Starting phenix.real_space_refine on Sat Aug 3 13:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqr_38586/08_2024/8xqr_38586.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqr_38586/08_2024/8xqr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqr_38586/08_2024/8xqr_38586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqr_38586/08_2024/8xqr_38586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqr_38586/08_2024/8xqr_38586.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqr_38586/08_2024/8xqr_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 Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "R PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.98, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.95 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: 2.58 Time building geometry restraints manager: 3.68 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: 98.38 - 105.51: 91 105.51 - 112.64: 4478 112.64 - 119.77: 2717 119.77 - 126.90: 4033 126.90 - 134.03: 98 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: 0.870 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.260 Find NCS groups from input model: 0.100 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 0.932 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: 0.2547 time to fit residues: 88.0762 Evaluate side-chains 263 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7870 (mtpt) REVERT: A 120 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7422 (mtt-85) REVERT: A 138 ARG cc_start: 0.7941 (ptm160) cc_final: 0.7454 (ptp-110) REVERT: A 236 ASP cc_start: 0.8649 (t0) cc_final: 0.8442 (t0) REVERT: B 155 ASN cc_start: 0.8009 (t0) cc_final: 0.7763 (t0) REVERT: B 186 ASP cc_start: 0.7616 (m-30) cc_final: 0.7293 (m-30) REVERT: B 303 ASP cc_start: 0.7095 (m-30) cc_final: 0.6790 (m-30) REVERT: N 50 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8400 (p) REVERT: N 113 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7867 (p) REVERT: R 62 ILE cc_start: 0.8366 (mm) cc_final: 0.7855 (tp) REVERT: R 131 LEU cc_start: 0.8710 (mm) cc_final: 0.8474 (mm) REVERT: R 205 MET cc_start: 0.8136 (mmm) cc_final: 0.7904 (tpp) REVERT: R 210 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7632 (mmtt) REVERT: R 212 MET cc_start: 0.7513 (mmm) cc_final: 0.7303 (mmp) REVERT: R 237 PHE cc_start: 0.8301 (m-80) cc_final: 0.7772 (m-80) REVERT: R 268 MET cc_start: 0.7859 (tmm) cc_final: 0.7647 (tmm) outliers start: 33 outliers final: 20 residues processed: 285 average time/residue: 0.2469 time to fit residues: 90.4584 Evaluate side-chains 287 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 264 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8441 Z= 0.171 Angle : 0.518 8.542 11417 Z= 0.272 Chirality : 0.040 0.152 1293 Planarity : 0.004 0.047 1439 Dihedral : 4.074 28.011 1129 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 5.10 % Allowed : 23.50 % 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: 1.31 (0.27), residues: 1030 helix: 2.55 (0.24), residues: 436 sheet: 0.17 (0.35), residues: 218 loop : -0.74 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 66 HIS 0.008 0.001 HIS R 94 PHE 0.015 0.001 PHE R 119 TYR 0.010 0.001 TYR N 96 ARG 0.008 0.000 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 315 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 269 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7437 (mtt-85) REVERT: A 135 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.7308 (tmm-80) REVERT: A 138 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7467 (ptp-110) REVERT: A 236 ASP cc_start: 0.8668 (t0) cc_final: 0.8456 (t0) REVERT: B 74 SER cc_start: 0.8274 (p) cc_final: 0.8024 (p) REVERT: B 137 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7948 (mmm-85) REVERT: B 155 ASN cc_start: 0.8003 (t0) cc_final: 0.7665 (t0) REVERT: B 186 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: B 271 CYS cc_start: 0.8568 (p) cc_final: 0.8324 (p) REVERT: B 303 ASP cc_start: 0.7074 (m-30) cc_final: 0.6780 (m-30) REVERT: N 50 SER cc_start: 0.8577 (m) cc_final: 0.8355 (p) REVERT: R 62 ILE cc_start: 0.8352 (mm) cc_final: 0.7892 (tp) REVERT: R 119 PHE cc_start: 0.8169 (t80) cc_final: 0.7787 (t80) REVERT: R 131 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8465 (mm) REVERT: R 205 MET cc_start: 0.8126 (mmm) cc_final: 0.7918 (tpp) REVERT: R 210 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7590 (mmtt) REVERT: R 268 MET cc_start: 0.7862 (tmm) cc_final: 0.7548 (tmm) REVERT: R 282 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7908 (tt) outliers start: 46 outliers final: 32 residues processed: 