Starting phenix.real_space_refine on Wed Jan 15 09:55:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqr_38586/01_2025/8xqr_38586.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqr_38586/01_2025/8xqr_38586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqr_38586/01_2025/8xqr_38586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqr_38586/01_2025/8xqr_38586.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqr_38586/01_2025/8xqr_38586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqr_38586/01_2025/8xqr_38586.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 48 5.16 5 C 5274 2.51 5 N 1432 2.21 5 O 1516 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8273 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1964 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "C" 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: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 981 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2256 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 3, 'TRANS': 275} Chain breaks: 2 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FLF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.55 Number of scatterers: 8273 At special positions: 0 Unit cell: (74.88, 99.84, 131.04, 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 48 16.00 F 3 9.00 O 1516 8.00 N 1432 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 100 " - pdb=" SG CYS N 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 973.3 milliseconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 45.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 Processing helix chain 'A' and resid 48 through 60 removed outlier: 3.920A pdb=" N ILE A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.634A pdb=" N ASN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.216A pdb=" N TYR A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.777A pdb=" N ALA A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.537A pdb=" N THR A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.943A pdb=" N ASN A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.640A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.608A pdb=" N ASN N 32 " --> pdb=" O THR N 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR N 33 " --> pdb=" O PHE N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 33' Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 72 Processing helix chain 'R' and resid 74 through 78 Processing helix chain 'R' and resid 80 through 112 Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.568A pdb=" N TRP R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 158 removed outlier: 4.096A pdb=" N VAL R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 215 Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 225 through 254 Processing helix chain 'R' and resid 258 through 284 removed outlier: 3.647A pdb=" N ILE R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.811A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 79 removed outlier: 9.316A pdb=" N ALA A 108 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A 38 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE A 110 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 40 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 112 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 42 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 109 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE A 145 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE A 111 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.206A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.700A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.572A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.141A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.626A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.747A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.687A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.620A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1335 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: 2.41 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2677 