Starting phenix.real_space_refine on Mon Mar 11 11:01:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h4k_34479/03_2024/8h4k_34479_neut_updated.pdb" } resolution = 3.1 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= 0.035 sd= 0.128 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 48 5.16 5 C 5158 2.51 5 N 1380 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 230": "OE1" <-> "OE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8078 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1857 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2533 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 402 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2316 Unusual residues: {'WPT': 1} Classifications: {'peptide': 299, 'undetermined': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 285, None: 1} Not linked: pdbres="LEU R 325 " pdbres="WPT R 401 " Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 4.79, per 1000 atoms: 0.59 Number of scatterers: 8078 At special positions: 0 Unit cell: (80.3, 102.3, 137.5, 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 48 16.00 O 1492 8.00 N 1380 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.5 seconds 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 36.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.999A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.545A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.725A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.943A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 36 through 67 removed outlier: 3.566A pdb=" N ARG R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 101 removed outlier: 4.208A pdb=" N SER R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 108 through 142 removed outlier: 5.481A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL R 141 " --> pdb=" O MET R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 168 Processing helix chain 'R' and resid 172 through 175 No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 201 through 215 Processing helix chain 'R' and resid 217 through 243 removed outlier: 3.590A pdb=" N LYS R 239 " --> pdb=" O LYS R 235 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG R 240 " --> pdb=" O ALA R 236 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 255 No H-bonds generated for 'chain 'R' and resid 252 through 255' Processing helix chain 'R' and resid 260 through 275 removed outlier: 4.168A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 292 Processing helix chain 'R' and resid 300 through 320 removed outlier: 4.211A pdb=" N ALA R 312 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.155A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.994A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.933A 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: 7.061A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.948A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.916A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.463A 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: 6.756A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.458A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.961A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 8 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.060A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 177 through 182 379 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2621 1.34 - 1.46: 1924 1.46 - 1.58: 3634 1.58 - 1.71: 0 1.71 - 1.83: 66 Bond restraints: 8245 Sorted by residual: bond pdb=" C12 WPT R 401 " pdb=" C14 WPT R 401 " ideal model delta sigma weight residual 1.530 1.564 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C08 WPT R 401 " pdb=" O07 WPT R 401 " ideal model delta sigma weight residual 1.402 1.433 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C20 WPT R 401 " pdb=" C21 WPT R 401 " ideal model delta sigma weight residual 1.386 1.415 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C17 WPT R 401 " pdb=" C18 WPT R 401 " ideal model delta sigma weight residual 1.386 1.415 -0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C23 WPT R 401 " pdb=" C24 WPT R 401 " ideal model delta sigma weight residual 1.528 1.556 -0.028 2.00e-02 2.50e+03 1.92e+00 ... (remaining 8240 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.16: 160 106.16 - 113.16: 4506 113.16 - 120.16: 2981 120.16 - 127.16: 3491 127.16 - 134.16: 88 Bond angle restraints: 11226 Sorted by residual: angle pdb=" C04 WPT R 401 " pdb=" O07 WPT R 401 " pdb=" C08 WPT R 