Starting phenix.real_space_refine on Thu Mar 14 13:22:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbh_38218/03_2024/8xbh_38218_updated.pdb" } resolution = 2.83 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 ------------------------------------------------------------------------------- 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= -0.004 sd= 0.523 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 67 5.16 5 C 5709 2.51 5 N 1514 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" 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: 8947 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'KW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.51, per 1000 atoms: 0.50 Number of scatterers: 8947 At special positions: 0 Unit cell: (90.37, 120.063, 135.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1 15.00 O 1656 8.00 N 1514 7.00 C 5709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 299 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 204 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 35.0% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.768A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 279 removed outlier: 4.105A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.689A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.830A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 30 through 43 removed outlier: 4.047A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 80 Processing helix chain 'R' and resid 88 through 116 Proline residue: R 108 - end of helix Processing helix chain 'R' and resid 124 through 156 removed outlier: 3.693A pdb=" N TYR R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 195 removed outlier: 3.675A pdb=" N LYS R 195 " --> pdb=" O ILE R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 251 Processing helix chain 'R' and resid 258 through 293 removed outlier: 4.113A pdb=" N ALA R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Proline residue: R 281 - end of helix removed outlier: 4.046A pdb=" N PHE R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 330 removed outlier: 4.203A pdb=" N ILE R 304 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS R 321 " --> pdb=" O SER R 317 " (cutoff:3.500A) Proline residue: R 324 - end of helix removed outlier: 3.548A pdb=" N TYR R 327 " --> pdb=" O ASP R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 341 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.580A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.836A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.961A 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: 7.463A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 150 through 153 removed outlier: 6.694A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A 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: 6.849A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.849A 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: 6.860A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.787A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.534A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.628A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1239 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: 2.42 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1572 1.33 - 1.45: 2425 1.45 - 1.57: 5032 1.57 - 1.69: 2 1.69 - 1.82: 98 Bond restraints: 9129 Sorted by residual: bond pdb=" C4 KW3 R 401 " pdb=" O6 KW3 R 401 " ideal model delta sigma weight residual 1.399 1.469 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C6 KW3 R 401 " pdb=" O2 KW3 R 401 " ideal model delta sigma weight residual 1.396 1.328 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 KW3 R 401 " pdb=" C2 KW3 R 401 " ideal model delta sigma weight residual 1.528 1.469 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" C28 KW3 R 401 " pdb=" O9 KW3 R 401 " ideal model delta sigma weight residual 1.399 1.448 -0.049 2.00e-02 2.50e+03 5.88e+00 bond pdb=" C5 KW3 R 401 " pdb=" O2 KW3 R 401 " ideal model delta sigma weight residual 1.396 1.443 -0.047 2.00e-02 2.50e+03 5.62e+00 ... (remaining 9124 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.14: 146 106.14 - 113.11: 4964 113.11 - 120.09: 3165 120.09 - 127.06: 3987 127.06 - 134.03: 84 Bond angle restraints: 12346 Sorted by residual: angle pdb=" CA CYS B 103 " pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 114.40 129.28 -14.88 2.30e+00 1.89e-01 4.19e+01 angle pdb=" N GLY B 115 " pdb=" CA GLY B 115 " pdb=" C GLY B 115 " ideal model delta sigma weight residual 110.80 117.25 -6.45 1.41e+00 5.03e-01 2.09e+01 angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.00 4.20 9.60e-01 1.09e+00 1.92e+01 angle pdb=" C20 KW3 R 401 " pdb=" O5 KW3 R 401 " pdb=" C21 KW3 R 401 " ideal model delta sigma weight residual 109.47 121.42 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N CYS B 103 " pdb=" CA CYS B 103 " pdb=" C CYS B 103 " ideal model delta sigma weight residual 107.73 113.98 -6.25 1.61e+00 3.86e-01 1.51e+01 ... (remaining 12341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4937 17.97 - 35.94: 414 35.94 - 53.91: 52 53.91 - 71.88: 11 71.88 - 89.85: 5 Dihedral angle restraints: 5419 sinusoidal: 2120 harmonic: 3299 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 145.80 -52.80 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA CYS B 103 " pdb=" C CYS B 103 " pdb=" N ALA B 104 " pdb=" CA ALA B 104 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1094 0.050 - 0.099: 251 0.099 - 0.149: 52 0.149 - 0.198: 3 0.198 - 0.248: 2 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA CYS B 103 " pdb=" N CYS B 103 " pdb=" C CYS B 103 " pdb=" CB CYS B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL R 280 " pdb=" CA VAL R 280 " pdb=" CG1 VAL R 280 " pdb=" CG2 VAL R 280 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 1399 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 318 " 0.013 2.00e-02 2.50e+03 1.29e-02 2.93e+00 pdb=" CG PHE R 318 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE R 318 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 318 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 318 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 318 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 318 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 247 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ASP B 247 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP B 247 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 248 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO G 55 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.023 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 246 2.70 - 3.25: 8774 3.25 - 3.80: 14380 3.80 - 4.35: 18894 4.35 - 4.90: 31727 Nonbonded interactions: 74021 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.151 2.440 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.192 2.520 nonbonded pdb=" NH1 ARG S 67 " pdb=" O SER S 85 " model vdw 2.199 2.520 nonbonded pdb=" OG SER R 54 " pdb=" O HIS R 114 " model vdw 2.218 2.440 nonbonded pdb=" OG SER R 331 " pdb=" OD1 ASN R 333 " model vdw 2.238 2.440 ... (remaining 74016 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: 0.120 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: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.130 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9129 Z= 0.235 Angle : 0.701 14.881 12346 Z= 0.382 Chirality : 0.044 0.248 1402 Planarity : 0.004 0.041 1548 Dihedral : 13.231 89.852 3278 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.30 (0.26), residues: 1121 helix: 1.85 (0.26), residues: 396 sheet: -0.26 (0.30), residues: 297 loop : -0.98 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 206 PHE 0.030 0.002 PHE R 318 TYR 0.020 0.002 TYR A 320 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6637 (mtp-110) REVERT: A 209 LYS cc_start: 0.7908 (tttt) cc_final: 0.7678 (tttm) REVERT: A 345 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7756 (tmtp) REVERT: B 155 ASN cc_start: 0.7936 (t0) cc_final: 0.7604 (t0) REVERT: B 220 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7125 (mp10) REVERT: B 280 LYS cc_start: 0.7968 (tttm) cc_final: 0.7742 (tttp) REVERT: B 301 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7860 (mttm) REVERT: B 325 MET cc_start: 0.7818 (mmm) cc_final: 0.7597 (mmm) REVERT: S 189 ASP cc_start: 0.7363 (p0) cc_final: 0.6965 (t0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.9883 time to fit residues: 239.6189 Evaluate side-chains 190 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 0.056 9129 Z= 0.149 Angle : 0.552 10.452 12346 Z= 0.286 Chirality : 0.042 0.197 1402 Planarity : 0.003 0.034 1548 Dihedral : 5.890 81.645 1245 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Rotamer: Outliers : 1.75 % Allowed : 11.72 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.38 (0.26), residues: 1121 helix: 1.94 (0.26), residues: 397 sheet: -0.11 (0.30), residues: 292 loop : -1.07 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 PHE 0.017 0.001 PHE B 151 TYR 0.020 0.001 TYR S 178 ARG 0.006 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.7789 (pttt) cc_final: 0.7335 (pttp) REVERT: A 308 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6994 (tp30) REVERT: A 345 LYS cc_start: 0.8126 (tmtt) cc_final: 0.7708 (tmtp) REVERT: B 155 ASN cc_start: 0.7785 (t0) cc_final: 0.7328 (t0) REVERT: B 200 VAL cc_start: 0.8611 (m) cc_final: 0.8317 (t) REVERT: B 228 ASP cc_start: 0.7337 (p0) cc_final: 0.6900 (p0) REVERT: B 280 LYS cc_start: 0.8001 (tttm) cc_final: 0.7683 (tttp) REVERT: S 189 ASP cc_start: 0.7475 (p0) cc_final: 0.7077 (t0) outliers start: 17 outliers final: 7 residues processed: 212 average time/residue: 0.9453 time to fit residues: 216.5844 Evaluate