294 average time/residue: 0.2385 time to fit residues: 90.4171 Evaluate side-chains 291 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 256 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 234 PHE 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 79 THR Chi-restraints excluded: chain N residue 100 CYS 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 139 VAL 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 282 LEU 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 69 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 0.0030 chunk 55 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 R 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1451 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= 0.209 Angle : 0.532 9.435 11417 Z= 0.277 Chirality : 0.040 0.163 1293 Planarity : 0.004 0.046 1439 Dihedral : 3.997 24.240 1129 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.23 % Favored : 97.67 % Rotamer: Outliers : 5.54 % Allowed : 22.95 % Favored : 71.51 % 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: 1.27 (0.27), residues: 1030 helix: 2.57 (0.24), residues: 436 sheet: 0.02 (0.34), residues: 222 loop : -0.73 (0.32), residues: 372 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 0.011 0.001 PHE B 253 TYR 0.012 0.001 TYR N 96 ARG 0.009 0.000 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 fitting. rotamer outliers: 50 poor density : 274 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7645 (tmmm) REVERT: A 47 SER cc_start: 0.8229 (p) cc_final: 0.8024 (p) REVERT: A 54 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7877 (mtpt) REVERT: A 120 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7467 (mtt-85) REVERT: A 138 ARG cc_start: 0.7955 (ptm160) cc_final: 0.7489 (ptp-110) REVERT: B 68 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.7301 (mtt-85) REVERT: B 74 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 118 ASP cc_start: 0.8050 (p0) cc_final: 0.7645 (p0) REVERT: B 153 ASP cc_start: 0.7785 (t0) cc_final: 0.7519 (t0) REVERT: B 155 ASN cc_start: 0.7992 (t0) cc_final: 0.7586 (t0) REVERT: B 186 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: B 271 CYS cc_start: 0.8568 (p) cc_final: 0.8312 (p) REVERT: B 303 ASP cc_start: 0.7098 (m-30) cc_final: 0.6796 (m-30) REVERT: N 6 GLN cc_start: 0.7086 (mt0) cc_final: 0.6855 (mt0) REVERT: N 50 SER cc_start: 0.8599 (m) cc_final: 0.8364 (p) REVERT: N 113 SER cc_start: 0.8161 (m) cc_final: 0.7834 (p) REVERT: R 62 ILE cc_start: 0.8368 (mm) cc_final: 0.7914 (tp) REVERT: R 119 PHE cc_start: 0.8216 (t80) cc_final: 0.7835 (t80) REVERT: R 131 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8473 (mm) REVERT: R 210 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7518 (mmtt) REVERT: R 237 PHE cc_start: 0.8295 (m-80) cc_final: 0.7953 (m-80) REVERT: R 239 LEU cc_start: 0.6783 (mt) cc_final: 0.6575 (mt) REVERT: R 248 PHE cc_start: 0.7910 (t80) cc_final: 0.7685 (t80) REVERT: R 268 MET cc_start: 0.7892 (tmm) cc_final: 0.7493 (tmm) REVERT: R 282 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7929 (tt) outliers start: 50 outliers final: 32 residues processed: 306 average time/residue: 0.2370 time to fit residues: 94.5755 Evaluate side-chains 309 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 39 LEU 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 74 SER 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 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 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 138 SER Chi-restraints excluded: chain R residue 139 VAL 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 282 LEU 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 1 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8441 Z= 0.252 Angle : 0.551 10.042 11417 Z= 0.289 Chirality : 0.041 0.157 1293 Planarity : 0.004 0.044 1439 Dihedral : 4.054 21.186 1129 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 6.54 % Allowed : 23.06 % 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: 1.17 (0.26), residues: 1030 helix: 2.54 (0.24), residues: 436 sheet: 0.02 (0.35), residues: 214 loop : -0.88 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.016 0.001 PHE R 26 TYR 0.014 0.002 TYR N 96 ARG 0.009 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 346 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 287 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7567 (tmmm) REVERT: A 95 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6974 (mm-30) REVERT: A 120 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7505 (mtt-85) REVERT: A 123 GLU cc_start: 0.7522 (tt0) cc_final: 0.7309 (tt0) REVERT: A 138 ARG cc_start: 0.7950 (ptm160) cc_final: 0.7745 (ptp-110) REVERT: A 219 THR cc_start: 0.7789 (t) cc_final: 0.7521 (m) REVERT: B 76 ASP cc_start: 0.7541 (p0) cc_final: 0.7010 (p0) REVERT: B 118 ASP cc_start: 0.8037 (p0) cc_final: 0.7674 (p0) REVERT: B 138 GLU cc_start: 0.7214 (pm20) cc_final: 0.6823 (pm20) REVERT: B 153 ASP cc_start: 0.7910 (t0) cc_final: 0.7549 (t0) REVERT: B 155 ASN cc_start: 0.7921 (t0) cc_final: 0.7565 (t0) REVERT: B 186 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: B 291 ASP cc_start: 0.7323 (p0) cc_final: 0.7011 (p0) REVERT: B 303 ASP cc_start: 0.7096 (m-30) cc_final: 0.6777 (m-30) REVERT: N 50 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8376 (p) REVERT: N 113 SER cc_start: 0.8169 (m) cc_final: 0.7910 (p) REVERT: R 31 ASN cc_start: 0.8244 (m-40) cc_final: 0.7816 (m-40) REVERT: R 62 ILE cc_start: 0.8361 (mm) cc_final: 0.7886 (tp) REVERT: R 111 ILE cc_start: 0.8812 (mt) cc_final: 0.8574 (mt) REVERT: R 119 PHE cc_start: 0.8219 (t80) cc_final: 0.7899 (t80) REVERT: R 131 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8486 (mm) REVERT: R 210 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7440 (mmtt) REVERT: R 237 PHE cc_start: 0.8382 (m-80) cc_final: 0.7843 (m-80) REVERT: R 248 PHE cc_start: 0.7931 (t80) cc_final: 0.7677 (t80) REVERT: R 268 MET cc_start: 0.7967 (tmm) cc_final: 0.7485 (tmm) REVERT: R 282 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7926 (tt) outliers start: 59 outliers final: 37 residues processed: 317 average time/residue: 0.2299 time to fit residues: 95.1503 Evaluate side-chains 326 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 284 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 37 ILE 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 221 THR Chi-restraints excluded: chain B residue 234 PHE 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 139 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 207 LYS Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 282 LEU 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 57 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 37 HIS A 134 ASN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8441 Z= 0.244 Angle : 0.552 9.832 11417 Z= 0.289 Chirality : 0.041 0.162 1293 Planarity : 0.004 0.044 1439 Dihedral : 4.052 18.580 1129 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 6.32 % Allowed : 23.95 % Favored : 69.73 % 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: 1.11 (0.26), residues: 1030 helix: 2.52 (0.24), residues: 436 sheet: -0.01 (0.34), residues: 214 loop : -0.96 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.012 0.001 PHE A 77 TYR 0.013 0.001 TYR N 96 ARG 0.008 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 341 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 284 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7555 (tmmm) REVERT: A 54 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7888 (mtpt) REVERT: A 95 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 104 ASN cc_start: 0.8568 (p0) cc_final: 0.8187 (p0) REVERT: A 120 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7494 (mtt-85) REVERT: A 138 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7756 (ptp-110) REVERT: A 219 THR cc_start: 0.7797 (t) cc_final: 0.7561 (m) REVERT: A 236 ASP cc_start: 0.8586 (t0) cc_final: 0.8338 (t0) REVERT: B 68 ARG cc_start: 0.7650 (mtt-85) cc_final: 0.7289 (mtt-85) REVERT: B 118 ASP cc_start: 0.8053 (p0) cc_final: 0.7680 (p0) REVERT: B 138 GLU cc_start: 0.7237 (pm20) cc_final: 0.6832 (pm20) REVERT: B 153 ASP cc_start: 0.7911 (t0) cc_final: 0.7490 (t0) REVERT: B 155 ASN cc_start: 0.7952 (t0) cc_final: 0.7526 (t0) REVERT: B 186 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: B 291 ASP cc_start: 0.7369 (p0) cc_final: 0.6975 (p0) REVERT: B 303 ASP cc_start: 0.7098 (m-30) cc_final: 0.6783 (m-30) REVERT: N 50 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8375 (p) REVERT: N 113 SER cc_start: 0.8240 (m) cc_final: 0.7921 (p) REVERT: R 31 ASN cc_start: 0.8247 (m-40) cc_final: 0.7824 (m-40) REVERT: R 62 ILE cc_start: 0.8356 (mm) cc_final: 0.7877 (tp) REVERT: R 111 ILE cc_start: 0.8800 (mt) cc_final: 0.8591 (mt) REVERT: R 119 PHE cc_start: 0.8218 (t80) cc_final: 0.7897 (t80) REVERT: R 210 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7512 (mmtt) REVERT: R 248 PHE cc_start: 0.7922 (t80) cc_final: 0.7660 (t80) REVERT: R 268 MET cc_start: 0.7990 (tmm) cc_final: 0.7492 (tmm) REVERT: R 282 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7935 (tt) outliers start: 57 outliers final: 43 residues processed: 314 average time/residue: 