401 " ideal model delta sigma weight residual 109.49 125.63 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" N GLU A 15 " pdb=" CA GLU A 15 " pdb=" C GLU A 15 " ideal model delta sigma weight residual 114.04 108.73 5.31 1.24e+00 6.50e-01 1.83e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.06 114.77 -4.71 1.43e+00 4.89e-01 1.09e+01 angle pdb=" C LEU B 261 " pdb=" N MET B 262 " pdb=" CA MET B 262 " ideal model delta sigma weight residual 121.85 116.49 5.36 1.77e+00 3.19e-01 9.16e+00 angle pdb=" C ASP A 252 " pdb=" N TYR A 253 " pdb=" CA TYR A 253 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.30e+00 ... (remaining 11221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4436 17.56 - 35.11: 348 35.11 - 52.67: 48 52.67 - 70.22: 17 70.22 - 87.78: 6 Dihedral angle restraints: 4855 sinusoidal: 1788 harmonic: 3067 Sorted by residual: dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA LEU B 308 " pdb=" C LEU B 308 " pdb=" N ALA B 309 " pdb=" CA ALA B 309 " ideal model delta harmonic sigma weight residual -180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 4852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 718 0.034 - 0.068: 413 0.068 - 0.102: 126 0.102 - 0.136: 54 0.136 - 0.170: 6 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 1314 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.051 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO G 53 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.57e+00 pdb=" N PRO R 172 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " -0.027 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 61 2.63 - 3.20: 6835 3.20 - 3.76: 11180 3.76 - 4.33: 15483 4.33 - 4.90: 27092 Nonbonded interactions: 60651 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.061 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.073 2.440 nonbonded pdb=" OG SER R 54 " pdb=" OG SER R 314 " model vdw 2.180 2.440 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.215 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.234 2.440 ... (remaining 60646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 3.880 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.750 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.006 0.043 8245 Z= 0.373 Angle : 0.756 16.135 11226 Z= 0.418 Chirality : 0.047 0.170 1317 Planarity : 0.005 0.078 1424 Dihedral : 13.503 87.778 2862 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.17 (0.26), residues: 1041 helix: 1.51 (0.27), residues: 392 sheet: 0.16 (0.32), residues: 244 loop : -1.31 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 82 HIS 0.018 0.002 HIS A 357 PHE 0.024 0.003 PHE B 151 TYR 0.020 0.002 TYR R 247 ARG 0.009 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.965 Fit side-chains REVERT: B 135 VAL cc_start: 0.8543 (t) cc_final: 0.8291 (p) REVERT: R 89 ILE cc_start: 0.8430 (tp) cc_final: 0.8172 (tp) REVERT: R 213 THR cc_start: 0.7620 (t) cc_final: 0.7395 (t) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1840 time to fit residues: 24.9279 Evaluate side-chains 85 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN R 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8245 Z= 0.185 Angle : 0.550 9.005 11226 Z= 0.293 Chirality : 0.043 0.150 1317 Planarity : 0.004 0.057 1424 Dihedral : 5.507 68.011 1139 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.82 % Allowed : 5.76 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1041 helix: 1.86 (0.28), residues: 395 sheet: 0.54 (0.32), residues: 250 loop : -1.33 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.015 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.974 Fit side-chains REVERT: B 135 VAL cc_start: 0.8517 (t) cc_final: 0.8258 (p) REVERT: R 89 ILE cc_start: 0.8399 (tp) cc_final: 0.8123 (tp) REVERT: R 137 MET cc_start: 0.7483 (tmm) cc_final: 0.7162 (tmm) REVERT: R 213 THR cc_start: 0.7636 (t) cc_final: 0.7384 (t) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.1712 time to fit residues: 23.9676 Evaluate side-chains 92 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 173 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8245 Z= 0.150 Angle : 0.493 5.691 11226 Z= 0.266 Chirality : 0.041 0.146 1317 Planarity : 0.004 0.049 1424 Dihedral : 5.267 73.549 1139 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.94 % Allowed : 8.35 % Favored : 90.71 % 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: 0.81 (0.27), residues: 1041 helix: 2.02 (0.27), residues: 400 sheet: 0.67 (0.32), residues: 245 loop : -1.13 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE