Starting phenix.real_space_refine on Sat Apr 6 02:38:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfw_29986/04_2024/8gfw_29986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfw_29986/04_2024/8gfw_29986.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/8gfw_29986/04_2024/8gfw_29986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfw_29986/04_2024/8gfw_29986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfw_29986/04_2024/8gfw_29986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfw_29986/04_2024/8gfw_29986_updated.pdb" } 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4322 2.51 5 N 1168 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6749 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1779 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2417 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 327} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 115 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 364 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2137 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 4.33, per 1000 atoms: 0.64 Number of scatterers: 6749 At special positions: 0 Unit cell: (82.4315, 130.155, 99.7855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1211 8.00 N 1168 7.00 C 4322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 42.7% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.680A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.641A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.631A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.930A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 25 removed outlier: 3.692A pdb=" N CYS B 25 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 46 removed outlier: 4.941A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 60 Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.180A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.511A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 164 removed outlier: 3.566A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 237 removed outlier: 3.714A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.642A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.690A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.317A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.799A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU R 310 " --> pdb=" O GLU R 306 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.056A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.633A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.141A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.850A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.818A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.826A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.512A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.591A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1467 1.33 - 1.45: 1579 1.45 - 1.57: 3777 1.57 - 1.69: 5 1.69 - 1.81: 63 Bond restraints: 6891 Sorted by residual: bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.467 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C4 GTP A 401 " pdb=" C5 GTP A 401 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C4 GTP A 401 " pdb=" N9 GTP A 401 " ideal model delta sigma weight residual 1.375 1.323 0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C6 GTP A 401 " pdb=" N1 GTP A 401 " ideal model delta sigma weight residual 1.380 1.329 0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.32e+00 ... (remaining 6886 not shown) Histogram of bond angle deviations from ideal: 100.00 - 107.20: 170 107.20 - 114.41: 4068 114.41 - 121.61: 3581 121.61 - 128.82: 1523 128.82 - 136.02: 62 Bond angle restraints: 9404 Sorted by residual: angle pdb=" N ARG R 239 " pdb=" CA ARG R 239 " pdb=" C ARG R 239 " ideal model delta sigma weight residual 111.71 116.73 -5.02 1.15e+00 7.56e-01 1.91e+01 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 121.47 -11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N VAL R 81 " pdb=" CA VAL R 81 " pdb=" C VAL R 81 " ideal model delta sigma weight residual 110.72 106.75 3.97 1.01e+00 9.80e-01 1.54e+01 angle pdb=" O1A GTP A 401 " pdb=" PA GTP A 401 " pdb=" O2A GTP A 401 " ideal model delta sigma weight residual 109.50 120.07 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N LEU R 340 " pdb=" CA LEU R 340 " pdb=" C LEU R 340 " ideal model delta sigma weight residual 110.55 106.70 3.85 1.35e+00 5.49e-01 8.15e+00 ... (remaining 9399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 3968 35.64 - 71.28: 43 71.28 - 106.91: 0 106.91 - 142.55: 2 142.55 - 178.19: 2 Dihedral angle restraints: 4015 sinusoidal: 1392 harmonic: 2623 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -112.54 -178.19 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -60.12 164.71 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual -56.21 -179.15 122.94 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 4012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 652 0.029 - 0.059: 294 0.059 - 0.088: 108 0.088 - 0.118: 46 0.118 - 0.147: 9 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1106 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ILE R 205 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 76 " 0.009 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C ALA R 76 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA R 76 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS R 77 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 194 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.017 5.00e-02 4.00e+02 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 