Starting phenix.real_space_refine on Fri Oct 11 01:10:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzi_38797/10_2024/8xzi_38797_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzi_38797/10_2024/8xzi_38797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzi_38797/10_2024/8xzi_38797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzi_38797/10_2024/8xzi_38797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzi_38797/10_2024/8xzi_38797_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xzi_38797/10_2024/8xzi_38797_trim.cif" } resolution = 2.7 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= 0.002 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 5758 2.51 5 N 1528 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9041 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2473 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2553 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 327} Chain breaks: 1 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'A1D5N': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.23, per 1000 atoms: 0.58 Number of scatterers: 9041 At special positions: 0 Unit cell: (101.352, 131.016, 115.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1682 8.00 N 1528 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.08 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.12 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 16 sheets defined 40.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'R' and resid 26 through 56 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.170A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.095A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 removed outlier: 3.535A pdb=" N VAL R 117 " --> pdb=" O MET R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.058A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.707A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 193 No H-bonds generated for 'chain 'R' and resid 191 through 193' Processing helix chain 'R' and resid 194 through 210 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 277 Proline residue: R 263 - end of helix removed outlier: 3.548A pdb=" N SER R 275 " --> pdb=" O TYR R 271 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 276 " --> pdb=" O MET R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 310 removed outlier: 3.640A pdb=" N CYS R 303 " --> pdb=" O TYR R 299 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.907A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.525A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.799A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.139A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.602A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.737A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.867A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.157A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.611A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.926A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.627A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.515A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 5 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.715A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.338A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.752A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.540A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1332 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: 2.63 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1510 1.30 - 1.43: 2567 1.43 - 1.56: 5024 1.56 - 1.69: 35 1.69 - 1.82: 101 Bond restraints: 9237 Sorted by residual: bond pdb=" C28 A1D5N R 401 " pdb=" S01 A1D5N R 401 " ideal model delta sigma weight residual 1.722 1.545 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C16 A1D5N R 401 " pdb=" C21 A1D5N R 401 " ideal model delta sigma weight residual 1.389 1.566 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C11 A1D5N R 401 " pdb=" C18 A1D5N R 401 " ideal model delta sigma weight residual 1.393 1.565 -0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" C30 A1D5N R 401 " pdb=" C31 A1D5N R 401 " ideal model delta sigma weight residual 1.422 1.593 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C32 A1D5N R 401 " pdb=" S01 A1D5N R 401 " ideal model delta sigma weight residual 1.714 1.551 0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 11561 3.09 - 6.19: 880 6.19 - 9.28: 61 9.28 - 12.37: 4 12.37 - 15.47: 5 Bond angle restraints: 12511 Sorted by residual: angle pdb=" N ARG R 91 " pdb=" CA ARG R 91 " pdb=" C ARG R 91 " ideal model delta sigma weight residual 110.53 97.92 12.61 1.32e+00 5.74e-01 9.12e+01 angle pdb=" C SER S 106 " pdb=" N PRO S 107 " pdb=" CA PRO S 107 " ideal model delta sigma weight residual 119.78 128.74 -8.96 1.03e+00 9.43e-01 7.56e+01 angle pdb=" N ARG S 179 " pdb=" CA ARG S 179 " pdb=" C ARG S 179 " ideal model delta sigma weight residual 110.14 96.83 13.31 1.55e+00 4.16e-01 7.37e+01 angle pdb=" C ASP G 48 " pdb=" N PRO G 49 " pdb=" CA PRO G 49 " ideal model delta sigma weight residual 119.56 128.03 -8.47 1.02e+00 9.61e-01 6.89e+01 angle pdb=" CA PHE B 199 " pdb=" CB PHE B 199 " pdb=" CG PHE B 199 " ideal model delta sigma weight residual 113.80 121.86 -8.06 1.00e+00 1.00e+00 6.50e+01 ... (remaining 12506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5304 17.23 - 34.46: 131 34.46 - 51.69: 17 51.69 - 68.92: 14 68.92 - 86.14: 4 Dihedral angle restraints: 5470 sinusoidal: 2137 harmonic: 3333 Sorted by residual: dihedral pdb=" C PHE B 241 " pdb=" N PHE B 241 " pdb=" CA PHE B 241 " pdb=" CB PHE B 241 " ideal model delta harmonic sigma weight residual -122.60 -106.76 -15.84 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C PHE B 199 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " pdb=" CB PHE B 199 " ideal model delta harmonic sigma weight residual -122.60 -107.20 -15.40 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" C TRP B 82 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " ideal model delta harmonic sigma weight residual -122.60 -114.04 -8.56 0 2.50e+00 1.60e-01 1.17e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 899 0.081 - 0.161: 395 0.161 - 0.242: 88 0.242 - 0.322: 25 0.322 - 0.403: 1 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA ASN R 112 " pdb=" N ASN R 112 " pdb=" C ASN R 112 " pdb=" CB ASN R 112 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA TYR R 221 " pdb=" N TYR R 221 " pdb=" C TYR R 221 " pdb=" CB TYR R 221 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB THR R 170 " pdb=" CA THR R 170 " pdb=" OG1 THR R 170 " pdb=" CG2 THR R 170 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1405 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.059 2.00e-02 2.50e+03 3.00e-02 1.80e+01 pdb=" CG TYR B 105 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 50 " -0.053 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR S 50 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR S 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR S 50 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR S 50 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR S 50 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR S 50 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR S 50 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 40 " 0.048 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" CG TYR G 40 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR G 40 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR G 40 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR G 40 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR G 40 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR G 40 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 40 " 0.044 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 1 1.96 - 2.70: 544 2.70 - 3.43: 12384 3.43 - 4.17: 23553 4.17 - 4.90: 40949 Nonbonded interactions: 77431 Sorted by model distance: nonbonded pdb=" O ASP R 23 " pdb=" N LYS R 25 " model vdw 1.226 3.120 nonbonded pdb=" C ASP R 23 " pdb=" N LYS R 25 " model vdw 2.118 3.350 nonbonded pdb=" O ASP R 23 " pdb=" CA LYS R 25 " model vdw 2.126 3.470 nonbonded pdb=" O ASP R 23 " pdb=" C TRP R 24 " model vdw 2.300 3.270 nonbonded pdb=" N ARG S 179 " pdb=" O ARG S 179 " model vdw 2.313 2.496 ... (remaining 77426 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: 0.010 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.021 0.181 9237 Z= 1.329 Angle : 1.723 15.465 12511 Z= 1.156 Chirality : 0.093 0.403 1408 Planarity : 0.009 0.041 1573 Dihedral : 9.398 86.144 3310 Min Nonbonded Distance : 1.226 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Rotamer: Outliers : 0.20 % Allowed : 0.41 % Favored : 99.39 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1131 helix: 0.55 (0.24), residues: 400 sheet: 1.25 (0.31), residues: 268 loop : 1.03 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP B 99 HIS 0.011 0.003 HIS A 213 PHE 0.039 0.006 PHE A 199 TYR 0.059 0.007 TYR B 105 ARG 0.013 0.001 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: R 62 ARG cc_start: 0.6894 (ptt180) cc_final: 0.6639 (mtt90) REVERT: R 271 TYR cc_start: 0.8235 (t80) cc_final: 0.7953 (t80) REVERT: A 195 HIS cc_start: 0.7655 (t70) cc_final: 0.7423 (t70) REVERT: A 271 LYS cc_start: 0.6732 (pttp) cc_final: 0.6530 (pttp) REVERT: B 129 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7513 (mmm-85) REVERT: B 199 PHE cc_start: 0.5958 (m-10) cc_final: 0.5608 (m-80) REVERT: S 23 SER cc_start: 0.8188 (t) cc_final: 0.7984 (m) REVERT: S 77 ASN cc_start: 0.8283 (m-40) cc_final: 0.8044 (m110) REVERT: S 113 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7729 (mm110) REVERT: S 207 LEU cc_start: 0.7344 (tp) cc_final: 0.6691 (tt) REVERT: S 212 VAL cc_start: 0.8049 (p) cc_final: 0.7722 (t) outliers start: 2 outliers final: 1 residues processed: 210 average time/residue: 1.4909 time to fit residues: 330.3347 Evaluate side-chains 144 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9237 Z= 0.221 Angle : 0.650 9.250 12511 Z= 0.353 Chirality : 0.045 0.174 1408 Planarity : 