Starting phenix.real_space_refine on Sat Apr 6 00:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/04_2024/8uo2_42425_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/04_2024/8uo2_42425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/04_2024/8uo2_42425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/04_2024/8uo2_42425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/04_2024/8uo2_42425_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/04_2024/8uo2_42425_updated.pdb" } resolution = 3.6 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= 0.018 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 32 5.16 5 C 4126 2.51 5 N 1154 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 22": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 1920 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 6, 'TRANS': 276} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 536 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 18, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 278 Chain: "B" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2396 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 5, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 145 Chain: "G" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 341 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1800 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 629 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 252 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} Time building chain proxies: 4.36, per 1000 atoms: 0.67 Number of scatterers: 6504 At special positions: 0 Unit cell: (84.1669, 135.361, 98.0501, 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 32 16.00 P 3 15.00 O 1189 8.00 N 1154 7.00 C 4126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 44.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.698A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.736A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 165' Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.692A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.503A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.507A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 390 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.370A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.760A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 32 through 60 removed outlier: 4.032A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.713A pdb=" N VAL R 86 " --> pdb=" O GLY R 83 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL R 87 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.736A pdb=" N THR R 96 " --> pdb=" O HIS R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.748A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 144 removed outlier: 4.281A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.635A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 207 Processing helix chain 'R' and resid 209 through 236 removed outlier: 3.746A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 4.025A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.858A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 325 removed outlier: 3.702A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.897A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.778A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.693A 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 103 removed outlier: 6.951A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.782A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.797A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.848A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 284 through 287 Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.810A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 909 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: 1.74 Time building geometry restraints manager: 2.56 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: 1697 1.33 - 1.45: 1252 1.45 - 1.57: 3635 1.57 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 6629 Sorted by residual: bond pdb=" C ALA A 366 " pdb=" N VAL A 367 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.26e-02 6.30e+03 8.45e+01 bond pdb=" CA LYS A 338 " pdb=" C LYS A 338 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.81e+00 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.19e-02 7.06e+03 9.42e+00 bond pdb=" CA SER B 245 " pdb=" CB SER B 245 " ideal model delta sigma weight residual 1.535 1.471 0.064 2.09e-02 2.29e+03 9.32e+00 ... (remaining 6624 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 144 106.83 - 113.62: 3688 113.62 - 120.41: 2413 120.41 - 127.21: 2784 127.21 - 134.00: 74 Bond angle restraints: 9103 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 104.51 6.77 1.09e+00 8.42e-01 3.86e+01 angle pdb=" N GLN A 267 " pdb=" CA GLN A 267 " pdb=" C GLN A 267 " ideal model delta sigma weight residual 111.71 105.87 5.84 1.15e+00 7.56e-01 2.57e+01 angle pdb=" N