483 2.74 - 3.28: 6390 3.28 - 3.82: 10582 3.82 - 4.36: 12258 4.36 - 4.90: 22605 Nonbonded interactions: 52318 Sorted by model distance: nonbonded pdb=" OH TYR R 219 " pdb=" O HOH R 601 " model vdw 2.197 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.268 2.440 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.307 2.440 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.341 2.520 ... (remaining 52313 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: 1.500 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: 7.560 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.570 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.004 0.077 6891 Z= 0.265 Angle : 0.574 11.969 9404 Z= 0.304 Chirality : 0.042 0.147 1109 Planarity : 0.003 0.030 1177 Dihedral : 13.587 178.192 2307 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 886 helix: 1.63 (0.27), residues: 392 sheet: 0.73 (0.44), residues: 160 loop : -0.63 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 105 HIS 0.007 0.001 HIS B 183 PHE 0.013 0.001 PHE R 101 TYR 0.020 0.001 TYR B 59 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.782 Fit side-chains REVERT: B 175 GLN cc_start: 0.8501 (pt0) cc_final: 0.8129 (pt0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.1829 time to fit residues: 123.7112 Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 75 GLN R 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6891 Z= 0.190 Angle : 0.477 5.520 9404 Z= 0.259 Chirality : 0.041 0.130 1109 Planarity : 0.004 0.038 1177 Dihedral : 9.946 173.455 992 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.15 % Allowed : 7.37 % Favored : 90.48 % 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: 1.12 (0.29), residues: 886 helix: 1.80 (0.27), residues: 384 sheet: 0.65 (0.42), residues: 175 loop : -0.43 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.013 0.001 TYR B 59 ARG 0.005 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.793 Fit side-chains REVERT: A 215 ASP cc_start: 0.8620 (m-30) cc_final: 0.8403 (m-30) REVERT: B 175 GLN cc_start: 0.8439 (pt0) cc_final: 0.8141 (pt0) outliers start: 14 outliers final: 2 residues processed: 89 average time/residue: 1.1597 time to fit residues: 109.3274 Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 0.0470 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6891 Z= 0.138 Angle : 0.435 6.271 9404 Z= 0.233 Chirality : 0.040 0.131 1109 Planarity : 0.003 0.029 1177 Dihedral : 9.451 173.699 992 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.84 % Allowed : 11.21 % Favored : 86.94 % 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: 1.19 (0.29), residues: 886 helix: 1.82 (0.27), residues: 386 sheet: 0.76 (0.42), residues: 169 loop : -0.38 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR R 132 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.799 Fit side-chains REVERT: B 175 GLN cc_start: 0.8350 (pt0) cc_final: 0.8092 (pt0) REVERT: R 228 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7132 (mtt-85) outliers start: 12 outliers final: 4 residues processed: 90 average time/residue: 1.0944 time to fit residues: 104.3372 Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 71 optimal weight: 0.0060 chunk 48 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6891 Z= 0.132 Angle : 0.431 6.526 9404 Z= 0.230 Chirality : 0.040 0.129 1109 Planarity : 0.003 0.028 1177 Dihedral : 9.291 177.294 992 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.54 % Allowed : 12.60 % Favored : 85.87 % 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: 1.25 (0.29), residues: 886 helix: 1.87 (0.27), residues: 386 sheet: 0.67 (0.41), residues: 175 loop : -0.28 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.008 0.001 TYR R 132 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.826 Fit side-chains REVERT: B 175 GLN cc_start: 0.8292 (pt0) cc_final: 0.8048 (pt0) REVERT: R 65 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8473 (mt0) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 1.1975 time to fit residues: 101.4745 Evaluate side-chains 78 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.0770 chunk 35 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 51 ASN R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6891 Z= 0.139 Angle : 0.431 6.535 9404 Z= 0.230 Chirality : 0.040 0.127 1109 Planarity : 0.003 0.029 1177 Dihedral : 9.235 178.885 992 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 12.75 % Favored : 85.25 % 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: 1.28 (0.29), residues: 886 helix: 1.89 (0.27), residues: 386 sheet: 0.75 (0.41), residues: 180 loop : -0.33 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR R 132 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.843 Fit side-chains REVERT: B 175 GLN cc_start: 0.8300 (pt0) cc_final: 0.8052 (pt0) REVERT: R 65 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: R 228 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7108 (mtt-85) outliers start: 13 outliers final: 5 residues processed: 81 average time/residue: 1.1818 time to fit residues: 101.2608 Evaluate side-chains 80 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 161 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 340 ASN R 51 ASN R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6891 Z= 0.144 Angle : 0.428 6.508 9404 Z= 0.229 Chirality : 0.040 0.127 1109 Planarity : 0.003 0.028 1177 Dihedral : 9.127 175.553 992 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.84 % Allowed : 12.75 % Favored : 85.41 % 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: 1.29 (0.29), residues: 886 helix: 1.89 (0.27), residues: 386 sheet: 0.76 (0.40), residues: 