Starting phenix.real_space_refine on Thu Mar 13 15:08:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dfl_30665/03_2025/7dfl_30665_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfl_30665/03_2025/7dfl_30665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2025/7dfl_30665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2025/7dfl_30665.map" model { file = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2025/7dfl_30665_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfl_30665/03_2025/7dfl_30665_neut.cif" } resolution = 3.3 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= 0.078 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 66 5.16 5 C 5729 2.51 5 N 1535 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2273 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} 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: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1847 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.21, per 1000 atoms: 0.58 Number of scatterers: 8987 At special positions: 0 Unit cell: (90.72, 119.88, 126.36, 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 66 16.00 O 1657 8.00 N 1535 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 180 " distance=2.04 Simple disulfide: pdb=" SG CYS R 441 " - pdb=" SG CYS R 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=1.95 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: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 38.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'R' and resid 28 through 53 removed outlier: 3.999A pdb=" N VAL R 32 " --> pdb=" O MET R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 80 removed outlier: 4.084A pdb=" N TYR R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 90 removed outlier: 3.612A pdb=" N ASN R 84 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 131 Processing helix chain 'R' and resid 140 through 157 Processing helix chain 'R' and resid 158 through 163 removed outlier: 4.403A pdb=" N ILE R 162 " --> pdb=" O TRP R 158 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 158 through 163' Processing helix chain 'R' and resid 168 through 172 removed outlier: 3.642A pdb=" N THR R 172 " --> pdb=" O MET R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 218 Processing helix chain 'R' and resid 408 through 439 Proline residue: R 430 - end of helix removed outlier: 3.735A pdb=" N PHE R 434 " --> pdb=" O PRO R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 464 removed outlier: 4.226A pdb=" N LEU R 449 " --> pdb=" O CYS R 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN R 460 " --> pdb=" O LEU R 456 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER R 461 " --> pdb=" O GLY R 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR R 462 " --> pdb=" O TYR R 458 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 467 No H-bonds generated for 'chain 'R' and resid 465 through 467' Processing helix chain 'R' and resid 468 through 472 removed outlier: 3.930A pdb=" N ASN R 472 " --> pdb=" O PRO R 469 " (cutoff:3.500A) Processing helix chain 'R' and resid 475 through 482 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'A' and resid 6 through 37 removed outlier: 4.128A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.762A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 219 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 260 removed outlier: 4.049A pdb=" N GLU A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.867A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.920A pdb=" N LEU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.671A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.537A pdb=" N VAL C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.630A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.520A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.047A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.513A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.220A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 