1.34 - 1.46: 1752 1.46 - 1.58: 3943 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 8441 Sorted by residual: bond pdb=" N FLF R 501 " pdb=" C1' FLF R 501 " ideal model delta sigma weight residual 1.377 1.414 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" CA ASN A 119 " pdb=" CB ASN A 119 " ideal model delta sigma weight residual 1.536 1.566 -0.031 2.01e-02 2.48e+03 2.33e+00 bond pdb=" N FLF R 501 " pdb=" C6 FLF R 501 " ideal model delta sigma weight residual 1.378 1.407 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 FLF R 501 " pdb=" C7 FLF R 501 " ideal model delta sigma weight residual 1.521 1.496 0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" CB ASN A 104 " pdb=" CG ASN A 104 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 8436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 11342 2.99 - 5.99: 66 5.99 - 8.98: 7 8.98 - 11.97: 1 11.97 - 14.97: 1 Bond angle restraints: 11417 Sorted by residual: angle pdb=" CA LEU R 257 " pdb=" CB LEU R 257 " pdb=" CG LEU R 257 " ideal model delta sigma weight residual 116.30 131.27 -14.97 3.50e+00 8.16e-02 1.83e+01 angle pdb=" CB LEU R 257 " pdb=" CG LEU R 257 " pdb=" CD1 LEU R 257 " ideal model delta sigma weight residual 110.70 119.47 -8.77 3.00e+00 1.11e-01 8.55e+00 angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 103.95 8.75 3.00e+00 1.11e-01 8.51e+00 angle pdb=" CA LYS R 210 " pdb=" CB LYS R 210 " pdb=" CG LYS R 210 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.98e+00 angle pdb=" CA LEU B 55 " pdb=" CB LEU B 55 " pdb=" CG LEU B 55 " ideal model delta sigma weight residual 116.30 125.45 -9.15 3.50e+00 8.16e-02 6.83e+00 ... (remaining 11412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4306 16.94 - 33.88: 534 33.88 - 50.81: 132 50.81 - 67.75: 21 67.75 - 84.69: 3 Dihedral angle restraints: 4996 sinusoidal: 1971 harmonic: 3025 Sorted by residual: dihedral pdb=" CB CYS N 100 " pdb=" SG CYS N 100 " pdb=" SG CYS N 108 " pdb=" CB CYS N 108 " ideal model delta sinusoidal sigma weight residual -86.00 -131.57 45.57 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CG ARG B 96 " pdb=" CD ARG B 96 " pdb=" NE ARG B 96 " pdb=" CZ ARG B 96 " ideal model delta sinusoidal sigma weight residual 90.00 38.08 51.92 2 1.50e+01 4.44e-03 1.32e+01 dihedral pdb=" SG CYS N 100 " pdb=" CB CYS N 108 " pdb=" SG CYS N 108 " pdb=" CA CYS N 108 " ideal model delta sinusoidal sigma weight residual 79.00 20.80 58.20 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 4993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1047 0.050 - 0.101: 188 0.101 - 0.151: 52 0.151 - 0.202: 3 0.202 - 0.252: 3 Chirality restraints: 1293 Sorted by residual: chirality pdb=" CG LEU R 131 " pdb=" CB LEU R 131 " pdb=" CD1 LEU R 131 " pdb=" CD2 LEU R 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA LYS R 210 " pdb=" N LYS R 210 " pdb=" C LYS R 210 " pdb=" CB LYS R 210 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU R 257 " pdb=" CB LEU R 257 " pdb=" CD1 LEU R 257 " pdb=" CD2 LEU R 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1290 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 72 " -0.058 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO R 73 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO R 73 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 73 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 340 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" CG ASN B 340 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 340 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 340 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 55 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.026 5.00e-02 4.00e+02 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 174 2.66 - 3.22: 8170 3.22 - 3.78: 13781 3.78 - 4.34: 17914 4.34 - 4.90: 29470 Nonbonded interactions: 69509 Sorted by model distance: nonbonded pdb=" NH1 ARG A 93 " pdb=" OD1 ASP B 186 " model vdw 2.104 3.120 nonbonded pdb=" O GLY B 162 " pdb=" OD1 ASP B 186 " model vdw 2.128 3.040 nonbonded pdb=" OD1 ASP B 153 " pdb=" N ASP B 154 " model vdw 2.160 3.120 nonbonded pdb=" O PRO A 187 " pdb=" OG1 