186 loop : -0.33 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.001 HIS R 296 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR R 132 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.776 Fit side-chains REVERT: B 175 GLN cc_start: 0.8304 (pt0) cc_final: 0.8056 (pt0) REVERT: R 65 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: R 228 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7230 (ttm110) outliers start: 12 outliers final: 6 residues processed: 78 average time/residue: 1.2105 time to fit residues: 99.7798 Evaluate side-chains 79 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 161 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 51 ASN R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6891 Z= 0.139 Angle : 0.432 6.457 9404 Z= 0.231 Chirality : 0.040 0.127 1109 Planarity : 0.003 0.028 1177 Dihedral : 9.051 172.187 992 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.00 % Allowed : 13.36 % Favored : 84.64 % 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 (0.29), residues: 886 helix: 1.90 (0.27), residues: 385 sheet: 0.78 (0.40), residues: 186 loop : -0.32 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.003 0.001 HIS R 296 PHE 0.017 0.001 PHE R 101 TYR 0.009 0.001 TYR R 132 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.809 Fit side-chains REVERT: B 175 GLN cc_start: 0.8325 (pt0) cc_final: 0.8066 (pt0) REVERT: R 65 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: R 228 ARG cc_start: 0.7555 (mtp85) cc_final: 0.7142 (ttm110) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 1.1956 time to fit residues: 102.3832 Evaluate side-chains 81 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 51 ASN R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6891 Z= 0.121 Angle : 0.421 6.401 9404 Z= 0.225 Chirality : 0.039 0.128 1109 Planarity : 0.003 0.028 1177 Dihedral : 8.940 168.825 992 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.15 % Allowed : 13.36 % Favored : 84.49 % 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: 1.33 (0.29), residues: 886 helix: 1.95 (0.27), residues: 385 sheet: 0.80 (0.41), residues: 180 loop : -0.35 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.001 HIS R 178 PHE 0.015 0.001 PHE R 101 TYR 0.008 0.001 TYR R 132 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.796 Fit side-chains REVERT: B 175 GLN cc_start: 0.8319 (pt0) cc_final: 0.8061 (pt0) REVERT: R 228 ARG cc_start: 0.7526 (mtp85) cc_final: 0.7126 (ttm110) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 1.2157 time to fit residues: 102.7183 Evaluate side-chains 83 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 72 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6891 Z= 0.120 Angle : 0.417 6.315 9404 Z= 0.223 Chirality : 0.039 0.128 1109 Planarity : 0.003 0.028 1177 Dihedral : 8.794 163.143 992 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.84 % Allowed : 14.13 % Favored : 84.02 % 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: 1.37 (0.29), residues: 886 helix: 2.01 (0.27), residues: 385 sheet: 0.79 (0.41), residues: 180 loop : -0.33 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.001 HIS R 178 PHE 0.014 0.001 PHE R 101 TYR 0.008 0.001 TYR R 132 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.759 Fit side-chains REVERT: A 221 MET cc_start: 0.8816 (ttp) cc_final: 0.8613 (ttp) REVERT: B 175 GLN cc_start: 0.8312 (pt0) cc_final: 0.8062 (pt0) REVERT: R 65 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8504 (mt0) REVERT: R 228 ARG cc_start: 0.7530 (mtp85) cc_final: 0.7157 (ttm110) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 1.2809 time to fit residues: 107.0728 Evaluate side-chains 83 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6891 Z= 0.179 Angle : 0.446 6.261 9404 Z= 0.238 Chirality : 0.040 0.125 1109 Planarity : 0.003 0.028 1177 Dihedral : 8.774 159.328 992 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.15 % Allowed : 13.67 % Favored : 84.18 % 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: 1.35 (0.29), residues: 886 helix: 1.99 (0.27), residues: 384 sheet: 0.81 (0.41), residues: 181 loop : -0.37 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.003 0.001 HIS R 178 PHE 0.015 0.001 PHE R 101 TYR 0.011 0.001 TYR R 132 ARG 0.004 0.000 ARG R 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.963 Fit side-chains REVERT: A 221 MET cc_start: 0.8852 (ttp) cc_final: 0.8629 (ttp) REVERT: B 175 GLN cc_start: 0.8336 (pt0) cc_final: 0.8080 (pt0) REVERT: R 228 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7219 (ttm110) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 1.1271 time to fit residues: 92.1016 Evaluate side-chains 77 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 190 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0060 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.101646 restraints weight = 8861.241| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.93 r_work: 0.3006 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6891 Z= 0.135 Angle : 0.427 6.150 9404 Z= 0.228 Chirality : 0.040 0.127 1109 Planarity : 0.003 0.028 1177 Dihedral : 8.666 157.213 992 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.84 % Allowed : 13.82 % Favored : 84.33 % 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: 1.39 (0.29), residues: 886 helix: 2.05 (0.27), residues: 384 sheet: 0.81 (0.41), residues: 181 loop : -0.36 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.002 0.001 HIS R 178 PHE 0.014 0.001 PHE R 101 TYR 0.009 0.001 TYR R 132 ARG 0.004 0.000 ARG R 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.83 seconds wall clock time: 47 minutes 42.05 seconds (2862.05 seconds total)