GLU A 268 " pdb=" CA GLU A 268 " pdb=" C GLU A 268 " ideal model delta sigma weight residual 111.28 106.51 4.77 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.23 115.77 -6.54 1.55e+00 4.16e-01 1.78e+01 angle pdb=" C SER R 236 " pdb=" N GLU R 237 " pdb=" CA GLU R 237 " ideal model delta sigma weight residual 123.11 117.24 5.87 1.42e+00 4.96e-01 1.71e+01 ... (remaining 9098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 3757 33.33 - 66.67: 62 66.67 - 100.00: 4 100.00 - 133.33: 1 133.33 - 166.67: 2 Dihedral angle restraints: 3826 sinusoidal: 1036 harmonic: 2790 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 -97.40 166.67 1 2.00e+01 2.50e-03 4.74e+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 -54.17 158.76 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 274.12 159.15 114.97 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 3823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 898 0.055 - 0.110: 165 0.110 - 0.165: 39 0.165 - 0.220: 5 0.220 - 0.275: 1 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE A 257 " pdb=" N ILE A 257 " pdb=" C ILE A 257 " pdb=" CB ILE A 257 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1105 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 366 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ALA A 366 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 366 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 367 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 219 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ARG B 219 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 219 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 220 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 266 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C LEU A 266 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 266 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 267 " -0.013 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1201 2.77 - 3.30: 6148 3.30 - 3.83: 10315 3.83 - 4.37: 10584 4.37 - 4.90: 19302 Nonbonded interactions: 47550 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.237 2.440 nonbonded pdb=" O LEU A 45 " pdb=" CG2 VAL A 224 " model vdw 2.274 3.460 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.309 2.440 nonbonded pdb=" NE2 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.374 2.520 nonbonded pdb=" N SER A 54 " pdb=" O1B GTP A 401 " model vdw 2.377 2.520 ... (remaining 47545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 7.670 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.010 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 0.116 6629 Z= 0.359 Angle : 0.761 10.646 9103 Z= 0.488 Chirality : 0.047 0.275 1108 Planarity : 0.003 0.035 1167 Dihedral : 13.649 166.667 2005 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.40 % Allowed : 1.20 % Favored : 98.40 % 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 (0.28), residues: 936 helix: 2.46 (0.25), residues: 414 sheet: -0.21 (0.42), residues: 168 loop : -0.52 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE A 246 TYR 0.011 0.001 TYR R 316 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.724 Fit side-chains REVERT: G 48 ASP cc_start: 0.9036 (t70) cc_final: 0.8362 (t0) REVERT: R 217 PHE cc_start: 0.7921 (t80) cc_final: 0.7677 (t80) outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.1359 time to fit residues: 19.3934 Evaluate side-chains 73 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6629 Z= 0.302 Angle : 0.526 5.881 9103 Z= 0.297 Chirality : 0.042 0.162 1108 Planarity : 0.004 0.034 1167 Dihedral : 9.161 158.944 1031 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.40 % Allowed : 11.42 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 936 helix: 2.28 (0.25), residues: 416 sheet: -0.60 (0.40), residues: 173 loop : -0.85 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.019 0.002 PHE B 235 TYR 0.023 0.001 TYR R 308 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.668 Fit side-chains REVERT: A 344 GLU cc_start: 0.8266 (tp30) cc_final: 0.7952 (tp30) REVERT: B 298 ASP cc_start: 0.8536 (t0) cc_final: 0.7968 (t0) REVERT: G 48 ASP cc_start: 0.9063 (t70) cc_final: 0.8395 (t0) REVERT: R 209 TYR cc_start: 0.8047 (m-80) cc_final: 0.7665 (m-10) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.1372 time to fit residues: 16.5644 Evaluate side-chains 80 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6629 Z= 0.288 Angle : 0.499 6.086 9103 Z= 0.280 Chirality : 0.042 0.135 1108 Planarity : 0.004 0.041 1167 Dihedral : 8.988 157.596 1031 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.40 % Allowed : 16.83 % Favored : 80.76 % 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: 0.82 (0.28), residues: 936 helix: 2.28 (0.26), residues: 413 sheet: -0.76 (0.38), residues: 170 loop : -0.87 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.002 PHE B 235 TYR 0.021 0.001 TYR R 308 ARG 0.008 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.741 Fit side-chains