side-chains 191 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 0.3980 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN S 39 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9129 Z= 0.166 Angle : 0.549 9.350 12346 Z= 0.285 Chirality : 0.042 0.225 1402 Planarity : 0.003 0.035 1548 Dihedral : 5.781 84.486 1245 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 2.36 % Allowed : 14.90 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.41 (0.26), residues: 1121 helix: 2.06 (0.26), residues: 390 sheet: -0.16 (0.29), residues: 295 loop : -1.06 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS S 220 PHE 0.019 0.001 PHE B 151 TYR 0.021 0.001 TYR S 178 ARG 0.003 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6131 (mmp) REVERT: A 248 LYS cc_start: 0.7829 (pttt) cc_final: 0.7399 (ptmm) REVERT: A 345 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7784 (tmtp) REVERT: B 200 VAL cc_start: 0.8639 (m) cc_final: 0.8388 (t) REVERT: B 228 ASP cc_start: 0.7415 (p0) cc_final: 0.6952 (p0) REVERT: B 280 LYS cc_start: 0.8041 (tttm) cc_final: 0.7718 (tttp) REVERT: R 169 LYS cc_start: 0.6083 (tttm) cc_final: 0.5736 (ttpt) REVERT: R 172 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6455 (mm) REVERT: R 183 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6770 (tm) REVERT: S 148 ARG cc_start: 0.5788 (ptp-110) cc_final: 0.5575 (ttp-110) REVERT: S 189 ASP cc_start: 0.7483 (p0) cc_final: 0.7067 (t0) outliers start: 23 outliers final: 11 residues processed: 205 average time/residue: 0.9791 time to fit residues: 216.9699 Evaluate side-chains 193 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 107 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9129 Z= 0.167 Angle : 0.549 9.889 12346 Z= 0.287 Chirality : 0.042 0.247 1402 Planarity : 0.003 0.038 1548 Dihedral : 5.754 87.495 1245 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.77 % Allowed : 15.93 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.43 (0.26), residues: 1121 helix: 2.04 (0.26), residues: 389 sheet: -0.14 (0.30), residues: 285 loop : -0.98 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS S 220 PHE 0.019 0.001 PHE B 151 TYR 0.020 0.001 TYR S 178 ARG 0.005 0.000 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 0.976 Fit side-chains REVERT: A 53 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6275 (mmp) REVERT: A 209 LYS cc_start: 0.7887 (tttm) cc_final: 0.7666 (mmmt) REVERT: A 248 LYS cc_start: 0.7875 (pttt) cc_final: 0.7423 (ptmm) REVERT: A 345 LYS cc_start: 0.8126 (tmtt) cc_final: 0.7776 (tmtp) REVERT: B 228 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.6990 (p0) REVERT: B 280 LYS cc_start: 0.8117 (tttm) cc_final: 0.7811 (tttp) REVERT: G 47 GLU cc_start: 0.6279 (tt0) cc_final: 0.5895 (mm-30) REVERT: R 169 LYS cc_start: 0.6190 (tttm) cc_final: 0.5768 (ttpt) REVERT: R 172 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6505 (mm) REVERT: R 183 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6776 (tm) REVERT: R 243 LYS cc_start: 0.7440 (mttm) cc_final: 0.6986 (mttp) REVERT: S 148 ARG cc_start: 0.5763 (ptp-110) cc_final: 0.5433 (ptp90) REVERT: S 189 ASP cc_start: 0.7493 (p0) cc_final: 0.7073 (t0) outliers start: 27 outliers final: 11 residues processed: 196 average time/residue: 0.9956 time to fit residues: 210.4042 Evaluate side-chains 194 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.0970 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN R 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9129 Z= 0.200 Angle : 0.582 12.437 12346 Z= 0.303 Chirality : 0.043 0.287 1402 Planarity : 0.004 0.041 1548 Dihedral : 5.875 92.145 1245 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 2.67 % Allowed : 17.27 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.42 (0.26), residues: 1121 helix: 1.96 (0.26), residues: 389 sheet: -0.13 (0.30), residues: 285 loop : -0.92 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.004 0.001 HIS B 62 PHE 0.020 0.002 PHE B 151 TYR 0.021 0.001 TYR S 178 ARG 0.006 0.000 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 0.997 Fit side-chains REVERT: A 53 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6169 (mmp) REVERT: A 245 GLU cc_start: 0.7676 (tp30) cc_final: 0.7460 (tp30) REVERT: A 248 LYS cc_start: 0.7887 (pttt) cc_final: 0.7418 (ptmm) REVERT: A 276 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6927 (tm-30) REVERT: A 345 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7756 (tmtp) REVERT: B 228 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.6932 (p0) REVERT: R 169 LYS cc_start: 0.6127 (tttm) cc_final: 0.5712 (ttpt) REVERT: R 172 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6385 (OUTLIER) REVERT: R 183 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6683 (tm) REVERT: R 189 MET cc_start: 0.5773 (tpp) cc_final: 0.5331 (mmp) REVERT: R 243 LYS cc_start: 0.7318 (mttm) cc_final: 0.6840 (mttp) REVERT: S 148 ARG cc_start: 0.5877 (ptp-110) cc_final: 0.5513 (ptp90) REVERT: S 189 ASP cc_start: 0.7404 (p0) cc_final: 0.6994 (t0) outliers start: 26 outliers final: 15 residues processed: 199 average time/residue: 1.0602 time to fit residues: 226.7726 Evaluate side-chains 191 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 87 ASN Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN B 340 ASN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 9129 Z= 0.443 Angle : 0.764 17.479 12346 Z= 0.403 Chirality : 0.049 0.367 1402 Planarity : 0.005 0.053 1548 Dihedral : 6.685 105.080 1245 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 4.11 % Allowed : 16.75 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.09 (0.25), residues: 1121 helix: 1.36 (0.26), residues: 390 sheet: -0.14 (0.30), residues: 288 loop : -0.91 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 99 HIS 0.007 0.002 HIS B 62 PHE 0.034 0.003 PHE B 151 TYR 0.032 0.003 TYR B 264 ARG 0.008 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 0.914 Fit side-chains REVERT: A 53 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6092 (mmp) REVERT: A 248 LYS cc_start: 0.7896 (pttt) cc_final: 0.7491 (ptmm) REVERT: B 155 ASN cc_start: 0.7766 (t0) cc_final: 0.7252 (t0) REVERT: B 220 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6719 (mp10) REVERT: B 228 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6879 (p0) REVERT: R 76 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7304 (mp) REVERT: R 172 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6509 (OUTLIER) REVERT: R 189 MET cc_start: 0.5799 (tpp) cc_final: 0.5467 (mmp) REVERT: R 203 MET cc_start: 0.5966 (mpp) cc_final: 0.5672 (mmp) REVERT: S 38 ARG cc_start: 0.7029 (ptt180) cc_final: 0.6755 (ptt180) REVERT: S 189 ASP cc_start: 0.7347 (p0) cc_final: 0.6830 (t0) outliers start: 40 outliers final: 24 residues processed: 198 average time/residue: 0.9755 time to fit residues: 208.2356 Evaluate side-chains 196 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 334 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 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 255 ASN A 333 GLN A 346 ASN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 ASN R 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9129 Z= 0.168 Angle : 0.589 10.742 12346 Z= 0.305 Chirality : 0.043 0.256 1402 Planarity : 0.004 0.041 1548 Dihedral : 5.987 101.085 1245 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Rotamer: Outliers : 2.47 % Allowed : 20.45 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.37 (0.26), residues: 1121 helix: 1.76 (0.26), residues: 391 sheet: -0.00 (0.30), residues: 281 loop : -0.92 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS S 220 PHE 0.028 0.002 PHE S 29 TYR 0.021 0.001 TYR S 178 ARG 0.007 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 0.977 Fit side-chains REVERT: A 248 LYS cc_start: 0.7864 (pttt) cc_final: 0.7477 (ptmm) REVERT: A 345 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7774 (tmtp) REVERT: B 220 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6714 (mp10) REVERT: B 228 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.6867 (p0) REVERT: B 268 ASN cc_start: 0.7040 (OUTLIER) cc_final: 0.6774 (t0) REVERT: R 172 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6551 (OUTLIER) REVERT: R 183 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6681 (tm) REVERT: R 189 MET cc_start: 0.5618 (tpp) cc_final: 0.5366 (mmp) REVERT: R 302 LYS cc_start: 0.7629 (tmmt) cc_final: 0.6357 (mtpt) REVERT: S 2 VAL cc_start: 0.8028 (t) cc_final: 0.7813 (m) REVERT: S 189 ASP cc_start: 0.7389 (p0) cc_final: 0.6891 (t0) outliers start: 24 outliers final: 10 residues processed: 185 average time/residue: 1.0178 time to fit residues: 202.6202 Evaluate side-chains 183 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9129 Z= 0.276 Angle : 0.661 18.095 12346 Z= 0.343 Chirality : 0.045 0.298 1402 Planarity : 0.004 0.045 1548 Dihedral : 6.218 104.757 1245 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.88 % Allowed : 20.66 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.35 (0.26), residues: 1121 helix: 1.70 (0.26), residues: 390 sheet: -0.06 (0.30), residues: 288 loop : -0.84 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.005 0.001 HIS S 220 PHE 0.027 0.002 PHE S 29 TYR 0.027 0.002 TYR B 264 ARG 0.006 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 0.834 Fit side-chains REVERT: A 207 GLU cc_start: 0.8041 (tt0) cc_final: 0.7607 (tt0) REVERT: A 248 LYS cc_start: 0.7868 (pttt) cc_final: 0.7468 (ptmm) REVERT: B 155 ASN cc_start: 0.7766 (t0) cc_final: 0.7260 (t0) REVERT: B 220 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6793 (mp10) REVERT: B 228 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.6952 (p0) REVERT: B 268 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6882 (t0) REVERT: R 76 