0.004 0.038 1573 Dihedral : 5.586 37.780 1277 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.88 % Rotamer: Outliers : 1.73 % Allowed : 8.34 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.54 (0.25), residues: 1131 helix: 1.70 (0.25), residues: 414 sheet: 1.25 (0.31), residues: 258 loop : 0.37 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 51 HIS 0.005 0.001 HIS G 44 PHE 0.018 0.002 PHE B 151 TYR 0.015 0.002 TYR S 59 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.022 Fit side-chains REVERT: R 30 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8160 (mt) REVERT: R 62 ARG cc_start: 0.7143 (ptt180) cc_final: 0.6677 (mtt90) REVERT: R 170 THR cc_start: 0.6736 (OUTLIER) cc_final: 0.6381 (p) REVERT: R 204 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8017 (m) REVERT: R 271 TYR cc_start: 0.8197 (t80) cc_final: 0.7923 (t80) REVERT: R 285 LEU cc_start: 0.7919 (mt) cc_final: 0.7668 (mm) REVERT: A 24 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.6991 (ttp-110) REVERT: A 33 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6732 (tt0) REVERT: A 186 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6950 (mt-10) REVERT: B 325 MET cc_start: 0.7903 (mmm) cc_final: 0.7318 (tpp) REVERT: S 207 LEU cc_start: 0.7864 (tp) cc_final: 0.7630 (tt) outliers start: 17 outliers final: 4 residues processed: 169 average time/residue: 1.4337 time to fit residues: 256.6971 Evaluate side-chains 145 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9237 Z= 0.329 Angle : 0.688 10.023 12511 Z= 0.368 Chirality : 0.047 0.192 1408 Planarity : 0.005 0.041 1573 Dihedral : 5.642 46.597 1275 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.75 % Allowed : 9.26 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1131 helix: 1.50 (0.25), residues: 424 sheet: 0.95 (0.30), residues: 277 loop : 0.09 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 51 HIS 0.007 0.002 HIS B 142 PHE 0.022 0.003 PHE B 151 TYR 0.017 0.002 TYR R 88 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.009 Fit side-chains REVERT: R 30 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7987 (mp) REVERT: R 62 ARG cc_start: 0.7120 (ptt180) cc_final: 0.6835 (mtt90) REVERT: R 285 LEU cc_start: 0.8003 (mt) cc_final: 0.7760 (mm) REVERT: A 24 ARG cc_start: 0.7497 (ttp-110) cc_final: 0.7073 (ttp-110) REVERT: A 33 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6543 (tt0) REVERT: A 192 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7128 (mptt) REVERT: B 146 LEU cc_start: 0.8603 (tp) cc_final: 0.8352 (mm) REVERT: B 172 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6689 (pt0) REVERT: S 23 SER cc_start: 0.8037 (t) cc_final: 0.7750 (m) outliers start: 27 outliers final: 13 residues processed: 156 average time/residue: 1.5202 time to fit residues: 251.1116 Evaluate side-chains 148 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 242 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9237 Z= 0.230 Angle : 0.599 9.998 12511 Z= 0.320 Chirality : 0.044 0.166 1408 Planarity : 0.004 0.042 1573 Dihedral : 5.309 43.313 1275 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.54 % Allowed : 10.78 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.30 (0.25), residues: 1131 helix: 1.78 (0.26), residues: 420 sheet: 0.90 (0.31), residues: 266 loop : 0.04 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 51 HIS 0.005 0.001 HIS B 142 PHE 0.017 0.002 PHE B 151 TYR 0.021 0.002 TYR R 90 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.036 Fit side-chains REVERT: R 62 ARG cc_start: 0.7066 (ptt180) cc_final: 0.6763 (mpt180) REVERT: R 204 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.7965 (m) REVERT: R 285 LEU cc_start: 0.8017 (mt) cc_final: 0.7754 (mm) REVERT: A 24 ARG cc_start: 0.7465 (ttp-110) cc_final: 0.7078 (ttp-110) REVERT: A 33 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6574 (tt0) REVERT: A 209 LYS cc_start: 0.8238 (ptmm) cc_final: 0.7658 (mmmm) REVERT: A 246 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.6933 (m) REVERT: B 146 LEU cc_start: 0.8553 (tp) cc_final: 0.8289 (mm) REVERT: S 76 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7598 (mptt) outliers start: 25 outliers final: 9 residues processed: 152 average time/residue: 1.5954 time to fit residues: 255.9686 Evaluate side-chains 147 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9237 Z= 0.355 Angle : 0.671 9.389 12511 Z= 0.358 Chirality : 0.047 0.191 1408 Planarity : 0.005 0.043 1573 Dihedral : 5.589 46.507 1275 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.15 % Allowed : 10.68 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1131 helix: 1.55 (0.25), residues: 422 sheet: 0.71 (0.30), residues: 280 loop : -0.12 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 51 HIS 0.006 0.002 HIS B 142 PHE 0.021 0.002 PHE B 151 TYR 0.025 0.002 TYR S 178 ARG 0.012 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 0.971 Fit side-chains REVERT: R 62 ARG cc_start: 0.7104 (ptt180) cc_final: 0.6845 (mtt90) REVERT: A 24 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.7087 (ttp-110) REVERT: A 33 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: A 186 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7006 (mt-10) REVERT: A 192 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7926 (mttm) REVERT: A 209 LYS cc_start: 0.8229 (ptmm) cc_final: 0.7642 (mmmm) REVERT: A 246 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.7243 (t) REVERT: A 247 MET cc_start: 0.8026 (mtm) cc_final: 0.7817 (mtp) REVERT: B 146 LEU cc_start: 0.8649 (tp) cc_final: 0.8383 (mm) REVERT: B 172 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6723 (pt0) REVERT: B 226 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: S 23 SER cc_start: 0.8082 (t) cc_final: 0.7774 (m) REVERT: S 76 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7590 (mptt) outliers start: 31 outliers final: 15 residues processed: 156 average time/residue: 1.5060 time to fit residues: 248.3048 Evaluate side-chains 157 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9237 Z= 0.210 Angle : 0.578 8.607 12511 Z= 0.308 Chirality : 0.043 0.169 1408 Planarity : 0.004 0.044 1573 Dihedral : 5.214 43.584 1275 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.54 % Allowed : 12.31 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1131 helix: 1.75 (0.26), residues: 423 sheet: 0.81 (0.31), residues: 266 loop : -0.13 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.002 PHE B 199 TYR 0.022 0.002 TYR R 90 ARG 0.012 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.090 Fit side-chains REVERT: R 62 ARG cc_start: 0.7043 (ptt180) cc_final: 0.6831 (mtt90) REVERT: R 186 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6914 (m) REVERT: R 204 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.7959 (m) REVERT: A 24 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7071 (ttp-110) REVERT: A 33 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: A 186 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7007 (mt-10) REVERT: A 192 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7897 (mttm) REVERT: A 209 LYS cc_start: 0.8221 (ptmm) cc_final: 0.7609 (mmmm) REVERT: A 247 MET cc_start: 0.8032 (mtm) cc_final: 0.7831 (mtp) REVERT: B 42 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6610 (tpp-160) REVERT: B 146 LEU cc_start: 0.8544 (tp) cc_final: 0.8302 (mm) REVERT: S 76 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7568 (mptt) REVERT: S 127 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8311 (t) REVERT: S 207 LEU cc_start: 0.7913 (tt) cc_final: 0.7086 (pp) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 1.4829 time to fit residues: 237.1839 Evaluate side-chains 149 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9237 Z= 0.213 Angle : 0.582 8.507 12511 Z= 0.310 Chirality : 0.043 0.163 1408 Planarity : 0.004 0.045 1573 Dihedral : 5.155 44.165 1275 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.85 % Allowed : 12.21 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1131 helix: 1.78 (0.26), residues: 423 sheet: 0.77 (0.31), residues: 266 loop : -0.14 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 51 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.002 PHE B 151 TYR 0.023 0.002 TYR R 90 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.981 Fit side-chains REVERT: R 62 ARG cc_start: 0.7073 (ptt180) cc_final: 0.6832 (mtt90) REVERT: R 186 SER cc_start: 0.7198 (OUTLIER) cc_final: 0.6926 (m) REVERT: R 204 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.7967 (m) REVERT: R 285 LEU cc_start: 0.7969 (mt) cc_final: 0.7725 (mm) REVERT: R 323 MET cc_start: 0.4630 (mtt) cc_final: 0.4307 (ttp) REVERT: A 24 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7071 (ttp-110) REVERT: A 33 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: A 186 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 192 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7911 (mttm) REVERT: A 209 LYS cc_start: 0.8206 (ptmm) cc_final: 0.7588 (mmmm) REVERT: B 42 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6605 (tpp-160) REVERT: B 146 LEU cc_start: 0.8614 (tp) cc_final: 0.8343 (mm) REVERT: B 226 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: S 127 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8317 (t) REVERT: S 207 LEU cc_start: 0.7926 (tt) cc_final: 0.7083 (pp) outliers start: 28 outliers final: 14 residues processed: 151 average time/residue: 1.5686 time to fit residues: 249.6299 Evaluate side-chains 152 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9237 Z= 0.251 Angle : 0.604 8.420 12511 Z= 0.322 Chirality : 0.044 0.187 1408 Planarity : 0.004 0.045 1573 Dihedral : 5.260 45.135 1275 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.54 % Allowed : 13.02 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1131 helix: 1.76 (0.26), residues: 420 sheet: 0.77 (0.31), residues: 266 loop : -0.19 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 51 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.002 PHE B 151 TYR 0.023 0.002 TYR R 90 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.048 Fit side-chains REVERT: R 