0.2373 time to fit residues: 96.7961 Evaluate side-chains 325 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain A residue 54 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 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 37 ILE 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 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 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 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 282 LEU Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8441 Z= 0.311 Angle : 0.576 7.553 11417 Z= 0.306 Chirality : 0.042 0.159 1293 Planarity : 0.004 0.048 1439 Dihedral : 4.152 17.503 1129 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 6.43 % Allowed : 23.28 % Favored : 70.29 % 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: 1.03 (0.26), residues: 1030 helix: 2.47 (0.24), residues: 435 sheet: 0.01 (0.34), residues: 210 loop : -1.04 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.014 0.002 PHE A 77 TYR 0.017 0.002 TYR R 272 ARG 0.008 0.001 ARG B 197 *********************** 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 348 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 290 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7252 (mmtm) REVERT: A 21 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7586 (tmmm) REVERT: A 54 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: A 95 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6842 (mm-30) REVERT: A 120 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7520 (mtt-85) REVERT: A 199 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 219 THR cc_start: 0.7788 (t) cc_final: 0.7569 (m) REVERT: A 236 ASP cc_start: 0.8598 (t0) cc_final: 0.8383 (t0) REVERT: B 76 ASP cc_start: 0.7604 (p0) cc_final: 0.7272 (p0) REVERT: B 96 ARG cc_start: 0.7311 (mtp85) cc_final: 0.7042 (mtp85) REVERT: B 118 ASP cc_start: 0.8059 (p0) cc_final: 0.7708 (p0) REVERT: B 153 ASP cc_start: 0.7997 (t0) cc_final: 0.7591 (t0) REVERT: B 155 ASN cc_start: 0.7944 (t0) cc_final: 0.7520 (t0) REVERT: B 186 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: B 291 ASP cc_start: 0.7383 (p0) cc_final: 0.6993 (p0) REVERT: B 303 ASP cc_start: 0.7088 (m-30) cc_final: 0.6777 (m-30) REVERT: N 50 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8384 (p) REVERT: N 113 SER cc_start: 0.8257 (m) cc_final: 0.7929 (p) REVERT: R 31 ASN cc_start: 0.8319 (m-40) cc_final: 0.7877 (m-40) REVERT: R 62 ILE cc_start: 0.8372 (mm) cc_final: 0.7887 (tp) REVERT: R 132 VAL cc_start: 0.8233 (p) cc_final: 0.7885 (m) REVERT: R 210 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7582 (mmtt) REVERT: R 232 SER cc_start: 0.7925 (t) cc_final: 0.7707 (p) REVERT: R 248 PHE cc_start: 0.7935 (t80) cc_final: 0.7667 (t80) REVERT: R 268 MET cc_start: 0.8011 (tmm) cc_final: 0.7496 (tmm) REVERT: R 282 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7945 (tt) outliers start: 58 outliers final: 45 residues processed: 319 average time/residue: 0.2267 time to fit residues: 94.2752 Evaluate side-chains 334 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 284 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain A residue 54 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 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 37 ILE 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 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 49 THR Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU 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 282 LEU 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 19 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8441 Z= 0.189 Angle : 0.555 10.783 11417 Z= 0.290 Chirality : 0.041 0.198 1293 Planarity : 0.004 0.044 1439 Dihedral : 4.024 16.077 1129 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % 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: 1.10 (0.26), residues: 1030 helix: 2.51 (0.24), residues: 436 sheet: 0.09 (0.34), residues: 208 loop : -1.02 (0.30), residues: 386 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 0.010 0.001 PHE R 119 TYR 0.011 0.001 TYR N 96 ARG 0.008 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 327 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 280 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7578 (tmmm) REVERT: A 54 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7862 (mtpt) REVERT: A 95 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6851 (mm-30) REVERT: A 104 ASN cc_start: 0.8517 (p0) cc_final: 0.8154 (p0) REVERT: A 120 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7478 (mtt-85) REVERT: A 138 ARG cc_start: 