R 263 TYR 0.010 0.001 TYR N 95 ARG 0.003 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.873 Fit side-chains REVERT: B 135 VAL cc_start: 0.8532 (t) cc_final: 0.8272 (p) REVERT: R 137 MET cc_start: 0.7291 (tmm) cc_final: 0.7062 (tmm) REVERT: R 213 THR cc_start: 0.7610 (t) cc_final: 0.7348 (t) outliers start: 8 outliers final: 8 residues processed: 94 average time/residue: 0.1714 time to fit residues: 23.4844 Evaluate side-chains 96 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 173 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.0870 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 0.0050 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8245 Z= 0.124 Angle : 0.473 7.646 11226 Z= 0.252 Chirality : 0.041 0.168 1317 Planarity : 0.003 0.045 1424 Dihedral : 5.117 76.037 1139 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.41 % Allowed : 9.29 % Favored : 89.29 % 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: 1.12 (0.27), residues: 1041 helix: 2.48 (0.28), residues: 383 sheet: 0.77 (0.32), residues: 245 loop : -0.98 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.009 0.001 TYR N 95 ARG 0.003 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.925 Fit side-chains REVERT: B 135 VAL cc_start: 0.8521 (t) cc_final: 0.8266 (p) REVERT: R 89 ILE cc_start: 0.8407 (tp) cc_final: 0.8176 (tp) REVERT: R 213 THR cc_start: 0.7537 (t) cc_final: 0.7264 (t) outliers start: 12 outliers final: 11 residues processed: 100 average time/residue: 0.1730 time to fit residues: 25.0515 Evaluate side-chains 99 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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: 0.7690 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8245 Z= 0.153 Angle : 0.486 5.770 11226 Z= 0.260 Chirality : 0.041 0.183 1317 Planarity : 0.004 0.045 1424 Dihedral : 5.078 75.134 1139 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.65 % Allowed : 10.35 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 1041 helix: 2.41 (0.27), residues: 387 sheet: 0.79 (0.32), residues: 245 loop : -0.96 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.011 0.001 TYR N 95 ARG 0.002 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.961 Fit side-chains REVERT: B 135 VAL cc_start: 0.8543 (t) cc_final: 0.8297 (p) REVERT: R 213 THR cc_start: 0.7551 (t) cc_final: 0.7269 (t) REVERT: R 296 LEU cc_start: 0.7096 (mt) cc_final: 0.6864 (tt) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.1707 time to fit residues: 24.6915 Evaluate side-chains 98 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 142 HIS Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 0.0270 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN R 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8245 Z= 0.248 Angle : 0.570 7.951 11226 Z= 0.303 Chirality : 0.044 0.196 1317 Planarity : 0.004 0.046 1424 Dihedral : 5.288 72.134 1139 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.00 % Allowed : 11.53 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 1041 helix: 2.09 (0.27), residues: 394 sheet: 0.67 (0.33), residues: 239 loop : -0.98 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.010 0.001 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.015 0.002 TYR N 95 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.888 Fit side-chains REVERT: A 230 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: B 135 VAL cc_start: 0.8548 (t) cc_final: 0.8323 (p) REVERT: B 262 MET cc_start: 0.7224 (tpp) cc_final: 0.6965 (ttm) REVERT: R 213 THR cc_start: 0.7623 (t) cc_final: 0.7341 (t) REVERT: R 247 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: R 296 LEU cc_start: 0.7192 (mt) cc_final: 0.6927 (tt) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.1761 time to fit residues: 25.0634 Evaluate side-chains 96 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 0.0270 chunk 62 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8245 Z= 0.132 Angle : 0.473 5.060 11226 Z= 0.255 Chirality : 0.041 0.201 1317 Planarity : 0.003 0.045 1424 Dihedral : 5.053 74.867 1139 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.41 % Allowed : 12.47 % Favored : 86.12 % 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: 1.10 (0.27), residues: 1041 helix: 2.40 (0.27), residues: 387 sheet: 0.70 (0.32), residues: 249 loop : -0.93 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 199 TYR 0.010 0.001 TYR N 95 ARG 0.002 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.983 Fit side-chains REVERT: B 135 VAL cc_start: 0.8508 (t) cc_final: 