196 removed outlier: 3.691A pdb=" N LEU A 42 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 9.973A pdb=" N SER A 225 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.446A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 149 removed outlier: 6.448A pdb=" N VAL C 147 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU C 174 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR C 190 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP C 176 " --> pdb=" O LEU C 188 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1185 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: 2.69 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2897 1.35 - 1.47: 2300 1.47 - 1.59: 3884 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 9181 Sorted by residual: bond pdb=" C VAL R 80 " pdb=" O VAL R 80 " ideal model delta sigma weight residual 1.233 1.285 -0.052 1.02e-02 9.61e+03 2.60e+01 bond pdb=" N THR C 118 " pdb=" CA THR C 118 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.23e-02 6.61e+03 1.76e+01 bond pdb=" N PRO C 236 " pdb=" CD PRO C 236 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N LEU C 187 " pdb=" CA LEU C 187 " ideal model delta sigma weight residual 1.456 1.503 -0.046 1.22e-02 6.72e+03 1.44e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.19e-02 7.06e+03 1.30e+01 ... (remaining 9176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 11990 2.21 - 4.42: 356 4.42 - 6.63: 66 6.63 - 8.84: 12 8.84 - 11.05: 3 Bond angle restraints: 12427 Sorted by residual: angle pdb=" N ARG R 218 " pdb=" CA ARG R 218 " pdb=" C ARG R 218 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 angle pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" C SER C 136 " ideal model delta sigma weight residual 110.80 100.47 10.33 2.13e+00 2.20e-01 2.35e+01 angle pdb=" N ARG R 134 " pdb=" CA ARG R 134 " pdb=" C ARG R 134 " ideal model delta sigma weight residual 108.58 99.99 8.59 1.82e+00 3.02e-01 2.23e+01 angle pdb=" N HIS R 406 " pdb=" CA HIS R 406 " pdb=" C HIS R 406 " ideal model delta sigma weight residual 108.02 116.30 -8.28 1.78e+00 3.16e-01 2.16e+01 angle pdb=" N CYS R 445 " pdb=" CA CYS R 445 " pdb=" C CYS R 445 " ideal model delta sigma weight residual 110.80 101.30 9.50 2.13e+00 2.20e-01 1.99e+01 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5048 16.82 - 33.65: 340 33.65 - 50.47: 54 50.47 - 67.29: 9 67.29 - 84.12: 6 Dihedral angle restraints: 5457 sinusoidal: 2162 harmonic: 3295 Sorted by residual: dihedral pdb=" C SER C 136 " pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" CB SER C 136 " ideal model delta harmonic sigma weight residual -122.60 -110.84 -11.76 0 2.50e+00 1.60e-01 2.21e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG R 134 " pdb=" C ARG R 134 " pdb=" N TYR R 135 " pdb=" CA TYR R 135 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1233 0.085 - 0.169: 142 0.169 - 0.254: 14 0.254 - 0.339: 2 0.339 - 0.423: 2 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA SER C 136 " pdb=" N SER C 136 " pdb=" C SER C 136 " pdb=" CB SER C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA SER B 67 " pdb=" N SER B 67 " pdb=" C SER B 67 " pdb=" CB SER B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ARG R 218 " pdb=" N ARG R 218 " pdb=" C ARG R 218 " pdb=" CB ARG R 218 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1390 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " 0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 236 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 435 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE R 435 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 435 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 435 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 435 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 435 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 435 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.025 2.00e-02 2.50e+03 2.02e-02 7.15e+00 pdb=" CG PHE B 234 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.004 