0.7953 (ptm160) cc_final: 0.7739 (ptp-110) REVERT: A 177 GLU cc_start: 0.6959 (pm20) cc_final: 0.6732 (pm20) REVERT: A 199 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6887 (mm-30) REVERT: B 38 ASP cc_start: 0.7982 (t0) cc_final: 0.7630 (p0) REVERT: B 96 ARG cc_start: 0.7293 (mtp85) cc_final: 0.7011 (mtp85) REVERT: B 118 ASP cc_start: 0.8054 (p0) cc_final: 0.7677 (p0) REVERT: B 137 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8121 (mmm-85) REVERT: B 153 ASP cc_start: 0.7954 (t0) cc_final: 0.7537 (t0) REVERT: B 155 ASN cc_start: 0.7905 (t0) cc_final: 0.7479 (t0) REVERT: B 186 ASP cc_start: 0.7623 (m-30) cc_final: 0.7254 (m-30) REVERT: B 291 ASP cc_start: 0.7367 (p0) cc_final: 0.6929 (p0) REVERT: B 303 ASP cc_start: 0.7073 (m-30) cc_final: 0.6774 (m-30) REVERT: B 337 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8369 (mtpp) REVERT: N 60 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7860 (p) REVERT: N 113 SER cc_start: 0.8250 (m) cc_final: 0.7919 (p) REVERT: R 31 ASN cc_start: 0.8300 (m-40) cc_final: 0.7917 (m-40) REVERT: R 62 ILE cc_start: 0.8339 (mm) cc_final: 0.7937 (tp) REVERT: R 210 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7627 (mmtt) REVERT: R 248 PHE cc_start: 0.7910 (t80) cc_final: 0.7638 (t80) REVERT: R 268 MET cc_start: 0.7961 (tmm) cc_final: 0.7429 (tmm) REVERT: R 270 MET cc_start: 0.8163 (mmm) cc_final: 0.7804 (mmm) REVERT: R 282 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7874 (tt) outliers start: 47 outliers final: 40 residues processed: 306 average time/residue: 0.2335 time to fit residues: 93.6843 Evaluate side-chains 318 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 274 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain A residue 145 PHE 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 37 ILE 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 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 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 49 THR Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU 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 282 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: 2.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 220 GLN R 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8441 Z= 0.284 Angle : 0.579 7.167 11417 Z= 0.306 Chirality : 0.043 0.237 1293 Planarity : 0.004 0.053 1439 Dihedral : 4.140 17.862 1129 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 4.77 % Allowed : 26.16 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1030 helix: 2.43 (0.24), residues: 435 sheet: -0.08 (0.34), residues: 212 loop : -1.02 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.012 0.001 PHE A 77 TYR 0.014 0.001 TYR R 272 ARG 0.008 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 325 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 282 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7595 (tmmm) REVERT: A 95 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6905 (mm-30) REVERT: A 120 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7505 (mtt-85) REVERT: A 177 GLU cc_start: 0.7049 (pm20) cc_final: 0.6822 (pm20) REVERT: A 199 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 38 ASP cc_start: 0.7974 (t0) cc_final: 0.7646 (p0) REVERT: B 68 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7197 (tpt-90) REVERT: B 96 ARG cc_start: 0.7315 (mtp85) cc_final: 0.7038 (mtp85) REVERT: B 118 ASP cc_start: 0.8071 (p0) cc_final: 0.7715 (p0) REVERT: B 153 ASP cc_start: 0.7985 (t0) cc_final: 0.7587 (t0) REVERT: B 155 ASN cc_start: 0.7949 (t0) cc_final: 0.7525 (t0) REVERT: B 186 ASP cc_start: 0.7764 (m-30) cc_final: 0.7362 (m-30) REVERT: B 291 ASP cc_start: 0.7383 (p0) cc_final: 0.6959 (p0) REVERT: B 303 ASP cc_start: 0.7092 (m-30) cc_final: 0.6783 (m-30) REVERT: N 113 SER cc_start: 0.8258 (m) cc_final: 0.7913 (p) REVERT: R 31 ASN cc_start: 0.8356 (m-40) cc_final: 0.7986 (m-40) REVERT: R 62 ILE cc_start: 0.8367 (mm) cc_final: 0.7966 (tp) REVERT: R 119 PHE cc_start: 0.8202 (t80) cc_final: 0.7872 (t80) REVERT: R 210 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7584 (mmtt) REVERT: R 248 PHE cc_start: 0.7924 (t80) cc_final: 0.7656 (t80) REVERT: R 268 MET cc_start: 0.7996 (tmm) cc_final: 0.7438 (tmm) REVERT: R 270 MET cc_start: 0.8232 (mmm) cc_final: 0.7901 (mmm) REVERT: R 282 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7939 (tt) outliers start: 43 outliers final: 41 residues processed: 306 average time/residue: 0.2333 time to fit residues: 93.2240 Evaluate side-chains 325 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 282 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 