THR A 190 " model vdw 2.165 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" O ILE B 273 " model vdw 2.194 3.120 ... (remaining 69504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.880 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 20.930 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 0.039 8441 Z= 0.262 Angle : 0.636 14.966 11417 Z= 0.334 Chirality : 0.043 0.252 1293 Planarity : 0.005 0.089 1439 Dihedral : 15.580 84.687 3030 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 30.04 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.27), residues: 1030 helix: 2.28 (0.24), residues: 428 sheet: -0.14 (0.36), residues: 221 loop : -0.60 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 66 HIS 0.011 0.002 HIS R 214 PHE 0.027 0.002 PHE R 119 TYR 0.011 0.001 TYR R 272 ARG 0.010 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ARG cc_start: 0.7863 (ptm160) cc_final: 0.7453 (ptp-110) REVERT: A 148 LYS cc_start: 0.8748 (mptt) cc_final: 0.8450 (mttt) REVERT: B 219 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7783 (ttm-80) REVERT: N 50 SER cc_start: 0.8688 (m) cc_final: 0.8393 (p) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2440 time to fit residues: 83.9649 Evaluate side-chains 263 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 155 ASN B 220 GLN B 259 GLN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128232 restraints weight = 12884.023| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.53 r_work: 0.3495 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8441 Z= 0.199 Angle : 0.562 9.652 11417 Z= 0.298 Chirality : 0.041 0.149 1293 Planarity : 0.005 0.057 1439 Dihedral : 4.317 38.590 1129 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 3.66 % Allowed : 24.94 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 1030 helix: 2.56 (0.24), residues: 429 sheet: 0.06 (0.36), residues: 215 loop : -0.69 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 66 HIS 0.008 0.001 HIS R 94 PHE 0.013 0.001 PHE B 253 TYR 0.012 0.001 TYR R 240 ARG 0.007 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7753 (mtpt) REVERT: A 120 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7458 (mtt-85) REVERT: A 138 ARG cc_start: 0.8003 (ptm160) cc_final: 0.7543 (ptp-110) REVERT: A 236 ASP cc_start: 0.8555 (t0) cc_final: 0.8326 (t0) REVERT: B 155 ASN cc_start: 0.8157 (t0) cc_final: 0.7897 (t0) REVERT: B 186 ASP cc_start: 0.7605 (m-30) cc_final: 0.7318 (m-30) REVERT: B 303 ASP cc_start: 0.7122 (m-30) cc_final: 0.6830 (m-30) REVERT: C 41 CYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7538 (p) REVERT: N 50 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8279 (p) REVERT: N 113 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7735 (p) REVERT: R 62 ILE cc_start: 0.8222 (mm) cc_final: 0.7766 (tp) REVERT: R 131 LEU cc_start: 0.8674 (mm) cc_final: 0.8435 (mm) REVERT: R 205 MET cc_start: 0.7902 (mmm) cc_final: 0.7669 (tpp) REVERT: R 210 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7799 (mmtt) REVERT: R 212 MET cc_start: 0.7766 (mmm) cc_final: 0.7486 (mmp) REVERT: R 237 PHE cc_start: 0.8305 (m-80) cc_final: 0.7764 (m-80) REVERT: R 268 MET cc_start: 0.8016 (tmm) cc_final: 0.7805 (tmm) outliers start: 33 outliers final: 20 residues processed: 285 average time/residue: 0.2553 time to fit residues: 93.3906 Evaluate side-chains 288 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 294 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 134 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.147331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126650 restraints weight = 13177.985| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.55 r_work: 0.3483 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8441 Z= 0.225 Angle : 0.538 8.599 11417 Z= 0.283 Chirality : 0.040 0.151 1293 Planarity : 0.004 0.045 1439 Dihedral : 4.150 26.526 1129 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 5.65 % Allowed : 23.06 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.27), residues: 1030 helix: 2.52 (0.24), residues: 435 sheet: 0.01 (0.34), residues: 227 loop : -0.77 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 