REVERT: A 344 GLU cc_start: 0.8261 (tp30) cc_final: 0.8018 (tp30) REVERT: B 262 MET cc_start: 0.8611 (tpp) cc_final: 0.8287 (tpp) REVERT: B 298 ASP cc_start: 0.8565 (t0) cc_final: 0.8078 (t0) REVERT: G 48 ASP cc_start: 0.9113 (t70) cc_final: 0.8392 (t0) outliers start: 12 outliers final: 12 residues processed: 84 average time/residue: 0.1549 time to fit residues: 18.3816 Evaluate side-chains 83 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6629 Z= 0.184 Angle : 0.442 5.918 9103 Z= 0.244 Chirality : 0.040 0.130 1108 Planarity : 0.003 0.038 1167 Dihedral : 8.693 155.001 1031 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.81 % Allowed : 17.84 % Favored : 79.36 % 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: 1.01 (0.28), residues: 936 helix: 2.47 (0.26), residues: 414 sheet: -0.63 (0.39), residues: 170 loop : -0.85 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 313 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE B 199 TYR 0.024 0.001 TYR R 308 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.801 Fit side-chains REVERT: A 344 GLU cc_start: 0.8227 (tp30) cc_final: 0.7949 (tp30) REVERT: B 61 MET cc_start: 0.9167 (tmm) cc_final: 0.8928 (tmm) REVERT: B 262 MET cc_start: 0.8594 (tpp) cc_final: 0.8274 (tpp) REVERT: G 48 ASP cc_start: 0.9062 (t70) cc_final: 0.8273 (t0) REVERT: R 312 ASN cc_start: 0.8448 (t0) cc_final: 0.7839 (t0) REVERT: R 316 TYR cc_start: 0.8575 (m-10) cc_final: 0.8316 (m-10) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1509 time to fit residues: 18.9445 Evaluate side-chains 85 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6629 Z= 0.199 Angle : 0.444 5.968 9103 Z= 0.246 Chirality : 0.040 0.130 1108 Planarity : 0.003 0.038 1167 Dihedral : 8.509 153.702 1031 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.21 % Allowed : 18.24 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 936 helix: 2.57 (0.26), residues: 414 sheet: -0.61 (0.38), residues: 170 loop : -0.89 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE B 199 TYR 0.023 0.001 TYR R 308 ARG 0.008 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.715 Fit side-chains REVERT: A 344 GLU cc_start: 0.8269 (tp30) cc_final: 0.7961 (tp30) REVERT: B 61 MET cc_start: 0.9199 (tmm) cc_final: 0.8991 (tmm) REVERT: B 262 MET cc_start: 0.8642 (tpp) cc_final: 0.8249 (tpp) REVERT: G 48 ASP cc_start: 0.9050 (t70) cc_final: 0.8187 (t0) REVERT: R 312 ASN cc_start: 0.8377 (t0) cc_final: 0.7573 (t0) REVERT: R 316 TYR cc_start: 0.8513 (m-10) cc_final: 0.8121 (m-10) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.1360 time to fit residues: 17.4304 Evaluate side-chains 87 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6629 Z= 0.147 Angle : 0.422 5.869 9103 Z= 0.231 Chirality : 0.040 0.131 1108 Planarity : 0.003 0.037 1167 Dihedral : 8.269 151.285 1031 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.81 % Allowed : 19.84 % Favored : 77.35 % 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: 1.21 (0.28), residues: 936 helix: 2.68 (0.26), residues: 415 sheet: -0.55 (0.39), residues: 170 loop : -0.83 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.002 0.001 HIS A 220 PHE 0.019 0.001 PHE R 217 TYR 0.024 0.001 TYR R 308 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.280 Fit side-chains REVERT: A 344 GLU cc_start: 0.8228 (tp30) cc_final: 0.7940 (tp30) REVERT: B 262 MET cc_start: 0.8594 (tpp) cc_final: 0.8233 (tpp) REVERT: B 333 ASP cc_start: 0.7855 (p0) cc_final: 0.7644 (p0) REVERT: G 48 ASP cc_start: 0.9049 (t70) cc_final: 0.8234 (t0) REVERT: R 212 LEU cc_start: 0.7069 (tt) cc_final: 0.6762 (tp) REVERT: R 312 ASN cc_start: 0.8401 (t0) cc_final: 0.7799 (t0) REVERT: R 316 TYR cc_start: 0.8498 (m-10) cc_final: 0.8266 (m-10) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.1630 time to fit residues: 21.1747 Evaluate side-chains 86 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6629 Z= 0.279 Angle : 0.487 5.892 9103 Z= 0.270 Chirality : 0.041 0.135 1108 Planarity : 0.003 0.041 1167 Dihedral : 8.318 152.872 1031 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.01 % Allowed : 20.64 % Favored : 75.35 % 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: 1.01 (0.28), residues: 936 helix: 2.59 (0.27), residues: 413 sheet: -0.68 (0.39), residues: 170 loop : -0.97 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 313 HIS 0.004 0.001 HIS B 183 PHE 0.018 0.002 PHE R 217 TYR 0.023 0.001 TYR R 308 ARG 0.004 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.743 Fit side-chains REVERT: A 344 GLU cc_start: 0.8273 (tp30) cc_final: 0.7943 (tp30) REVERT: B 147 SER cc_start: 0.9215 (m) cc_final: 0.8997 (p) REVERT: B 262 MET cc_start: 0.8653 (tpp) cc_final: 0.8309 (tpp) REVERT: G 48 ASP cc_start: 0.9043 (t70) cc_final: 0.8152 (t0) REVERT: R 212 LEU cc_start: 0.7131 (tt) cc_final: 0.6865 (tp) REVERT: R 312 ASN cc_start: 0.8421 (t0) cc_final: 0.7524 (t0) REVERT: R 316 TYR cc_start: 0.8536 (m-10) cc_final: 0.8078 (m-10) outliers start: 20 outliers final: 14 residues processed: 