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 34 2.51 - 3.11: 7003 3.11 - 3.70: 13351 3.70 - 4.30: 19365 4.30 - 4.90: 32412 Nonbonded interactions: 72165 Sorted by model distance: nonbonded pdb=" SD MET A 203 " pdb=" CE MET A 227 " model vdw 1.910 3.820 nonbonded pdb=" O ILE B 43 " pdb=" NH2 ARG B 304 " model vdw 2.129 3.120 nonbonded pdb=" O ILE R 37 " pdb=" OG1 THR R 41 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 247 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" N GLU B 215 " model vdw 2.297 3.120 ... (remaining 72160 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: 1.400 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.008 0.072 9181 Z= 0.520 Angle : 0.951 11.046 12427 Z= 0.557 Chirality : 0.057 0.423 1393 Planarity : 0.006 0.089 1568 Dihedral : 11.969 84.118 3319 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.96 (0.24), residues: 1115 helix: 0.54 (0.27), residues: 363 sheet: -0.92 (0.32), residues: 252 loop : -1.31 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 216 HIS 0.013 0.002 HIS A 327 PHE 0.057 0.003 PHE R 435 TYR 0.025 0.003 TYR R 138 ARG 0.010 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8031 (mt) cc_final: 0.7708 (mt) REVERT: R 179 LYS cc_start: 0.5155 (pttm) cc_final: 0.4651 (mttp) REVERT: R 436 MET cc_start: 0.7342 (mtp) cc_final: 0.7061 (mmp) REVERT: B 32 GLN cc_start: 0.7585 (tt0) cc_final: 0.7350 (tm-30) REVERT: B 118 ASP cc_start: 0.7398 (p0) cc_final: 0.7161 (p0) REVERT: B 255 LEU cc_start: 0.8060 (mt) cc_final: 0.7798 (mt) REVERT: A 311 LYS cc_start: 0.8097 (tptm) cc_final: 0.7812 (tptm) REVERT: C 80 PHE cc_start: 0.6826 (m-10) cc_final: 0.6553 (m-10) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2427 time to fit residues: 109.6236 Evaluate side-chains 225 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111132 restraints weight = 14204.309| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.90 r_work: 0.3346 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9181 Z= 0.226 Angle : 0.687 9.298 12427 Z= 0.355 Chirality : 0.045 0.195 1393 Planarity : 0.005 0.065 1568 Dihedral : 5.438 46.233 1239 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.54 % Allowed : 12.21 % Favored : 85.25 % 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: -0.30 (0.25), residues: 1115 helix: 1.04 (0.27), residues: 371 sheet: -0.53 (0.32), residues: 246 loop : -0.90 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 297 HIS 0.003 0.001 HIS C 35 PHE 0.030 0.002 PHE R 435 TYR 0.020 0.002 TYR R 50 ARG 0.005 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.8096 (pmm) cc_final: 0.6344 (mpp) REVERT: R 50 TYR cc_start: 0.8107 (t80) cc_final: 0.7582 (t80) REVERT: R 130 GLN cc_start: 0.8156 (tp40) cc_final: 0.7588 (tm-30) REVERT: R 133 LEU cc_start: 0.5959 (mp) cc_final: 0.5445 (tp) REVERT: R 179 LYS cc_start: 0.5237 (pttm) cc_final: 0.4371 (mttp) REVERT: R 436 MET cc_start: 0.8143 (mtp) cc_final: 0.7502 (mmp) REVERT: R 481 ARG cc_start: 0.8747 (mtt90) cc_final: 0.7655 (tpt170) REVERT: B 15 LYS cc_start: 0.9290 (mmtp) cc_final: 0.9059 (mmtp) REVERT: B 29 THR cc_start: 0.7106 (t) cc_final: 0.6904 (t) REVERT: B 32 GLN cc_start: 0.8140 (tt0) cc_final: 0.7432 (tm-30) REVERT: B 57 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8219 (mtpt) REVERT: B 172 GLU cc_start: 0.8616 (tp30) cc_final: 0.8393 (tp30) REVERT: B 197 ARG cc_start: 0.8595 (mmp80) cc_final: 0.8350 (mmp80) REVERT: B 217 MET cc_start: 0.7606 (tmm) cc_final: 0.7158 (tmm) REVERT: B 254 ASP cc_start: 0.7937 (t70) cc_final: 0.7600 (t70) REVERT: B 297 TRP cc_start: 0.7704 (m100) cc_final: 0.7185 (m-10) REVERT: G 13 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8091 (mtm-85) REVERT: G 18 GLN cc_start: 0.7397 (tp40) cc_final: 0.6750 (tp-100) REVERT: G 28 ILE cc_start: 0.8648 (tp) cc_final: 0.8207 (tt) REVERT: G 29 LYS cc_start: 0.7352 (mtmm) cc_final: 0.7132 (mptt) REVERT: A 9 ASP cc_start: 0.8281 (m-30) cc_final: 0.7962 (m-30) REVERT: A 38 ARG cc_start: 0.7289 (ptp90) cc_final: 0.6852 (ptp-170) REVERT: A 57 LYS cc_start: 0.8446 (tttt) cc_final: 0.8204 (mttp) REVERT: A 212 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6531 (tm-30) REVERT: A 234 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7384 (mt-10) REVERT: A 265 GLN cc_start: 0.8159 (mt0) cc_final: 0.7857 (mt0) REVERT: A 287 HIS cc_start: 0.7381 (m90) cc_final: 0.7015 (m-70) REVERT: A 295 TYR cc_start: 0.8232 (t80) cc_final: 0.7972 (t80) REVERT: A 311 LYS cc_start: 0.8313 (tptm) cc_final: 0.8102 (tptm) REVERT: A 346 ASP cc_start: 0.8110 (m-30) cc_final: 0.7420 (t70) REVERT: A 350 GLN cc_start: 0.7447 (tp40) cc_final: 0.6665 (mm110) REVERT: C 113 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 153 GLU cc_start: 0.8786 (tp30) cc_final: 0.8524 (tp30) REVERT: C 218 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.7586 (tpp-160) REVERT: C 219 LEU cc_start: 0.7979 (tt) cc_final: 0.6898 (tt) REVERT: C 220 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7326 (mp0) REVERT: C 223 ASP cc_start: 0.7707 (m-30) cc_final: 0.7371 (p0) REVERT: C 230 MET cc_start: 0.7911 (ttp) cc_final: 0.7547 (ttt) REVERT: C 234 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7845 (pt0) outliers start: 25 outliers final: 15 residues processed: 285 average time/residue: 0.2406 time to fit residues: 92.7760 Evaluate side-chains 241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 225 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.0050 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN A 287 HIS A 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111758 restraints weight = 14631.210| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.90 r_work: 0.3373 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9181 Z= 0.196 Angle : 0.637 10.502 12427 Z= 0.329 Chirality : 0.044 0.159 1393 Planarity : 0.004 0.066 1568 Dihedral : 4.970 44.683 1239 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.36 % Allowed : 13.94 % Favored : 82.71 % 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: -0.07 (0.25), residues: 1115 helix: 1.06 (0.27), residues: 368 sheet: -0.24 (0.34), residues: 235 loop : -0.71 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 287 PHE 0.031 0.002 PHE R 435 TYR 0.017 0.001 TYR A 235 ARG 0.007 0.001 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7945 (pmm) cc_final: 0.6410 (mpp) REVERT: R 50 TYR cc_start: 0.8127 (t80) cc_final: 0.7783 (t80) REVERT: R 93 TRP cc_start: 0.6108 (t-100) cc_final: 0.5383 (t-100) REVERT: R 130 GLN cc_start: 0.8258 (tp40) cc_final: 0.7832 (tm-30) REVERT: R 133 LEU cc_start: 0.5967 (mp) cc_final: 0.5154 (tp) REVERT: R 179 LYS cc_start: 0.5124 (pttm) cc_final: 0.4274 (mttp) REVERT: R 436 MET cc_start: 0.8090 (mtp) cc_final: 0.7507 (mmp) REVERT: R 450 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7355 (m90) REVERT: R 481 ARG cc_start: 0.8798 (mtt90) cc_final: 0.7653 (tpt170) REVERT: B 13 GLN cc_start: 0.8234 (mp10) cc_final: 0.8033 (mp10) REVERT: B 20 ASP cc_start: 0.8408 (m-30) cc_final: 0.8148 (m-30) REVERT: B 29 THR cc_start: 0.7079 (t) cc_final: 0.6867 (t) REVERT: B 32 GLN cc_start: 0.8116 (tt0) cc_final: 0.7341 (tm-30) REVERT: B 42 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7347 (tpp80) REVERT: B 44 GLN cc_start: 0.7198 (mp10) cc_final: 0.6910 (mp10) REVERT: B 57 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8261 (mtpt) REVERT: B 197 ARG cc_start: 0.8653 (mmp80) cc_final: 0.8379 (mmp80) REVERT: B 217 MET cc_start: 0.7360 (tmm) cc_final: 0.7151 (tmm) REVERT: B 254 ASP cc_start: 0.7965 (t70) cc_final: 0.7557 (t70) REVERT: B 260 GLU cc_start: 0.8417 (tt0) cc_final: 0.7924 (tt0) REVERT: B 297 TRP cc_start: 0.7488 (m100) cc_final: 0.6828 (m-10) REVERT: B 325 MET cc_start: 0.8615 (tpp) cc_final: 0.8348 (tpt) REVERT: G 13 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8084 (mtm-85) REVERT: G 18 GLN cc_start: 0.7466 (tp40) cc_final: 0.7134 (tp-100) REVERT: G 28 ILE cc_start: 0.8628 (tp) cc_final: 0.8236 (tt) REVERT: A 9 ASP cc_start: 0.8279 (m-30) cc_final: 0.7918 (m-30) REVERT: A 