Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 23:53:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/10_2023/7xov_33360_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 61 5.16 5 Cl 1 4.86 5 C 5217 2.51 5 N 1427 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8218 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1884 Classifications: {'peptide': 227} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118} Chain: "R" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2336 Unusual residues: {'IA1': 1} Classifications: {'peptide': 288, 'undetermined': 1, 'water': 1} Link IDs: {'PTRANS': 11, 'TRANS': 276, None: 2} Not linked: pdbres="PHE R 385 " pdbres="IA1 R 501 " Not linked: pdbres="IA1 R 501 " pdbres="HOH R 601 " Chain breaks: 1 Time building chain proxies: 4.67, per 1000 atoms: 0.57 Number of scatterers: 8218 At special positions: 0 Unit cell: (90.246, 95.316, 134.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 61 16.00 O 1512 8.00 N 1427 7.00 C 5217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " 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: 3.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.515A pdb=" N LYS A 17 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A 38 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.027A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.575A pdb=" N ILE A 383 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.983A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.400A pdb=" N ARG G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL G 16 " --> pdb=" O ARG G 13 " (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 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' 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 44 through 68 removed outlier: 3.548A pdb=" N ILE R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 94 Processing helix chain 'R' and resid 99 through 104 removed outlier: 3.551A pdb=" N LEU R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 144 Processing helix chain 'R' and resid 146 through 152 removed outlier: 4.351A pdb=" N VAL R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 172 removed outlier: 4.140A pdb=" N LYS R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR R 171 " --> pdb=" O CYS R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 176 No H-bonds generated for 'chain 'R' and resid 174 through 176' Processing helix chain 'R' and resid 204 through 217 removed outlier: 3.702A pdb=" N TRP R 209 " --> pdb=" O GLN R 206 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE R 216 " --> pdb=" O LEU R 213 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU R 217 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 243 Processing helix chain 'R' and resid 302 through 338 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 340 through 349 removed outlier: 3.632A pdb=" N GLY R 349 " --> pdb=" O ARG R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 370 removed outlier: 3.804A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS R 364 " --> pdb=" O TYR R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 379 through 384 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.146A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.838A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.246A 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: 6.902A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.364A 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 152 removed outlier: 6.856A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.616A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.867A 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: 6.749A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.701A 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: 6.522A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.144A 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: 6.870A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.722A 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 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.837A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 180 through 182 390 hydrogen bonds defined for protein. 939 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: 2.09 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1400 1.31 - 1.44: 2275 1.44 - 1.57: 4588 1.57 - 1.70: 29 1.70 - 1.83: 89 Bond restraints: 8381 Sorted by residual: bond pdb=" C23 IA1 R 501 " pdb=" C30 IA1 R 501 " ideal model delta sigma weight residual 1.411 1.572 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C25 IA1 R 501 " pdb=" C32 IA1 R 501 " ideal model delta sigma weight residual 1.411 1.565 -0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" C26 IA1 R 501 " pdb=" C36 IA1 R 501 " ideal model delta sigma weight residual 1.391 1.537 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C22 IA1 R 501 " pdb=" C26 IA1 R 501 " ideal model delta sigma weight residual 1.391 1.534 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C22 IA1 R 501 " pdb=" C27 IA1 R 501 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.79e+01 ... (remaining 8376 not shown) Histogram of bond angle deviations from ideal: 96.53 - 108.16: 648 108.16 - 119.80: 6942 119.80 - 131.43: 3730 131.43 - 143.07: 24 143.07 - 154.71: 2 Bond angle restraints: 11346 Sorted by residual: angle pdb=" C LYS R 187 " pdb=" N ASN R 188 " pdb=" CA ASN R 188 " ideal model delta sigma weight residual 120.72 154.71 -33.99 1.67e+00 3.59e-01 4.14e+02 angle pdb=" C THR N 28 " pdb=" N PHE N 29 " pdb=" CA PHE N 29 " ideal model delta sigma weight residual 122.85 96.53 26.32 1.39e+00 5.18e-01 3.59e+02 angle pdb=" C GLN N 120 " pdb=" N GLY N 121 " pdb=" CA GLY N 121 " ideal model delta sigma weight residual 121.70 151.55 -29.85 1.80e+00 3.09e-01 2.75e+02 angle pdb=" C36 IA1 R 501 " pdb=" C26 IA1 R 501 " pdb=" O3 IA1 R 501 " ideal model delta sigma weight residual 70.88 120.41 -49.53 3.00e+00 