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7101 (mp) REVERT: R 172 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6598 (OUTLIER) REVERT: R 189 MET cc_start: 0.5684 (tpp) cc_final: 0.5407 (mmp) REVERT: R 203 MET cc_start: 0.6078 (mpp) cc_final: 0.5749 (mmp) REVERT: R 302 LYS cc_start: 0.7636 (tmmt) cc_final: 0.6355 (mtpt) REVERT: S 189 ASP cc_start: 0.7330 (p0) cc_final: 0.6814 (t0) outliers start: 28 outliers final: 18 residues processed: 190 average time/residue: 1.0937 time to fit residues: 222.9303 Evaluate side-chains 194 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9129 Z= 0.171 Angle : 0.614 15.311 12346 Z= 0.314 Chirality : 0.043 0.256 1402 Planarity : 0.004 0.040 1548 Dihedral : 6.075 103.988 1245 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 21.89 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.40 (0.26), residues: 1121 helix: 1.76 (0.26), residues: 391 sheet: 0.04 (0.31), residues: 281 loop : -0.90 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 220 PHE 0.024 0.002 PHE S 29 TYR 0.020 0.001 TYR S 178 ARG 0.008 0.001 ARG R 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 0.979 Fit side-chains REVERT: A 209 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7610 (mmmt) REVERT: A 248 LYS cc_start: 0.7835 (pttt) cc_final: 0.7440 (ptmm) REVERT: A 345 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7744 (tmtp) REVERT: B 220 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6641 (mp10) REVERT: B 228 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6877 (p0) REVERT: B 268 ASN cc_start: 0.6979 (OUTLIER) cc_final: 0.6751 (t0) REVERT: R 172 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6539 (OUTLIER) REVERT: R 189 MET cc_start: 0.5533 (tpp) cc_final: 0.5323 (mmp) REVERT: R 302 LYS cc_start: 0.7468 (tmmt) cc_final: 0.6269 (mtpt) REVERT: S 189 ASP cc_start: 0.7312 (p0) cc_final: 0.6838 (t0) outliers start: 20 outliers final: 12 residues processed: 185 average time/residue: 1.0535 time to fit residues: 209.3638 Evaluate side-chains 184 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN B 340 ASN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9129 Z= 0.233 Angle : 0.666 16.789 12346 Z= 0.342 Chirality : 0.044 0.296 1402 Planarity : 0.004 0.057 1548 Dihedral : 6.177 106.150 1245 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 2.36 % Allowed : 22.61 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.37 (0.26), residues: 1121 helix: 1.69 (0.26), residues: 391 sheet: -0.03 (0.30), residues: 287 loop : -0.83 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS S 220 PHE 0.026 0.002 PHE S 29 TYR 0.022 0.002 TYR S 178 ARG 0.015 0.001 ARG R 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 0.966 Fit side-chains REVERT: A 209 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7676 (mmmt) REVERT: A 248 LYS cc_start: 0.7870 (pttt) cc_final: 0.7476 (ptmm) REVERT: B 155 ASN cc_start: 0.7754 (t0) cc_final: 0.7255 (t0) REVERT: B 220 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6748 (mp10) REVERT: B 228 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.6950 (p0) REVERT: B 268 ASN cc_start: 0.6981 (OUTLIER) cc_final: 0.6752 (t0) REVERT: R 172 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6576 (OUTLIER) REVERT: R 189 MET cc_start: 0.5651 (tpp) cc_final: 0.5276 (mmp) REVERT: R 203 MET cc_start: 0.5955 (mpp) cc_final: 0.5715 (mmp) REVERT: S 189 ASP cc_start: 0.7364 (p0) cc_final: 0.6931 (t0) outliers start: 23 outliers final: 16 residues processed: 180 average time/residue: 1.1153 time to fit residues: 215.1902 Evaluate side-chains 187 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 167 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 249 SER Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 211 ASP Chi-restraints excluded: chain S residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 333 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** R 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.214810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.177713 restraints weight = 10269.264| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.00 r_work: 0.3759 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9129 Z= 0.207 Angle : 0.652 15.197 12346 Z= 0.332 Chirality : 0.043 0.286 1402 Planarity : 0.004 0.058 1548 Dihedral : 6.093 106.457 1245 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 2.26 % Allowed : 22.40 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.38 (0.25), residues: 1121 helix: 1.69 (0.26), residues: 391 sheet: -0.02 (0.30), residues: 286 loop : -0.82 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.005 0.001 HIS S 220 PHE 0.025 0.002 PHE S 29 TYR 0.021 0.001 TYR S 178 ARG 0.016 0.001 ARG R 86 =============================================================================== Job complete usr+sys time: 3748.92 seconds wall clock time: 66 minutes 47.62 seconds (4007.62 seconds total)