57 LYS cc_start: 0.8392 (tttt) cc_final: 0.8158 (mttp) REVERT: A 265 GLN cc_start: 0.8203 (mt0) cc_final: 0.7921 (mt0) REVERT: A 280 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8279 (pp20) REVERT: A 284 MET cc_start: 0.8679 (mtt) cc_final: 0.8467 (mtm) REVERT: A 350 GLN cc_start: 0.7564 (tp40) cc_final: 0.6747 (mm110) REVERT: C 82 GLN cc_start: 0.7731 (mt0) cc_final: 0.7518 (mt0) REVERT: C 113 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8262 (tp40) REVERT: C 153 GLU cc_start: 0.8604 (tp30) cc_final: 0.8258 (tp30) REVERT: C 218 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.7940 (ttm-80) REVERT: C 220 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7742 (mp0) REVERT: C 230 MET cc_start: 0.8082 (ttp) cc_final: 0.7801 (ttp) REVERT: C 234 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7871 (pt0) outliers start: 33 outliers final: 21 residues processed: 274 average time/residue: 0.2132 time to fit residues: 79.2055 Evaluate side-chains 241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109160 restraints weight = 14621.130| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.90 r_work: 0.3315 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9181 Z= 0.251 Angle : 0.646 10.161 12427 Z= 0.332 Chirality : 0.044 0.182 1393 Planarity : 0.004 0.066 1568 Dihedral : 4.851 37.228 1239 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.17 % Allowed : 14.95 % Favored : 80.87 % 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: -0.03 (0.25), residues: 1115 helix: 1.16 (0.27), residues: 368 sheet: -0.27 (0.33), residues: 241 loop : -0.72 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 47 HIS 0.003 0.001 HIS C 232 PHE 0.043 0.002 PHE R 435 TYR 0.028 0.002 TYR A 295 ARG 0.005 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7747 (pmm) cc_final: 0.6448 (mpp) REVERT: R 93 TRP cc_start: 0.5756 (t-100) cc_final: 0.5016 (t-100) REVERT: R 130 GLN cc_start: 0.8195 (tp40) cc_final: 0.7732 (tm-30) REVERT: R 133 LEU cc_start: 0.6282 (mp) cc_final: 0.5096 (tp) REVERT: R 158 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.5470 (t60) REVERT: R 179 LYS cc_start: 0.5344 (pttm) cc_final: 0.4042 (mttp) REVERT: R 186 ASP cc_start: 0.7775 (p0) cc_final: 0.7442 (p0) REVERT: R 436 MET cc_start: 0.8136 (mtp) cc_final: 0.7495 (mmp) REVERT: R 450 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7276 (m90) REVERT: R 481 ARG cc_start: 0.8807 (mtt90) cc_final: 0.7713 (tpt170) REVERT: B 20 ASP cc_start: 0.8381 (m-30) cc_final: 0.8137 (m-30) REVERT: B 29 THR cc_start: 0.7136 (t) cc_final: 0.6900 (t) REVERT: B 32 GLN cc_start: 0.8065 (tt0) cc_final: 0.7325 (tm-30) REVERT: B 42 ARG cc_start: 0.7470 (tpp80) cc_final: 0.7261 (tpp80) REVERT: B 44 GLN cc_start: 0.7360 (mp10) cc_final: 0.7046 (mp10) REVERT: B 57 LYS cc_start: 0.8541 (mtmm) cc_final: 0.8241 (mtmt) REVERT: B 160 SER cc_start: 0.8951 (m) cc_final: 0.8192 (p) REVERT: B 217 MET cc_start: 0.7268 (tmm) cc_final: 0.7054 (tmm) REVERT: B 226 GLU cc_start: 0.8282 (mp0) cc_final: 0.7946 (mp0) REVERT: B 234 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8273 (m-10) REVERT: B 254 ASP cc_start: 0.8033 (t70) cc_final: 0.7527 (t70) REVERT: B 260 GLU cc_start: 0.8307 (tt0) cc_final: 0.7815 (tt0) REVERT: B 293 ASN cc_start: 0.7214 (m-40) cc_final: 0.6693 (p0) REVERT: G 18 GLN cc_start: 0.7510 (tp40) cc_final: 0.7000 (tp-100) REVERT: G 21 MET cc_start: 0.7979 (ptt) cc_final: 0.7634 (ptt) REVERT: A 9 ASP cc_start: 0.8346 (m-30) cc_final: 0.8061 (m-30) REVERT: A 57 LYS cc_start: 0.8355 (tttt) cc_final: 0.8132 (mttp) REVERT: A 234 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 265 GLN cc_start: 0.8201 (mt0) cc_final: 0.7861 (mt0) REVERT: A 350 GLN cc_start: 0.7544 (tp40) cc_final: 0.6758 (mm110) REVERT: C 82 GLN cc_start: 0.7652 (mt0) cc_final: 0.7433 (mt0) REVERT: C 86 LEU cc_start: 0.8213 (mt) cc_final: 0.8007 (mt) REVERT: C 113 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8355 (tp40) REVERT: C 153 GLU cc_start: 0.8627 (tp30) cc_final: 0.8259 (tp30) REVERT: C 160 