Starting phenix.real_space_refine on Sat Apr 6 00:19:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge2_29953/04_2024/8ge2_29953_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge2_29953/04_2024/8ge2_29953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge2_29953/04_2024/8ge2_29953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge2_29953/04_2024/8ge2_29953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge2_29953/04_2024/8ge2_29953_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge2_29953/04_2024/8ge2_29953_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4174 2.51 5 N 1136 2.21 5 O 1123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6473 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1679 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 172 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2349 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 5, 'TRANS': 327} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 6, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 149 Chain: "G" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 356 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 2074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2074 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 126 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: 4.10, per 1000 atoms: 0.63 Number of scatterers: 6473 At special positions: 0 Unit cell: (72.08, 97.52, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1123 8.00 N 1136 7.00 C 4174 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 8 sheets defined 44.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'A' and resid 53 through 61 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 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.592A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 9 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.910A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 60 Processing helix chain 'R' and resid 67 through 96 removed outlier: 3.653A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.423A 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 Processing helix chain 'R' and resid 138 through 144 removed outlier: 4.041A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.903A 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 236 removed outlier: 5.114A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 269 through 298 removed outlier: 4.445A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 305 through 326 removed outlier: 4.070A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.446A 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 339 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.961A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.967A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.021A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.522A 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: 6.815A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 3.504A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.058A 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: 6.468A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.577A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.924A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 1017 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: 1.85 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2103 1.34 - 1.46: 1519 1.46 - 1.58: 2936 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6614 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.568 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.562 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" CAD G1I R 501 " pdb=" OAK G1I R 501 " ideal model delta sigma weight residual 1.353 1.322 0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.45: 135 106.45 - 113.34: 3647 113.34 - 120.24: 2218 120.24 - 127.14: 2971 127.14 - 134.04: 74 Bond angle restraints: 9045 Sorted by residual: angle pdb=" CA LEU R 144 " pdb=" CB LEU R 144 " pdb=" CG LEU R 144 " ideal model delta sigma weight residual 116.30 123.53 -7.23 3.50e+00 8.16e-02 4.26e+00 angle pdb=" N GLN R 231 " pdb=" CA GLN R 231 " pdb=" CB GLN R 231 " ideal model delta sigma weight residual 110.16 112.88 -2.72 1.48e+00 4.57e-01 3.37e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.97 -5.34 3.00e+00 1.11e-01 3.17e+00 angle pdb=" C GLY A 49 " pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 122.08 124.65 -2.57 1.47e+00 4.63e-01 3.05e+00 angle pdb=" N HIS R 296 " pdb=" CA HIS R 296 " pdb=" CB HIS R 296 " ideal model delta sigma weight residual 110.30 112.83 -2.53 1.54e+00 4.22e-01 2.70e+00 ... (remaining 9040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3481 