66 HIS 0.008 0.001 HIS R 94 PHE 0.016 0.001 PHE R 119 TYR 0.011 0.001 TYR N 96 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7524 (mtt-85) REVERT: A 129 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7876 (mtpp) REVERT: A 138 ARG cc_start: 0.8013 (ptm160) cc_final: 0.7587 (ptp-110) REVERT: A 236 ASP cc_start: 0.8576 (t0) cc_final: 0.8203 (t0) REVERT: A 238 ILE cc_start: 0.8074 (mm) cc_final: 0.7830 (mt) REVERT: B 74 SER cc_start: 0.8143 (p) cc_final: 0.7936 (p) REVERT: B 76 ASP cc_start: 0.7375 (p0) cc_final: 0.6818 (p0) REVERT: B 153 ASP cc_start: 0.7858 (t0) cc_final: 0.7629 (t0) REVERT: B 155 ASN cc_start: 0.8157 (t0) cc_final: 0.7805 (t0) REVERT: B 271 CYS cc_start: 0.8345 (p) cc_final: 0.8119 (p) REVERT: B 303 ASP cc_start: 0.7147 (m-30) cc_final: 0.6848 (m-30) REVERT: C 41 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7549 (p) REVERT: N 50 SER cc_start: 0.8492 (m) cc_final: 0.8239 (p) REVERT: R 62 ILE cc_start: 0.8195 (mm) cc_final: 0.7776 (tp) REVERT: R 131 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8425 (mm) REVERT: R 210 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7730 (mmtt) REVERT: R 212 MET cc_start: 0.7796 (mmm) cc_final: 0.7548 (mmp) REVERT: R 268 MET cc_start: 0.8019 (tmm) cc_final: 0.7648 (tmm) outliers start: 51 outliers final: 34 residues processed: 305 average time/residue: 0.2585 time to fit residues: 101.8417 Evaluate side-chains 305 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 134 ASN B 220 GLN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.147076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126631 restraints weight = 13004.068| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.53 r_work: 0.3496 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8441 Z= 0.198 Angle : 0.539 9.646 11417 Z= 0.280 Chirality : 0.040 0.161 1293 Planarity : 0.004 0.046 1439 Dihedral : 4.044 24.140 1129 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.43 % Favored : 97.48 % Rotamer: Outliers : 5.88 % Allowed : 22.84 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1030 helix: 2.53 (0.24), residues: 436 sheet: -0.01 (0.34), residues: 222 loop : -0.79 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.017 0.001 PHE R 119 TYR 0.011 0.001 TYR N 96 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7532 (tmmm) REVERT: A 54 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7712 (mtpt) REVERT: A 120 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7522 (mtt-85) REVERT: A 138 ARG cc_start: 0.8017 (ptm160) cc_final: 0.7574 (ptp-110) REVERT: A 236 ASP cc_start: 0.8555 (t0) cc_final: 0.8160 (t0) REVERT: A 240 LYS cc_start: 0.8456 (mttm) cc_final: 0.8244 (mttm) REVERT: B 68 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7280 (mtt-85) REVERT: B 76 ASP cc_start: 0.7406 (p0) cc_final: 0.6836 (p0) REVERT: B 118 ASP cc_start: 0.7898 (p0) cc_final: 0.7513 (p0) REVERT: B 153 ASP cc_start: 0.7928 (t0) cc_final: 0.7614 (t0) REVERT: B 155 ASN cc_start: 0.8051 (t0) cc_final: 0.7690 (t0) REVERT: B 186 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: B 303 ASP cc_start: 0.7139 (m-30) cc_final: 0.6835 (m-30) REVERT: C 41 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7600 (p) REVERT: N 50 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8236 (p) REVERT: R 62 ILE cc_start: 0.8255 (mm) cc_final: 0.7828 (tp) REVERT: R 119 PHE cc_start: 0.8117 (t80) cc_final: 0.7782 (t80) REVERT: R 131 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8459 (mm) REVERT: R 205 MET cc_start: 0.7969 (mmm) cc_final: 0.7768 (tpp) REVERT: R 210 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7733 (mmtt) REVERT: R 212 MET cc_start: 0.7790 (mmm) cc_final: 0.7471 (mmp) REVERT: R 237 PHE cc_start: 0.8378 (m-80) cc_final: 0.7933 (m-80) REVERT: R 248 PHE cc_start: 0.7829 (t80) cc_final: 0.7596 (t80) REVERT: R 268 MET cc_start: 0.8049 (tmm) cc_final: 0.7641 (tmm) outliers start: 53 outliers final: 32 residues processed: 303 average time/residue: 0.2554 time to fit residues: 100.6127 Evaluate side-chains 304 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 294 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 