62 ARG cc_start: 0.7111 (ptt180) cc_final: 0.6828 (mtt90) REVERT: R 186 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.6992 (m) REVERT: R 204 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7963 (m) REVERT: A 24 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.7110 (ttp-110) REVERT: A 33 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: A 186 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7016 (mt-10) REVERT: A 209 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7591 (mmmm) REVERT: B 146 LEU cc_start: 0.8605 (tp) cc_final: 0.8371 (mm) REVERT: B 226 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: S 127 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (t) REVERT: S 207 LEU cc_start: 0.7907 (tt) cc_final: 0.7068 (pp) outliers start: 25 outliers final: 13 residues processed: 142 average time/residue: 1.5683 time to fit residues: 235.2550 Evaluate side-chains 147 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9237 Z= 0.271 Angle : 0.618 8.461 12511 Z= 0.331 Chirality : 0.045 0.200 1408 Planarity : 0.004 0.045 1573 Dihedral : 5.334 45.545 1275 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.14 % Allowed : 13.53 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.06 (0.25), residues: 1131 helix: 1.73 (0.26), residues: 420 sheet: 0.74 (0.31), residues: 273 loop : -0.27 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 95 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.002 PHE B 151 TYR 0.023 0.002 TYR R 90 ARG 0.015 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.976 Fit side-chains REVERT: R 62 ARG cc_start: 0.7112 (ptt180) cc_final: 0.6825 (mtt90) REVERT: R 186 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.7024 (m) REVERT: R 323 MET cc_start: 0.4639 (mtt) cc_final: 0.4310 (ttp) REVERT: A 24 ARG cc_start: 0.7476 (ttp-110) cc_final: 0.7112 (ttp-110) REVERT: A 33 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: A 186 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 209 LYS cc_start: 0.8211 (ptmm) cc_final: 0.7598 (mmmm) REVERT: B 146 LEU cc_start: 0.8628 (tp) cc_final: 0.8372 (mm) REVERT: B 226 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: S 76 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7609 (mptt) REVERT: S 127 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8364 (t) REVERT: S 207 LEU cc_start: 0.7896 (tt) cc_final: 0.7070 (pp) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 1.5440 time to fit residues: 238.0979 Evaluate side-chains 150 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9237 Z= 0.289 Angle : 0.629 8.522 12511 Z= 0.336 Chirality : 0.045 0.196 1408 Planarity : 0.005 0.044 1573 Dihedral : 5.410 45.916 1275 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.83 % Allowed : 14.34 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.06 (0.25), residues: 1131 helix: 1.76 (0.26), residues: 420 sheet: 0.71 (0.31), residues: 278 loop : -0.29 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 51 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.002 PHE B 151 TYR 0.024 0.002 TYR R 90 ARG 0.015 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.068 Fit side-chains REVERT: R 62 ARG cc_start: 0.7120 (ptt180) cc_final: 0.6791 (mpt90) REVERT: R 186 SER cc_start: 0.7255 (OUTLIER) cc_final: 0.7031 (m) REVERT: R 323 MET cc_start: 0.4721 (mtt) cc_final: 0.4391 (ttp) REVERT: A 24 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.7113 (ttp-110) REVERT: A 33 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6577 (tt0) REVERT: A 186 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 209 LYS cc_start: 0.8226 (ptmm) cc_final: 0.7610 (mmmm) REVERT: B 146 LEU cc_start: 0.8632 (tp) cc_final: 0.8382 (mm) REVERT: B 226 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: S 18 ARG cc_start: 0.8283 (tpt-90) cc_final: 0.8071 (tpt170) REVERT: S 76 LYS cc_start: 0.7977 (mmmm) cc_final: 0.7579 (mptt) REVERT: S 127 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8360 (t) REVERT: S 207 LEU cc_start: 0.7880 (tt) cc_final: 0.7057 (pp) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 1.6055 time to fit residues: 242.8105 Evaluate side-chains 150 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.128252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102743 restraints weight = 12768.920| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.82 r_work: 0.3184 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9237 Z= 0.206 Angle : 0.578 8.283 12511 Z= 0.310 Chirality : 0.043 0.191 1408 Planarity : 0.004 0.045 1573 Dihedral : 5.167 43.724 1275 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.73 % Allowed : 14.45 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1131 helix: 1.91 (0.26), residues: 420 sheet: 0.75 (0.31), residues: 266 loop : -0.27 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 51 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.002 PHE B 151 TYR 0.023 0.002 TYR R 90 ARG 0.016 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4194.69 seconds wall clock time: 75 minutes 28.02 seconds (4528.02 seconds total)