16.18 - 32.35: 272 32.35 - 48.53: 56 48.53 - 64.71: 7 64.71 - 80.88: 4 Dihedral angle restraints: 3820 sinusoidal: 1172 harmonic: 2648 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LEU R 144 " pdb=" C LEU R 144 " pdb=" N LEU R 145 " pdb=" CA LEU R 145 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CG LYS B 209 " pdb=" CD LYS B 209 " pdb=" CE LYS B 209 " pdb=" NZ LYS B 209 " ideal model delta sinusoidal sigma weight residual 180.00 127.61 52.39 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 3817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 738 0.034 - 0.069: 240 0.069 - 0.103: 75 0.103 - 0.138: 26 0.138 - 0.172: 1 Chirality restraints: 1080 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 2.57 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE G 25 " pdb=" N ILE G 25 " pdb=" C ILE G 25 " pdb=" CB ILE G 25 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1077 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.06e+00 pdb=" C ILE R 205 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.009 2.00e-02 2.50e+03 7.38e-03 1.09e+00 pdb=" CG TYR B 59 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.87e-01 pdb=" N PRO R 168 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " 0.012 5.00e-02 4.00e+02 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 565 2.74 - 3.28: 6440 3.28 - 3.82: 11002 3.82 - 4.36: 11996 4.36 - 4.90: 22125 Nonbonded interactions: 52128 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR R 98 " pdb=" O THR R 189 " model vdw 2.295 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.314 2.440 nonbonded pdb=" O ARG A 283 " pdb=" OG1 THR A 284 " model vdw 2.332 2.440 nonbonded pdb=" NE2 GLN A 19 " pdb=" OD2 ASP B 83 " model vdw 2.338 2.520 ... (remaining 52123 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=0.00 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: 1.620 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: 6.510 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 21.960 Find NCS groups from input model: 0.210 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.003 0.053 6614 Z= 0.195 Angle : 0.451 7.228 9045 Z= 0.238 Chirality : 0.040 0.172 1080 Planarity : 0.003 0.029 1143 Dihedral : 12.658 80.883 2097 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.64 (0.28), residues: 892 helix: 2.55 (0.26), residues: 392 sheet: 0.34 (0.38), residues: 167 loop : -0.28 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE B 234 TYR 0.018 0.001 TYR B 59 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 278 ASN cc_start: 0.9113 (m-40) cc_final: 0.8857 (m-40) REVERT: B 147 SER cc_start: 0.8963 (m) cc_final: 0.8699 (m) REVERT: B 175 GLN cc_start: 0.8308 (pm20) cc_final: 0.8038 (pm20) REVERT: B 259 GLN cc_start: 0.8241 (pt0) cc_final: 0.8024 (pt0) REVERT: R 111 SER cc_start: 0.8965 (m) cc_final: 0.8726 (m) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1687 time to fit residues: 25.2374 Evaluate side-chains 86 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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: 0.0970 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6614 Z= 0.228 Angle : 0.461 6.726 9045 Z= 0.245 Chirality : 0.041 0.125 1080 Planarity : 0.003 0.023 1143 Dihedral : 3.843 18.283 981 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.72 % Allowed : 9.40 % Favored : 89.87 % 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: 1.88 (0.29), residues: 892 helix: 2.76 (0.26), residues: 391 sheet: 0.36 (0.37), residues: 181 loop : -0.10 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE R 240 TYR 0.023 0.001 TYR B 59 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 278 ASN cc_start: 0.9162 (m-40) cc_final: 0.8883 (m-40) REVERT: B 175 GLN cc_start: 0.8256 (pm20) cc_final: 0.7990 (pm20) REVERT: R 111 SER cc_start: 0.8939 (m) cc_final: 0.8705 (m) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.1684 time to fit residues: 20.9511 Evaluate side-chains 84 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 72 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6614 Z= 0.134 Angle : 0.412 6.770 9045 Z= 0.218 Chirality : 0.039 0.129 1080 Planarity : 0.002 0.021 1143 Dihedral : 3.627 17.481 981 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.63 % Allowed : 12.48 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.29), residues: 892 helix: 2.89 (0.26), residues: 390 sheet: 0.46 (0.37), residues: 184 loop : -0.09 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 PHE 0.007 0.001 PHE B 241 TYR 0.014 0.001 TYR B 59 ARG 0.001 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.781 Fit side-chains REVERT: B 175 GLN cc_start: 0.8241 (pm20) cc_final: 0.8012 (pm20) REVERT: B 259 GLN cc_start: 0.8211 (pt0) cc_final: 0.7923 (pt0) REVERT: R 