220 GLN R 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128942 restraints weight = 12921.022| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.50 r_work: 0.3494 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8441 Z= 0.206 Angle : 0.537 10.392 11417 Z= 0.279 Chirality : 0.040 0.166 1293 Planarity : 0.004 0.045 1439 Dihedral : 4.020 21.782 1129 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 5.99 % Allowed : 23.61 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1030 helix: 2.56 (0.24), residues: 436 sheet: -0.05 (0.34), residues: 222 loop : -0.83 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.011 0.001 PHE R 236 TYR 0.012 0.001 TYR N 96 ARG 0.010 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7480 (tmmm) REVERT: A 120 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7573 (mtt-85) REVERT: A 138 ARG cc_start: 0.8010 (ptm160) cc_final: 0.7600 (ptp-110) REVERT: A 236 ASP cc_start: 0.8518 (t0) cc_final: 0.8170 (t0) REVERT: A 238 ILE cc_start: 0.8118 (mm) cc_final: 0.7894 (mt) REVERT: B 118 ASP cc_start: 0.7906 (p0) cc_final: 0.7528 (p0) REVERT: B 153 ASP cc_start: 0.7908 (t0) cc_final: 0.7558 (t0) REVERT: B 155 ASN cc_start: 0.8060 (t0) cc_final: 0.7640 (t0) REVERT: B 186 ASP cc_start: 0.7684 (m-30) cc_final: 0.7285 (m-30) REVERT: B 303 ASP cc_start: 0.7127 (m-30) cc_final: 0.6818 (m-30) REVERT: N 50 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8220 (p) REVERT: N 113 SER cc_start: 0.7969 (m) cc_final: 0.7695 (p) REVERT: R 62 ILE cc_start: 0.8234 (mm) cc_final: 0.7806 (tp) REVERT: R 119 PHE cc_start: 0.8191 (t80) cc_final: 0.7843 (t80) REVERT: R 131 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8446 (mm) REVERT: R 210 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7723 (mmtt) REVERT: R 212 MET cc_start: 0.7804 (mmm) cc_final: 0.7533 (mmp) REVERT: R 237 PHE cc_start: 0.8400 (m-80) cc_final: 0.7889 (m-80) REVERT: R 248 PHE cc_start: 0.7859 (t80) cc_final: 0.7619 (t80) REVERT: R 268 MET cc_start: 0.8091 (tmm) cc_final: 0.7612 (tmm) outliers start: 54 outliers final: 39 residues processed: 302 average time/residue: 0.2438 time to fit residues: 95.6284 Evaluate side-chains 306 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 134 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125130 restraints weight = 12824.359| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.52 r_work: 0.3471 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8441 Z= 0.268 Angle : 0.565 10.265 11417 Z= 0.295 Chirality : 0.041 0.167 1293 Planarity : 0.004 0.043 1439 Dihedral : 4.101 18.207 1129 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 5.99 % Allowed : 23.84 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1030 helix: 2.56 (0.24), residues: 435 sheet: -0.11 (0.34), residues: 219 loop : -0.90 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.011 0.001 PHE B 253 TYR 0.014 0.002 TYR R 272 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7456 (tmmm) REVERT: A 95 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6921 (mm-30) REVERT: A 104 ASN cc_start: 0.8556 (p0) cc_final: 0.8210 (p0) REVERT: A 120 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7580 (mtt-85) REVERT: A 138 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7848 (ptp-110) REVERT: A 177 GLU cc_start: 0.7122 (pm20) cc_final: 0.6922 (pm20) REVERT: A 236 ASP cc_start: 0.8529 (t0) cc_final: 0.8185 (t0) REVERT: A 238 ILE cc_start: 0.8190 (mm) cc_final: 0.7943 (mt) REVERT: B 68 ARG cc_start: 0.7724 (mtt-85) cc_final: 0.7398 (mtt-85) REVERT: B 118 ASP cc_start: 0.7914 (p0) cc_final: 0.7556 (p0) REVERT: B 153 ASP cc_start: 0.8036 (t0) cc_final: 0.7639 (t0) REVERT: B 155 ASN cc_start: 0.8054 (t0) cc_final: 0.7690 (t0) REVERT: B 186 ASP cc_start: 0.7741 (m-30) cc_final: 0.7357 (m-30) REVERT: B 291 ASP cc_start: 0.7244 (p0) cc_final: 0.6842 (p0) REVERT: B 303 ASP cc_start: 0.7143 (m-30) cc_final: 0.6835 (m-30) REVERT: N 50 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8246 (p) REVERT: N 113 SER cc_start: 0.7989 (m) cc_final: 0.7724 (p) REVERT: R 31 ASN cc_start: 0.8261 (m-40) cc_final: 0.7862 (m-40) REVERT: R 62 