90 average time/residue: 0.1322 time to fit residues: 17.6976 Evaluate side-chains 87 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.0370 chunk 84 optimal weight: 0.8980 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6629 Z= 0.135 Angle : 0.420 5.756 9103 Z= 0.231 Chirality : 0.040 0.132 1108 Planarity : 0.003 0.036 1167 Dihedral : 8.045 149.683 1031 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.21 % Allowed : 21.24 % Favored : 75.55 % 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: 1.22 (0.28), residues: 936 helix: 2.75 (0.26), residues: 415 sheet: -0.59 (0.39), residues: 170 loop : -0.86 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 313 HIS 0.002 0.001 HIS A 220 PHE 0.020 0.001 PHE R 217 TYR 0.024 0.001 TYR R 308 ARG 0.004 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.767 Fit side-chains REVERT: A 344 GLU cc_start: 0.8234 (tp30) cc_final: 0.7947 (tp30) REVERT: B 262 MET cc_start: 0.8573 (tpp) cc_final: 0.8258 (tpp) REVERT: B 308 LEU cc_start: 0.8322 (mt) cc_final: 0.7970 (mp) REVERT: B 333 ASP cc_start: 0.7874 (p0) cc_final: 0.7642 (p0) REVERT: G 48 ASP cc_start: 0.9020 (t70) cc_final: 0.8528 (t0) REVERT: R 212 LEU cc_start: 0.7069 (tt) cc_final: 0.6813 (tp) REVERT: R 312 ASN cc_start: 0.8409 (t0) cc_final: 0.7517 (t0) REVERT: R 316 TYR cc_start: 0.8421 (m-10) cc_final: 0.7991 (m-10) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.1421 time to fit residues: 19.1356 Evaluate side-chains 88 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 0.0070 chunk 76 optimal weight: 0.4980 chunk 79 optimal weight: 0.0370 chunk 84 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.2892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 6629 Z= 0.099 Angle : 0.398 5.816 9103 Z= 0.215 Chirality : 0.039 0.124 1108 Planarity : 0.003 0.034 1167 Dihedral : 7.576 143.958 1031 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.81 % Allowed : 22.24 % Favored : 74.95 % 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 (0.28), residues: 936 helix: 2.78 (0.26), residues: 421 sheet: -0.37 (0.40), residues: 167 loop : -0.81 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 313 HIS 0.002 0.000 HIS A 362 PHE 0.019 0.001 PHE R 217 TYR 0.023 0.001 TYR R 308 ARG 0.005 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.697 Fit side-chains REVERT: A 344 GLU cc_start: 0.8205 (tp30) cc_final: 0.7947 (tp30) REVERT: B 262 MET cc_start: 0.8496 (tpp) cc_final: 0.8192 (tpp) REVERT: B 298 ASP cc_start: 0.8455 (t0) cc_final: 0.7589 (t0) REVERT: B 333 ASP cc_start: 0.7735 (p0) cc_final: 0.7448 (p0) REVERT: R 316 TYR cc_start: 0.8316 (m-10) cc_final: 0.7963 (m-80) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 0.1213 time to fit residues: 17.1043 Evaluate side-chains 89 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6629 Z= 0.123 Angle : 0.412 5.840 9103 Z= 0.223 Chirality : 0.039 0.131 1108 Planarity : 0.003 0.032 1167 Dihedral : 7.485 143.774 1031 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.00 % Allowed : 23.25 % Favored : 74.75 % 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: 1.42 (0.28), residues: 936 helix: 2.87 (0.26), residues: 416 sheet: -0.41 (0.39), residues: 169 loop : -0.75 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.000 HIS B 142 PHE 0.020 0.001 PHE R 217 TYR 0.023 0.001 TYR R 308 ARG 0.004 0.000 ARG R 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.733 Fit side-chains REVERT: A 344 GLU cc_start: 0.8220 (tp30) cc_final: 0.7951 (tp30) REVERT: B 262 MET cc_start: 0.8537 (tpp) cc_final: 0.8204 (tpp) REVERT: B 333 ASP cc_start: 0.7846 (p0) cc_final: 0.7539 (p0) REVERT: R 212 LEU cc_start: 0.7108 (tt) cc_final: 0.6804 (tp) REVERT: R 316 TYR cc_start: 0.8418 (m-10) cc_final: 0.8088 (m-80) outliers start: 10 outliers final: 9 residues processed: 86 average time/residue: 0.1435 time to fit residues: 18.4304 Evaluate side-chains 84 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.0050 chunk 76 optimal weight: 0.0570 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.7916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092380 restraints weight = 14001.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095031 restraints weight = 7720.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096896 restraints weight = 5284.280| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6629 Z= 0.136 Angle : 0.414 5.792 9103 Z= 0.225 Chirality : 0.040 0.134 1108 Planarity : 0.003 0.033 1167 Dihedral : 7.397 144.063 1031 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.40 % Allowed : 23.05 % Favored : 74.55 % 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: 1.45 (0.28), residues: 936 helix: 2.91 (0.26), residues: 415 sheet: -0.39 (0.39), residues: 169 loop : -0.76 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS B 142 PHE 0.020 0.001 PHE R 217 TYR 0.023 0.001 TYR R 308 ARG 0.004 0.000 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.88 seconds wall clock time: 29 minutes 4.17 seconds (1744.17 seconds total)