111 SER cc_start: 0.8889 (m) cc_final: 0.8681 (m) REVERT: R 228 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7579 (ttp-110) REVERT: R 279 MET cc_start: 0.8651 (mmm) cc_final: 0.8338 (mmm) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.1762 time to fit residues: 24.6982 Evaluate side-chains 96 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6614 Z= 0.221 Angle : 0.441 6.747 9045 Z= 0.234 Chirality : 0.041 0.148 1080 Planarity : 0.003 0.023 1143 Dihedral : 3.703 14.445 981 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.71 % Allowed : 13.38 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.29), residues: 892 helix: 2.91 (0.26), residues: 389 sheet: 0.52 (0.37), residues: 186 loop : -0.04 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE R 289 TYR 0.019 0.001 TYR B 59 ARG 0.006 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.846 Fit side-chains REVERT: B 175 GLN cc_start: 0.8233 (pm20) cc_final: 0.8026 (pm20) REVERT: B 262 MET cc_start: 0.8834 (tpp) cc_final: 0.8531 (tpp) REVERT: R 228 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7285 (ttp-110) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 0.1812 time to fit residues: 24.5799 Evaluate side-chains 90 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 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: 2.9990 chunk 35 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6614 Z= 0.194 Angle : 0.433 7.335 9045 Z= 0.229 Chirality : 0.040 0.129 1080 Planarity : 0.003 0.021 1143 Dihedral : 3.676 14.548 981 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.17 % Allowed : 15.19 % Favored : 82.64 % 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: 1.99 (0.29), residues: 892 helix: 2.84 (0.26), residues: 390 sheet: 0.49 (0.37), residues: 186 loop : -0.09 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 172 PHE 0.008 0.001 PHE R 240 TYR 0.015 0.001 TYR B 59 ARG 0.006 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.718 Fit side-chains REVERT: B 259 GLN cc_start: 0.8074 (pt0) cc_final: 0.7717 (pt0) REVERT: B 262 MET cc_start: 0.8859 (tpp) cc_final: 0.8533 (tpp) REVERT: G 48 ASP cc_start: 0.8793 (t0) cc_final: 0.8499 (t0) REVERT: R 228 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7325 (ttp-110) outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.1606 time to fit residues: 21.4600 Evaluate side-chains 95 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6614 Z= 0.203 Angle : 0.439 7.643 9045 Z= 0.232 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.021 1143 Dihedral : 3.681 14.459 981 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.35 % Allowed : 16.27 % Favored : 81.37 % 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: 1.97 (0.29), residues: 892 helix: 2.83 (0.26), residues: 390 sheet: 0.46 (0.37), residues: 186 loop : -0.09 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.000 HIS B 225 PHE 0.010 0.001 PHE R 289 TYR 0.016 0.001 TYR B 59 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.698 Fit side-chains REVERT: B 259 GLN cc_start: 0.7982 (pt0) cc_final: 0.7629 (pt0) REVERT: B 262 MET cc_start: 0.8874 (tpp) cc_final: 0.8559 (tpp) REVERT: G 38 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7946 (mtp) REVERT: G 48 ASP cc_start: 0.8748 (t0) cc_final: 0.8473 (t0) REVERT: R 228 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7606 (ttp-110) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 0.1667 time to fit residues: 22.2292 Evaluate side-chains 95 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6614 Z= 0.204 Angle : 0.437 7.876 9045 Z= 0.231 Chirality : 0.040 0.133 1080 Planarity : 0.003 0.022 1143 Dihedral : 3.690 14.474 981 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.89 % Allowed : 16.27 % Favored : 80.83 % 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: 1.98 (0.29), residues: 892 helix: 2.81 (0.26), residues: 391 sheet: 0.63 (0.37), residues: 179 loop : -0.16 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.010 0.001 PHE R 289 TYR 0.016 0.001 TYR B 59 ARG 0.008 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.604 Fit side-chains REVERT: B 259 GLN cc_start: 0.8017 (pt0) cc_final: 0.7683 (pt0) REVERT: B 262 MET cc_start: 0.8874 (tpp) cc_final: 0.8556 (tpp) REVERT: B 316 SER cc_start: 0.9160 (t) cc_final: 0.8882 (t) REVERT: G 38 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.8002 (mtp) REVERT: G 48 ASP cc_start: 0.8757 (t0) cc_final: 0.8494 (t0) REVERT: R 228 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7602 (ttp-110) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.1682 time to fit residues: 23.1020 Evaluate side-chains 99 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 0.0470 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6614 Z= 