ILE cc_start: 0.8218 (mm) cc_final: 0.7787 (tp) REVERT: R 210 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7823 (mmtt) REVERT: R 212 MET cc_start: 0.7712 (mmm) cc_final: 0.7423 (mmp) REVERT: R 248 PHE cc_start: 0.7876 (t80) cc_final: 0.7624 (t80) REVERT: R 268 MET cc_start: 0.8141 (tmm) cc_final: 0.7638 (tmm) outliers start: 54 outliers final: 44 residues processed: 306 average time/residue: 0.2425 time to fit residues: 96.1401 Evaluate side-chains 317 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 50 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 294 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.0770 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 0.0060 chunk 0 optimal weight: 8.9990 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 134 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130227 restraints weight = 12928.301| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.54 r_work: 0.3504 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8441 Z= 0.158 Angle : 0.539 10.173 11417 Z= 0.277 Chirality : 0.040 0.168 1293 Planarity : 0.004 0.044 1439 Dihedral : 3.943 17.195 1129 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 5.21 % Allowed : 25.83 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1030 helix: 2.59 (0.24), residues: 436 sheet: 0.05 (0.34), residues: 217 loop : -0.91 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.025 0.001 PHE R 119 TYR 0.009 0.001 TYR N 96 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7123 (mmtm) REVERT: A 21 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7429 (tmmm) REVERT: A 93 ARG cc_start: 0.8025 (ptm-80) cc_final: 0.7556 (ptm-80) REVERT: A 104 ASN cc_start: 0.8520 (p0) cc_final: 0.8090 (p0) REVERT: A 120 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7560 (mtt-85) REVERT: A 236 ASP cc_start: 0.8514 (t0) cc_final: 0.8225 (t0) REVERT: B 68 ARG cc_start: 0.7549 (mtt-85) cc_final: 0.7236 (mtt-85) REVERT: B 118 ASP cc_start: 0.7895 (p0) cc_final: 0.7539 (p0) REVERT: B 137 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7618 (mmm-85) REVERT: B 153 ASP cc_start: 0.7957 (t0) cc_final: 0.7551 (t0) REVERT: B 155 ASN cc_start: 0.8042 (t0) cc_final: 0.7559 (t0) REVERT: B 303 ASP cc_start: 0.7163 (m-30) cc_final: 0.6851 (m-30) REVERT: B 337 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8275 (mtpp) REVERT: N 60 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.7905 (p) REVERT: N 113 SER cc_start: 0.8005 (m) cc_final: 0.7717 (p) REVERT: R 31 ASN cc_start: 0.8230 (m-40) cc_final: 0.7865 (m-40) REVERT: R 62 ILE cc_start: 0.8250 (mm) cc_final: 0.7904 (tp) REVERT: R 93 ASN cc_start: 0.8432 (t0) cc_final: 0.8222 (t0) REVERT: R 119 PHE cc_start: 0.8171 (t80) cc_final: 0.7865 (t80) REVERT: R 210 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7810 (mmtt) REVERT: R 212 MET cc_start: 0.7757 (mmm) cc_final: 0.7430 (mmp) REVERT: R 248 PHE cc_start: 0.7899 (t80) cc_final: 0.7648 (t80) REVERT: R 268 MET cc_start: 0.8077 (tmm) cc_final: 0.7582 (tmm) REVERT: R 270 MET cc_start: 0.8136 (mmm) cc_final: 0.7779 (mmm) outliers start: 47 outliers final: 35 residues processed: 300 average time/residue: 0.2437 time to fit residues: 94.6650 Evaluate side-chains 300 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128586 restraints weight = 13006.041| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.55 r_work: 0.3479 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8441 Z= 0.219 Angle : 0.559 10.505 11417 Z= 0.291 Chirality : 0.041 0.201 1293 Planarity : 0.004 0.043 1439 Dihedral : 3.990 16.484 1129 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 4.88 % Allowed : 26.16 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1030 helix: 2.56 (0.24), residues: 435 sheet: -0.02 (0.34), residues: 218 loop : -0.90 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.018 0.001 PHE R 119 TYR 0.013 0.001 TYR N 96 ARG 0.009 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.7727 (mmtm) cc_final: 0.7149 (mmtm) REVERT: A 21 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7490 (tmmm) REVERT: A 95 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6762 (mm-30) REVERT: A 104 ASN cc_start: 0.8528 (p0) cc_final: 0.8148 (p0) REVERT: A 120 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7542 (mtt-85) REVERT: A 138 ARG cc_start: 0.8021 (ptm160) cc_final: 0.7578 (ptp-110) REVERT: A 236 ASP cc_start: 0.8535 (t0) cc_final: 0.8204 (t0) REVERT: B 49 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7635 (mtm-85) REVERT: B 68 ARG cc_start: 0.7739 (mtt-85) cc_final: 0.7474 (mtt-85) REVERT: B 118 ASP cc_start: 0.7910 (p0) cc_final: 0.7559 (p0) REVERT: B 137 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7847 (mmm-85) REVERT: B 153 ASP cc_start: 0.8009 (t0) cc_final: 0.7631 (t0) REVERT: B 155 ASN cc_start: 0.8056 (t0) cc_final: 0.7589 (t0) REVERT: B 186 ASP cc_start: 0.7701 (m-30) cc_final: 0.7283 (m-30) REVERT: B 303 ASP cc_start: 0.7175 (m-30) cc_final: 0.6872 (m-30) REVERT: N 60 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7876 (p) REVERT: N 113 SER cc_start: 0.8009 (m) cc_final: 0.7708 (p) REVERT: R 31 ASN cc_start: 0.8282 (m-40) cc_final: 0.7918 (m-40) REVERT: R 62 ILE cc_start: 0.8275 (mm) cc_final: 0.7925 (tp) REVERT: R 119 PHE cc_start: 0.8236 (t80) cc_final: 0.7916 (t80) REVERT: R 210 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7850 (mmtt) REVERT: R 212 MET cc_start: 0.7713 (mmm) cc_final: 0.7398 (mmp) REVERT: R 248 PHE cc_start: 0.7897 (t80) cc_final: 0.7649 (t80) REVERT: R 268 MET cc_start: 0.8098 (tmm) cc_final: 0.7552 (tmm) REVERT: R 270 MET cc_start: 0.8147 (mmm) cc_final: 0.7837 (mmm) outliers start: 44 outliers final: 37 residues processed: 295 average time/residue: 0.2498 time to fit residues: 95.5711 Evaluate side-chains 308 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.0050 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.0070 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 134 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.149755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129966 restraints weight = 13105.498| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.56 r_work: 0.3502 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8441 Z= 0.169 Angle : 0.552 10.554 11417 Z= 0.286 Chirality : 0.041 0.234 1293 Planarity : 0.004 0.043 1439 Dihedral : 3.951 16.180 1129 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 4.55 % Allowed : 26.61 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1030 helix: 2.55 (0.24), residues: 436 sheet: 0.04 (0.34), residues: 217 loop : -0.84 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.016 0.001 PHE R 119 TYR 0.010 0.001 TYR N 96 ARG 0.009 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7449 (tmmm) REVERT: A 104 ASN cc_start: 0.8488 (p0) cc_final: 0.8134 (p0) REVERT: A 120 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7517 (mtt-85) REVERT: A 138 ARG cc_start: 0.7989 (ptm160) cc_final: 0.7560 (ptp-110) REVERT: A 236 ASP cc_start: 0.8542 (t0) cc_final: 0.8204 (t0) REVERT: B 38 ASP cc_start: 0.7944 (t0) cc_final: 0.7564 (p0) REVERT: B 49 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7572 (mtm-85) REVERT: B 68 ARG cc_start: 0.7573 (mtt-85) cc_final: 0.7351 (mtt-85) REVERT: B 118 ASP cc_start: 0.7885 (p0) cc_final: 0.7529 (p0) REVERT: B 137 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7728 (mmm-85) REVERT: B 153 ASP cc_start: 0.7950 (t0) cc_final: 0.7564 (t0) REVERT: B 155 ASN cc_start: 0.7982 (t0) cc_final: 0.7515 (t0) REVERT: B 186 ASP cc_start: 0.7647 (m-30) cc_final: 0.7264 (m-30) REVERT: B 303 ASP cc_start: 0.7174 (m-30) cc_final: 0.6855 (m-30) REVERT: N 60 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7860 (p) REVERT: N 113 SER cc_start: 0.8025 (m) cc_final: 0.7693 (p) REVERT: R 31 ASN cc_start: 0.8269 (m-40) cc_final: 0.7934 (m-40) REVERT: R 61 LEU cc_start: 0.7958 (tp) cc_final: 0.7748 (tt) REVERT: R 93 ASN cc_start: 0.8433 (t0) cc_final: 0.8223 (t0) REVERT: R 119 PHE cc_start: 0.8227 (t80) cc_final: 0.7892 (t80) REVERT: R 210 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7827 (mmtt) REVERT: R 212 MET cc_start: 0.7745 (mmm) cc_final: 0.7418 (mmp) REVERT: R 248 PHE cc_start: 0.7865 (t80) cc_final: 0.7625 (t80) REVERT: R 268 MET cc_start: 0.8092 (tmm) cc_final: 