145 PHE 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 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 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 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 49 THR Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU 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 282 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 101 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 134 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8441 Z= 0.235 Angle : 0.579 10.977 11417 Z= 0.302 Chirality : 0.042 0.238 1293 Planarity : 0.004 0.045 1439 Dihedral : 4.115 16.932 1129 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 4.66 % Allowed : 27.27 % Favored : 68.07 % 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: 1.02 (0.26), residues: 1030 helix: 2.45 (0.24), residues: 435 sheet: -0.00 (0.34), residues: 210 loop : -1.02 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 66 HIS 0.009 0.001 HIS R 94 PHE 0.013 0.001 PHE R 26 TYR 0.012 0.001 TYR N 96 ARG 0.008 0.001 ARG A 96 ********************** 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 324 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 282 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7545 (tmmm) REVERT: A 54 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7870 (mtpt) REVERT: A 95 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 120 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7479 (mtt-85) REVERT: A 177 GLU cc_start: 0.7030 (pm20) cc_final: 0.6795 (pm20) REVERT: A 199 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6885 (mm-30) REVERT: B 38 ASP cc_start: 0.7973 (t0) cc_final: 0.7656 (p0) REVERT: B 68 ARG cc_start: 0.7665 (mtt-85) cc_final: 0.7195 (tpt-90) REVERT: B 96 ARG cc_start: 0.7315 (mtp85) cc_final: 0.7032 (mtp85) REVERT: B 118 ASP cc_start: 0.8059 (p0) cc_final: 0.7703 (p0) REVERT: B 153 ASP cc_start: 0.7950 (t0) cc_final: 0.7554 (t0) REVERT: B 155 ASN cc_start: 0.7916 (t0) cc_final: 0.7478 (t0) REVERT: B 186 ASP cc_start: 0.7737 (m-30) cc_final: 0.7368 (m-30) REVERT: B 291 ASP cc_start: 0.7370 (p0) cc_final: 0.6933 (p0) REVERT: B 303 ASP cc_start: 0.7089 (m-30) cc_final: 0.6779 (m-30) REVERT: B 337 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8378 (mtpp) REVERT: N 60 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7876 (p) REVERT: N 113 SER cc_start: 0.8279 (m) cc_final: 0.7938 (p) REVERT: R 31 ASN cc_start: 0.8327 (m-40) cc_final: 0.7966 (m-40) REVERT: R 62 ILE cc_start: 0.8353 (mm) cc_final: 0.7951 (tp) REVERT: R 132 VAL cc_start: 0.8318 (p) cc_final: 0.7941 (m) REVERT: R 210 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7577 (mmtt) REVERT: R 239 LEU cc_start: 0.6959 (mt) cc_final: 0.6743 (mt) REVERT: R 248 PHE cc_start: 0.7883 (t80) cc_final: 0.7622 (t80) REVERT: R 268 MET cc_start: 0.7985 (tmm) cc_final: 0.7421 (tmm) REVERT: R 270 MET cc_start: 0.8204 (mmm) cc_final: 0.7869 (mmm) REVERT: R 282 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7934 (tt) outliers start: 42 outliers final: 37 residues processed: 306 average time/residue: 0.2295 time to fit residues: 91.4578 Evaluate side-chains 316 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 275 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 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 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 49 THR Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 122 LEU 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 282 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 22 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 92 optimal weight: 0.0070 chunk 54 optimal weight: 4.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.148931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129170 restraints weight = 12870.335| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.51 r_work: 0.3486 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2039 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= 0.197 Angle : 0.563 8.400 11417 Z= 0.295 Chirality : 0.042 0.233 1293 Planarity : 0.004 0.051 1439 Dihedral : 4.038 15.781 1129 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 4.77 % Allowed : 27.83 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1030 helix: 2.48 (0.24), residues: 435 sheet: -0.04 (0.34), residues: 218 loop : -0.94 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 66 HIS 0.010 0.001 HIS R 94 PHE 0.014 0.001 PHE R 26 TYR 0.011 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: 2464.83 seconds wall clock time: 44 minutes 25.54 seconds (2665.54 seconds total)