0.173 Angle : 0.441 8.259 9045 Z= 0.231 Chirality : 0.040 0.131 1080 Planarity : 0.003 0.022 1143 Dihedral : 3.644 14.513 981 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.07 % Allowed : 16.46 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.29), residues: 892 helix: 2.90 (0.26), residues: 386 sheet: 0.51 (0.37), residues: 177 loop : -0.19 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.008 0.001 PHE R 290 TYR 0.017 0.001 TYR A 253 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.671 Fit side-chains REVERT: B 59 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: B 259 GLN cc_start: 0.8003 (pt0) cc_final: 0.7658 (pt0) REVERT: B 262 MET cc_start: 0.8865 (tpp) cc_final: 0.8557 (tpp) REVERT: B 316 SER cc_start: 0.9157 (t) cc_final: 0.8873 (t) REVERT: G 48 ASP cc_start: 0.8721 (t0) cc_final: 0.8454 (t0) REVERT: R 228 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7707 (ttp-110) REVERT: R 279 MET cc_start: 0.8730 (mmm) cc_final: 0.8514 (mmm) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.1585 time to fit residues: 22.2174 Evaluate side-chains 101 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 75 optimal weight: 0.0060 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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** R 172 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6614 Z= 0.130 Angle : 0.434 8.752 9045 Z= 0.227 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.035 1143 Dihedral : 3.518 14.631 981 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.35 % Allowed : 17.00 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.29), residues: 892 helix: 3.00 (0.26), residues: 385 sheet: 0.58 (0.37), residues: 177 loop : -0.18 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.007 0.001 HIS R 172 PHE 0.007 0.001 PHE R 290 TYR 0.018 0.001 TYR A 253 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.659 Fit side-chains REVERT: B 59 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: B 175 GLN cc_start: 0.8274 (pm20) cc_final: 0.7972 (pm20) REVERT: B 262 MET cc_start: 0.8789 (tpp) cc_final: 0.8480 (tpp) REVERT: B 316 SER cc_start: 0.9115 (t) cc_final: 0.8845 (t) REVERT: G 48 ASP cc_start: 0.8726 (t0) cc_final: 0.8456 (t0) REVERT: G 50 LEU cc_start: 0.7927 (mt) cc_final: 0.7626 (mt) REVERT: R 228 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7434 (ttp-110) REVERT: R 293 ASN cc_start: 0.7330 (t0) cc_final: 0.7117 (t0) outliers start: 13 outliers final: 10 residues processed: 99 average time/residue: 0.1550 time to fit residues: 21.4883 Evaluate side-chains 98 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 59 GLN B 88 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6614 Z= 0.174 Angle : 0.445 8.652 9045 Z= 0.234 Chirality : 0.040 0.181 1080 Planarity : 0.003 0.022 1143 Dihedral : 3.555 14.606 981 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.53 % Allowed : 17.18 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.29), residues: 892 helix: 2.94 (0.26), residues: 386 sheet: 0.58 (0.37), residues: 177 loop : -0.20 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.000 HIS B 225 PHE 0.008 0.001 PHE R 240 TYR 0.018 0.001 TYR A 253 ARG 0.006 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.722 Fit side-chains REVERT: B 59 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: B 175 GLN cc_start: 0.8256 (pm20) cc_final: 0.7994 (pm20) REVERT: B 262 MET cc_start: 0.8873 (tpp) cc_final: 0.8615 (tpp) REVERT: B 316 SER cc_start: 0.9134 (t) cc_final: 0.8862 (t) REVERT: B 322 ASP cc_start: 0.8312 (m-30) cc_final: 0.7950 (m-30) REVERT: G 48 ASP cc_start: 0.8783 (t0) cc_final: 0.8478 (t0) REVERT: R 228 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7264 (ttp-110) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.1517 time to fit residues: 20.5495 Evaluate side-chains 96 residues out of total 785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 0.0170 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.096216 restraints weight = 10734.721| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.72 r_work: 0.3089 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6614 Z= 0.146 Angle : 0.437 8.681 9045 Z= 0.229 Chirality : 0.040 0.173 1080 Planarity : 0.003 0.022 1143 Dihedral : 3.529 14.610 981 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.71 % Allowed : 16.82 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.29), residues: 892 helix: 2.98 (0.26), residues: 385 sheet: 0.60 (0.37), residues: 177 loop : -0.20 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS B 225 PHE 0.007 0.001 PHE R 290 TYR 0.018 0.001 TYR A 253 ARG 0.007 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.25 seconds wall clock time: 31 minutes 1.20 seconds (1861.20 seconds total)