1.11e-01 2.73e+02 angle pdb=" C22 IA1 R 501 " pdb=" C26 IA1 R 501 " pdb=" O3 IA1 R 501 " ideal model delta sigma weight residual 81.60 120.41 -38.81 3.00e+00 1.11e-01 1.67e+02 ... (remaining 11341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4802 17.11 - 34.22: 142 34.22 - 51.34: 33 51.34 - 68.45: 24 68.45 - 85.56: 7 Dihedral angle restraints: 5008 sinusoidal: 1992 harmonic: 3016 Sorted by residual: dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta harmonic sigma weight residual 180.00 -141.20 -38.80 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA ASN N 84 " pdb=" C ASN N 84 " pdb=" N SER N 85 " pdb=" CA SER N 85 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual -86.00 -144.12 58.12 1 1.00e+01 1.00e-02 4.53e+01 ... (remaining 5005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 824 0.080 - 0.160: 347 0.160 - 0.239: 95 0.239 - 0.319: 15 0.319 - 0.399: 1 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA GLU A 230 " pdb=" N GLU A 230 " pdb=" C GLU A 230 " pdb=" CB GLU A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA TYR B 111 " pdb=" N TYR B 111 " pdb=" C TYR B 111 " pdb=" CB TYR B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ILE B 171 " pdb=" N ILE B 171 " pdb=" C ILE B 171 " pdb=" CB ILE B 171 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1279 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 237 " 0.072 2.00e-02 2.50e+03 1.48e-01 2.19e+02 pdb=" C ASN B 237 " -0.256 2.00e-02 2.50e+03 pdb=" O ASN B 237 " 0.096 2.00e-02 2.50e+03 pdb=" N GLY B 238 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 66 " 0.067 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C ASP B 66 " -0.249 2.00e-02 2.50e+03 pdb=" O ASP B 66 " 0.098 2.00e-02 2.50e+03 pdb=" N SER B 67 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 276 " 0.066 2.00e-02 2.50e+03 1.44e-01 2.07e+02 pdb=" C ILE A 276 " -0.249 2.00e-02 2.50e+03 pdb=" O ILE A 276 " 0.099 2.00e-02 2.50e+03 pdb=" N TRP A 277 " 0.084 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2598 2.84 - 3.35: 7991 3.35 - 3.87: 13718 3.87 - 4.38: 16957 4.38 - 4.90: 27124 Nonbonded interactions: 68388 Sorted by model distance: nonbonded pdb=" O THR N 28 " pdb=" CA PHE N 29 " model vdw 2.322 2.776 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.342 2.520 nonbonded pdb=" N SER N 30 " pdb=" N ASN N 31 " model vdw 2.344 2.560 nonbonded pdb=" CD1 LEU R 347 " pdb=" C39 IA1 R 501 " model vdw 2.346 3.880 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.352 2.440 ... (remaining 68383 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: 0.370 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: 2.000 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.240 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0298 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 : 0.019 0.161 8381 Z= 1.231 Angle : 1.976 49.535 11346 Z= 1.261 Chirality : 0.091 0.399 1282 Planarity : 0.017 0.148 1440 Dihedral : 10.839 85.562 3043 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 0.90 % Allowed : 1.01 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: 0.50 (0.25), residues: 1018 helix: -0.26 (0.23), residues: 388 sheet: 1.46 (0.33), residues: 215 loop : 0.54 (0.31), residues: 415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 1.2608 time to fit residues: 118.0444 Evaluate side-chains 59 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.2633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN R 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1166 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8381 Z= 0.250 Angle : 0.942 36.724 11346 Z= 0.444 Chirality : 0.048 0.235 1282 Planarity : 0.006 0.065 1440 Dihedral : 7.243 86.030 1135 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.45 % Rotamer: Outliers : 1.23 % Allowed : 5.94 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.67 (0.26), residues: 1018 helix: 1.00 (0.26), residues: 379 sheet: 1.00 (0.34), residues: 208 loop : -0.24 (0.31), residues: 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.850 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 75 average time/residue: 1.2200 time to fit residues: 97.9524 Evaluate side-chains 56 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.2882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 ASN R 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2757 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 8381 Z= 0.372 Angle : 1.057 36.698 11346 Z= 0.505 Chirality : 0.052 0.402 1282 Planarity : 0.007 0.075 1440 Dihedral : 6.310 79.545 1135 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.80 % Allowed : 7.61 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: -0.03 (0.26), residues: 1018 helix: 0.34 (0.26), residues: 382 sheet: 0.49 (0.36), residues: 205 loop : -0.47 (0.32), residues: 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.826 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 112 average time/residue: 1.0437 time to fit residues: 125.9256 Evaluate side-chains 68 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.7863 time to fit residues: 3.8535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 0.0370 chunk 92 optimal weight: 0.0570 chunk 97 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 0.0030 chunk 81 optimal weight: 0.9990 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 91 HIS R 69 ASN R 77 ASN R 153 GLN R 304 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2818 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8381 Z= 0.160 Angle : 0.840 36.156 11346 Z= 0.373 Chirality : 0.044 0.261 1282 Planarity : 0.005 0.067 1440 Dihedral : 5.656 78.080 1135 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.80 % Allowed : 11.09 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.39 (0.27), residues: 1018 helix: 0.83 (0.27), residues: 385 sheet: 0.45 (0.35), residues: 199 loop : -0.23 (0.31), residues: 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 0.835 