0.7537 (tmm) REVERT: R 270 MET cc_start: 0.8147 (mmm) cc_final: 0.7940 (mmm) outliers start: 41 outliers final: 36 residues processed: 302 average time/residue: 0.2439 time to fit residues: 97.2447 Evaluate side-chains 303 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 59 optimal weight: 0.0030 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 134 ASN A 226 ASN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129366 restraints weight = 12932.285| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.54 r_work: 0.3495 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8441 Z= 0.210 Angle : 0.577 10.802 11417 Z= 0.299 Chirality : 0.042 0.225 1293 Planarity : 0.004 0.051 1439 Dihedral : 3.981 16.250 1129 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 4.43 % Allowed : 27.16 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1030 helix: 2.54 (0.24), residues: 435 sheet: -0.03 (0.34), residues: 219 loop : -0.84 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 66 HIS 0.010 0.001 HIS R 94 PHE 0.014 0.001 PHE R 119 TYR 0.012 0.001 TYR N 96 ARG 0.009 0.001 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7139 (mmtm) REVERT: A 21 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7480 (tmmm) REVERT: A 104 ASN cc_start: 0.8505 (p0) cc_final: 0.8119 (p0) REVERT: A 120 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7540 (mtt-85) REVERT: A 135 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7556 (tmm-80) REVERT: A 186 ASP cc_start: 0.7825 (t0) cc_final: 0.7568 (t70) REVERT: A 236 ASP cc_start: 0.8524 (t0) cc_final: 0.8070 (t0) REVERT: A 240 LYS cc_start: 0.8230 (mttp) cc_final: 0.8006 (mttp) REVERT: B 38 ASP cc_start: 0.7965 (t0) cc_final: 0.7571 (p0) REVERT: B 49 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7779 (mtt90) REVERT: B 68 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7485 (mtt-85) REVERT: B 118 ASP cc_start: 0.7907 (p0) cc_final: 0.7557 (p0) REVERT: B 137 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: B 153 ASP cc_start: 0.7981 (t0) cc_final: 0.7606 (t0) REVERT: B 155 ASN cc_start: 0.8000 (t0) cc_final: 0.7538 (t0) REVERT: B 186 ASP cc_start: 0.7657 (m-30) cc_final: 0.7363 (m-30) REVERT: B 303 ASP cc_start: 0.7160 (m-30) cc_final: 0.6855 (m-30) REVERT: N 54 GLN cc_start: 0.7976 (mp10) cc_final: 0.7717 (mp10) REVERT: N 60 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7898 (p) REVERT: N 113 SER cc_start: 0.8031 (m) cc_final: 0.7797 (p) REVERT: R 31 ASN cc_start: 0.8260 (m-40) cc_final: 0.7934 (m-40) REVERT: R 62 ILE cc_start: 0.8206 (mm) cc_final: 0.7892 (tp) REVERT: R 119 PHE cc_start: 0.8230 (t80) cc_final: 0.7897 (t80) REVERT: R 210 LYS cc_start: 0.8428 (mmtt) cc_final: 0.7792 (mmtt) REVERT: R 212 MET cc_start: 0.7797 (mmm) cc_final: 0.7497 (mmp) REVERT: R 248 PHE cc_start: 0.7904 (t80) cc_final: 0.7664 (t80) REVERT: R 268 MET cc_start: 0.8117 (tmm) cc_final: 0.7553 (tmm) REVERT: R 270 MET cc_start: 0.8137 (mmm) cc_final: 0.7866 (mmm) outliers start: 40 outliers final: 37 residues processed: 293 average time/residue: 0.2461 time to fit residues: 93.4140 Evaluate side-chains 308 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 62 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 81 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 134 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129555 restraints weight = 13112.353| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.56 r_work: 0.3494 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8441 Z= 0.199 Angle : 0.579 10.666 11417 Z= 0.299 Chirality : 0.042 0.222 1293 Planarity : 0.004 0.066 1439 Dihedral : 4.008 16.303 1129 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer: Outliers : 4.43 % Allowed : 27.72 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1030 helix: 2.51 (0.24), residues: 436 sheet: 0.01 (0.34), residues: 218 loop : -0.85 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 66 HIS 0.011 0.001 HIS R 94 PHE 0.014 0.001 PHE R 119 TYR 0.012 0.001 TYR N 96 ARG 0.010 0.001 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4081.17 seconds wall clock time: 73 minutes 29.48 seconds (4409.48 seconds total)