 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 = 0.3355 r_free = 0.3355 target = 0.079732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058960 restraints weight = 21825.871| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.11 r_work: 0.2771 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9192 Z= 0.165 Angle : 0.595 8.468 12544 Z= 0.311 Chirality : 0.042 0.244 1468 Planarity : 0.004 0.054 1546 Dihedral : 6.366 55.508 1644 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.30 % Allowed : 19.00 % Favored : 79.70 % 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: 1.31 (0.26), residues: 1144 helix: 2.02 (0.27), residues: 393 sheet: 0.54 (0.33), residues: 254 loop : 0.22 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 211 HIS 0.003 0.000 HIS A 324 PHE 0.009 0.001 PHE R 279 TYR 0.017 0.001 TYR E 235 ARG 0.013 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.99 seconds wall clock time: 62 minutes 56.55 seconds (3776.55 seconds total)