0.8264 (p) REVERT: B 262 MET cc_start: 0.7276 (tpp) cc_final: 0.6931 (ttm) REVERT: R 213 THR cc_start: 0.7515 (t) cc_final: 0.7224 (t) REVERT: R 247 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6234 (m-10) REVERT: R 296 LEU cc_start: 0.7104 (mt) cc_final: 0.6858 (tt) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 0.1810 time to fit residues: 24.7627 Evaluate side-chains 97 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 49 optimal weight: 0.0020 chunk 9 optimal weight: 0.4980 chunk 78 optimal weight: 0.0040 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.3202 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8245 Z= 0.115 Angle : 0.462 9.098 11226 Z= 0.244 Chirality : 0.041 0.204 1317 Planarity : 0.003 0.045 1424 Dihedral : 4.855 76.475 1139 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.53 % Allowed : 12.59 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 1041 helix: 2.64 (0.27), residues: 382 sheet: 0.76 (0.32), residues: 249 loop : -0.81 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE R 263 TYR 0.008 0.001 TYR N 95 ARG 0.002 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.915 Fit side-chains REVERT: B 135 VAL cc_start: 0.8522 (t) cc_final: 0.8274 (p) REVERT: N 20 LEU cc_start: 0.7642 (mt) cc_final: 0.7409 (mp) REVERT: R 213 THR cc_start: 0.7403 (t) cc_final: 0.7099 (t) REVERT: R 247 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6227 (m-10) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1701 time to fit residues: 23.8859 Evaluate side-chains 99 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8245 Z= 0.184 Angle : 0.536 13.335 11226 Z= 0.278 Chirality : 0.042 0.210 1317 Planarity : 0.004 0.044 1424 Dihedral : 4.972 74.574 1139 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.41 % Allowed : 12.71 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1041 helix: 2.54 (0.27), residues: 382 sheet: 0.78 (0.32), residues: 256 loop : -0.86 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 104 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.014 0.001 TYR N 95 ARG 0.002 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.910 Fit side-chains REVERT: B 135 VAL cc_start: 0.8531 (t) cc_final: 0.8292 (p) REVERT: N 83 MET cc_start: 0.7995 (mtt) cc_final: 0.7620 (ptp) REVERT: R 213 THR cc_start: 0.7538 (t) cc_final: 0.7238 (t) REVERT: R 247 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6299 (m-10) outliers start: 12 outliers final: 9 residues processed: 96 average time/residue: 0.1760 time to fit residues: 24.2283 Evaluate side-chains 97 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8245 Z= 0.175 Angle : 0.526 7.824 11226 Z= 0.275 Chirality : 0.042 0.209 1317 Planarity : 0.004 0.045 1424 Dihedral : 4.956 74.453 1139 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.53 % Allowed : 12.94 % Favored : 85.53 % 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: 1.24 (0.27), residues: 1041 helix: 2.53 (0.27), residues: 382 sheet: 0.71 (0.32), residues: 258 loop : -0.82 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 104 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.012 0.001 TYR N 95 ARG 0.002 0.000 ARG R 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.883 Fit side-chains REVERT: A 230 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: B 135 VAL cc_start: 0.8525 (t) cc_final: 0.8285 (p) REVERT: R 213 THR cc_start: 0.7529 (t) cc_final: 0.7229 (t) REVERT: R 247 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6270 (m-10) outliers start: 13 outliers final: 11 residues processed: 94 average time/residue: 0.1706 time to fit residues: 23.2079 Evaluate side-chains 98 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 247 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096487 restraints weight = 12894.105| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.49 r_work: 0.3160 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8245 Z= 0.139 Angle : 0.493 7.328 11226 Z= 0.260 Chirality : 0.041 0.214 1317 Planarity : 0.003 0.045 1424 Dihedral : 4.872 75.464 1139 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.53 % Allowed : 12.82 % Favored : 85.65 % 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: 1.28 (0.27), residues: 1041 helix: 2.58 (0.27), residues: 382 sheet: 0.73 (0.32), residues: 256 loop : -0.80 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.010 0.001 TYR N 95 ARG 0.002 0.000 ARG R 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.67 seconds wall clock time: 35 minutes 23.34 seconds (2123.34 seconds total)