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 91 average time/residue: 0.9222 time to fit residues: 91.6928 Evaluate side-chains 70 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.2991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 220 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 259 GLN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3737 moved from start: 1.0234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8381 Z= 0.260 Angle : 0.904 35.974 11346 Z= 0.420 Chirality : 0.046 0.256 1282 Planarity : 0.006 0.133 1440 Dihedral : 5.596 71.999 1135 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.36 % Allowed : 11.87 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.13 (0.26), residues: 1018 helix: 0.65 (0.26), residues: 385 sheet: 0.40 (0.35), residues: 205 loop : -0.48 (0.31), residues: 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 101 average time/residue: 0.8061 time to fit residues: 89.7427 Evaluate side-chains 76 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1212 time to fit residues: 2.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS N 82 GLN R 131 ASN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3904 moved from start: 1.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8381 Z= 0.181 Angle : 0.837 36.043 11346 Z= 0.366 Chirality : 0.043 0.229 1282 Planarity : 0.004 0.067 1440 Dihedral : 5.292 69.618 1135 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.13 % Allowed : 14.11 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.42 (0.27), residues: 1018 helix: 0.97 (0.27), residues: 387 sheet: 0.42 (0.36), residues: 199 loop : -0.32 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.880 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 88 average time/residue: 0.8541 time to fit residues: 82.4760 Evaluate side-chains 78 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0737 time to fit residues: 1.3418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 0.0020 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5011 moved from start: 1.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8381 Z= 0.297 Angle : 0.957 36.298 11346 Z= 0.450 Chirality : 0.048 0.215 1282 Planarity : 0.006 0.078 1440 Dihedral : 5.986 79.293 1135 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.91 % Allowed : 14.11 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: -0.14 (0.27), residues: 1018 helix: 0.66 (0.27), residues: 387 sheet: 0.03 (0.37), residues: 204 loop : -0.75 (0.32), residues: 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 114 average time/residue: 0.8793 time to fit residues: 109.5229 Evaluate side-chains 75 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.3028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.0050 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.0010 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 1.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8381 Z= 0.176 Angle : 0.875 36.343 11346 Z= 0.385 Chirality : 0.042 0.187 1282 Planarity : 0.004 0.064 1440 Dihedral : 5.503 79.724 1135 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.57 % Allowed : 17.47 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.05 (0.27), residues: 1018 helix: 0.85 (0.27), residues: 391 sheet: -0.04 (0.37), residues: 196 loop : -0.59 (0.31), residues: 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 92 average time/residue: 0.8014 time to fit residues: 81.4682 Evaluate side-chains 72 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.2976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 0.0470 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 GLN R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5244 moved from start: 1.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8381 Z= 0.205 Angle : 0.878 36.238 11346 Z= 0.393 Chirality : 0.044 0.186 1282 Planarity : 0.005 0.078 1440 Dihedral : 5.450 78.963 1135 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.90 % Allowed : 18.48 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: -0.06 (0.26), residues: 1018 helix: 0.86 (0.27), residues: 391 sheet: -0.06 (0.35), residues: 200 loop : -0.79 (0.30), residues: 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 92 average time/residue: 0.9308 time to fit residues: 93.1445 Evaluate side-chains 78 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.0070 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5251 moved from start: 1.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8381 Z= 0.172 Angle : 0.851 36.532 11346 Z= 0.370 Chirality : 0.043 0.185 1282 Planarity : 0.004 0.070 1440 Dihedral : 5.336 79.086 1135 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 0.90 % Allowed : 20.83 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.04 (0.26), residues: 1018 helix: 1.05 (0.27), residues: 393 sheet: -0.12 (0.35), residues: 207 loop : -0.81 (0.30), residues: 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 1.0319 time to fit residues: 102.5381 Evaluate side-chains 84 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6528 time to fit residues: 2.7123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.285560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.234658 restraints weight = 9374.277| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 2.93 r_work: 0.4454 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 1.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8381 Z= 0.175 Angle : 0.852 36.562 11346 Z= 0.374 Chirality : 0.043 0.170 1282 Planarity : 0.005 0.078 1440 Dihedral : 5.326 78.656 1135 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 0.67 % Allowed : 21.61 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.04 (0.26), residues: 1018 helix: 1.13 (0.27), residues: 389 sheet: -0.16 (0.35), residues: 207 loop : -0.86 (0.30), residues: 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.25 seconds wall clock time: 48 minutes 31.99 seconds (2911.99 seconds total)