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7548 (ttm-80) REVERT: C 218 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8254 (mmm160) REVERT: C 230 MET cc_start: 0.8204 (ttp) cc_final: 0.7744 (ttp) outliers start: 41 outliers final: 26 residues processed: 256 average time/residue: 0.2220 time to fit residues: 76.9763 Evaluate side-chains 243 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 437 VAL Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain R residue 462 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.144943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108528 restraints weight = 14674.199| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.88 r_work: 0.3323 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9181 Z= 0.269 Angle : 0.653 9.529 12427 Z= 0.336 Chirality : 0.044 0.183 1393 Planarity : 0.004 0.068 1568 Dihedral : 4.822 33.409 1239 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.17 % Allowed : 16.07 % Favored : 79.76 % 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: -0.05 (0.25), residues: 1115 helix: 1.20 (0.27), residues: 368 sheet: -0.49 (0.32), residues: 253 loop : -0.64 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 47 HIS 0.004 0.001 HIS B 62 PHE 0.036 0.002 PHE R 435 TYR 0.029 0.002 TYR A 295 ARG 0.007 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7706 (pmm) cc_final: 0.6524 (mpp) REVERT: R 103 TRP cc_start: 0.7302 (t60) cc_final: 0.7020 (t60) REVERT: R 130 GLN cc_start: 0.8214 (tp40) cc_final: 0.7885 (tm-30) REVERT: R 158 TRP cc_start: 0.7585 (OUTLIER) cc_final: 0.5391 (t60) REVERT: R 179 LYS cc_start: 0.5689 (pttm) cc_final: 0.4721 (mttp) REVERT: R 436 MET cc_start: 0.8158 (mtp) cc_final: 0.7143 (tpp) REVERT: R 450 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.7364 (m90) REVERT: R 481 ARG cc_start: 0.8826 (mtt90) cc_final: 0.7862 (tpt170) REVERT: B 20 ASP cc_start: 0.8316 (m-30) cc_final: 0.8109 (m-30) REVERT: B 32 GLN cc_start: 0.8011 (tt0) cc_final: 0.7325 (tm-30) REVERT: B 42 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7352 (tpp80) REVERT: B 44 GLN cc_start: 0.7357 (mp10) cc_final: 0.7049 (mp10) REVERT: B 57 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8501 (mtmt) REVERT: B 75 GLN cc_start: 0.8641 (tt0) cc_final: 0.8408 (tt0) REVERT: B 160 SER cc_start: 0.9032 (m) cc_final: 0.8296 (p) REVERT: B 217 MET cc_start: 0.7342 (tmm) cc_final: 0.7106 (tmm) REVERT: B 234 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8304 (m-10) REVERT: B 254 ASP cc_start: 0.8121 (t70) cc_final: 0.7641 (t70) REVERT: B 260 GLU cc_start: 0.8336 (tt0) cc_final: 0.7901 (tt0) REVERT: B 293 ASN cc_start: 0.7327 (m-40) cc_final: 0.6770 (p0) REVERT: A 9 ASP cc_start: 0.8431 (m-30) cc_final: 0.8157 (m-30) REVERT: A 57 LYS cc_start: 0.8411 (tttt) cc_final: 0.8154 (mttp) REVERT: A 265 GLN cc_start: 0.8164 (mt0) cc_final: 0.7816 (mt0) REVERT: A 315 ASP cc_start: 0.8898 (m-30) cc_final: 0.8348 (m-30) REVERT: A 333 ASP cc_start: 0.3240 (OUTLIER) cc_final: 0.2149 (t70) REVERT: A 350 GLN cc_start: 0.7516 (tp40) cc_final: 0.6714 (mm110) REVERT: C 73 ASP cc_start: 0.7004 (t0) cc_final: 0.6469 (t0) REVERT: C 82 GLN cc_start: 0.7603 (mt0) cc_final: 0.7393 (mt0) REVERT: C 113 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8375 (tp40) REVERT: C 153 GLU cc_start: 0.8558 (tp30) cc_final: 0.8236 (tp30) REVERT: C 160 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7662 (ttm-80) REVERT: C 202 ARG cc_start: 0.7664 (mpp80) cc_final: 0.7026 (mtm-85) REVERT: C 218 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.7840 (mpp80) REVERT: C 230 MET cc_start: 0.8245 (ttp) cc_final: 0.8021 (ttp) outliers start: 41 outliers final: 31 residues processed: 249 average time/residue: 0.2371 time to fit residues: 80.8806 Evaluate side-chains 254 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 183 ASP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 421 MET Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 437 VAL Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain R residue 462 THR Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.0020 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110922 restraints weight = 14309.307| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.79 r_work: 0.3364 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9181 Z= 0.197 Angle : 0.625 10.087 12427 Z= 0.320 Chirality : 0.043 0.185 1393 Planarity : 0.004 0.063 1568 Dihedral : 4.636 27.608 1239 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.66 % Allowed : 17.29 % Favored : 79.04 % 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: 0.10 (0.26), residues: 1115 helix: 1.35 (0.27), residues: 367 sheet: -0.53 (0.31), residues: 272 loop : -0.48 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS C 35 PHE 0.034 0.002 PHE R 435 TYR 0.013 0.001 TYR A 295 ARG 0.005 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7640 (pmm) cc_final: 0.6502 (mpp) REVERT: R 93 TRP cc_start: 0.5900 (t-100) cc_final: 0.5621 (t-100) REVERT: R 130 GLN cc_start: 0.8224 (tp40) cc_final: 0.7945 (tm-30) REVERT: R 158 TRP cc_start: 0.7508 (OUTLIER) cc_final: 0.5340 (t60) REVERT: R 179 LYS cc_start: 0.5700 (pttm) cc_final: 0.4675 (mttp) REVERT: R 181 GLU cc_start: 0.5272 (OUTLIER) cc_final: 0.4942 (tp30) REVERT: R 436 MET cc_start: 0.8095 (mtp) cc_final: 0.7867 (tpp) REVERT: R 481 ARG cc_start: 0.8824 (mtt90) cc_final: 0.7884 (tpt170) REVERT: B 20 ASP cc_start: 0.8277 (m-30) cc_final: 0.8047 (m-30) REVERT: B 32 GLN cc_start: 0.8026 (tt0) cc_final: 0.7310 (tm-30) REVERT: B 42 ARG cc_start: 0.7415 (tpp80) cc_final: 0.7128 (tpp80) REVERT: B 44 GLN cc_start: 0.7340 (mp10) cc_final: 0.7013 (mp10) REVERT: B 57 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8513 (mtmt) REVERT: B 137 ARG cc_start: 0.7184 (mmt-90) cc_final: 0.6746 (mmm-85) REVERT: B 160 SER cc_start: 0.8950 (m) cc_final: 0.8165 (p) REVERT: B 234 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: B 254 ASP cc_start: 0.8075 (t70) cc_final: 0.7627 (t70) REVERT: B 260 GLU cc_start: 0.8331 (tt0) cc_final: 0.7899 (tt0) REVERT: B 293 ASN cc_start: 0.7242 (m-40) cc_final: 0.6706 (p0) REVERT: B 297 TRP cc_start: 0.7717 (m100) cc_final: 0.7477 (m100) REVERT: G 18 GLN cc_start: 0.7341 (tp40) cc_final: 0.6992 (tp-100) REVERT: A 9 ASP cc_start: 0.8417 (m-30) cc_final: 0.8155 (m-30) REVERT: A 57 LYS cc_start: 0.8378 (tttt) cc_final: 0.8127 (mttp) REVERT: A 265 GLN cc_start: 0.8151 (mt0) cc_final: 0.7791 (mt0) REVERT: A 275 LYS cc_start: 0.8298 (tttp) cc_final: 0.7887 (tttp) REVERT: A 280 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8260 (pp20) REVERT: A 311 LYS cc_start: 0.8293 (tptm) cc_final: 0.8052 (tptm) REVERT: A 315 ASP cc_start: 0.8878 (m-30) cc_final: 0.8411 (m-30) REVERT: A 333 ASP cc_start: 0.3128 (OUTLIER) cc_final: 0.2119 (t70) REVERT: A 350 GLN cc_start: 0.7459 (tp40) cc_final: 0.6673 (mm110) REVERT: C 73 ASP cc_start: 0.7097 (t0) cc_final: 0.6533 (t0) REVERT: C 82 GLN cc_start: 0.7508 (mt0) cc_final: 0.7189 (mt0) REVERT: C 113 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8333 (tp40) REVERT: C 153 GLU cc_start: 0.8459 (tp30) cc_final: 0.8133 (tp30) REVERT: C 160 ARG cc_start: 0.7958 (ttp-110) cc_final: 0.7717 (ttm-80) REVERT: C 195 LEU cc_start: 0.7071 (mp) cc_final: 0.6746 (mt) REVERT: C 202 ARG cc_start: 0.7449 (mpp80) cc_final: 0.6770 (mtm-85) REVERT: C 218 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.7906 (mpp80) REVERT: C 234 GLU cc_start: 0.7553 (pt0) cc_final: 0.6987 (pm20) outliers start: 36 outliers final: 24 residues processed: 259 average time/residue: 0.2222 time to fit residues: 77.6851 Evaluate side-chains 251 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 183 ASP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.145807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109041 restraints weight = 14878.160| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.96 r_work: 0.3320 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9181 Z= 0.234 Angle : 0.648 10.359 12427 Z= 0.333 Chirality : 0.044 0.202 1393 Planarity : 0.004 0.064 1568 Dihedral : 4.622 27.260 1239 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.07 % Allowed : 17.60 % Favored : 78.33 % 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: 0.07 (0.26), residues: 1115 helix: 1.32 (0.27), residues: 369 sheet: -0.58 (0.31), residues: 272 loop : -0.49 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 287 PHE 0.035 0.002 PHE R 435 TYR 0.027 0.002 TYR A 295 ARG 0.004 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7649 (pmm) cc_final: 0.6501 (mpp) REVERT: R 83 MET cc_start: 0.8206 (mmm) cc_final: 0.7954 (mmt) REVERT: R 93 TRP cc_start: 0.6144 (t-100) cc_final: 0.5673 (t-100) REVERT: R 130 GLN cc_start: 0.8256 (tp40) cc_final: 0.7832 (tm-30) REVERT: R 158 TRP cc_start: 0.7563 (OUTLIER) cc_final: 0.5428 (t60) REVERT: R 179 LYS cc_start: 0.5790 (pttm) cc_final: 0.4930 (mttp) REVERT: R 181 GLU cc_start: 0.5109 (OUTLIER) cc_final: 0.4826 (tp30) REVERT: R 438 ILE cc_start: 0.6591 (tp) cc_final: 0.6317 (tt) REVERT: R 481 ARG cc_start: 0.8821 (mtt90) cc_final: 0.7785 (tpt90) REVERT: B 20 ASP cc_start: 0.8233 (m-30) cc_final: 0.8020 (m-30) REVERT: B 32 GLN cc_start: 0.8041 (tt0) cc_final: 0.7361 (tm-30) REVERT: B 42 ARG cc_start: 0.7325 (tpp80) cc_final: 0.7050 (tpp80) REVERT: B 44 GLN cc_start: 0.7485 (mp10) cc_final: 0.7151 (mp10) REVERT: B 57 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8449 (mtmt) REVERT: B 137 ARG cc_start: 0.7254 (mmt-90) cc_final: 0.6779 (mmm-85) REVERT: B 160 SER cc_start: 0.9027 (m) cc_final: 0.8224 (p) REVERT: B 234 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8281 (m-10) REVERT: B 254 ASP cc_start: 0.8079 (t70) cc_final: 0.7607 (t70) REVERT: B 260 GLU cc_start: 0.8331 (tt0) cc_final: 0.7857 (tt0) REVERT: B 293 ASN cc_start: 0.7223 (m-40) cc_final: 0.6637 (p0) REVERT: G 18 GLN cc_start: 0.7225 (tp40) cc_final: 0.6730 (tp-100) REVERT: G 21 MET cc_start: 0.8033 (ptp) cc_final: 0.7258 (ptt) REVERT: G 32 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7988 (ttpp) REVERT: A 9 ASP cc_start: 0.8476 (m-30) cc_final: 0.8199 (m-30) REVERT: A 57 LYS cc_start: 0.8381 (tttt) cc_final: 0.8118 (mttp) REVERT: A 265 GLN cc_start: 0.8228 (mt0) cc_final: 0.7858 (mt0) REVERT: A 275 LYS cc_start: 0.8310 (tttp) cc_final: 0.7878 (tttp) REVERT: A 280 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: A 333 ASP cc_start: 0.3158 (OUTLIER) cc_final: 0.2066 (t70) REVERT: A 350 GLN cc_start: 0.7424 (tp40) cc_final: 0.6649 (mm110) REVERT: C 73 ASP cc_start: 0.6908 (t0) cc_final: 0.6389 (t0) REVERT: C 82 GLN cc_start: 0.7522 (mt0) cc_final: 0.7216 (mt0) REVERT: C 113 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8350 (tp40) REVERT: C 153 GLU cc_start: 0.8515 (tp30) cc_final: 0.8181 (tp30) REVERT: C 160 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7822 (ttm-80) REVERT: C 202 ARG cc_start: 0.7388 (mpp80) cc_final: 0.6515 (mtp180) REVERT: C 218 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.7803 (mpp80) outliers start: 40 outliers final: 30 residues processed: 250 average time/residue: 0.2256 time to fit residues: 76.5645 Evaluate side-chains 253 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 183 ASP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 421 MET Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 0.0770 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.147273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110500 restraints weight = 14861.552| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.98 r_work: 0.3326 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9181 Z= 0.207 Angle : 0.652 10.938 12427 Z= 0.331 Chirality : 0.044 0.211 1393 Planarity : 0.004 0.063 1568 Dihedral : 4.512 27.240 1239 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.76 % Allowed : 18.01 % Favored : 78.23 % 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: 0.05 (0.25), residues: 1115 helix: 1.33 (0.27), residues: 368 sheet: -0.69 (0.30), residues: 272 loop : -0.45 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS A 287 PHE 0.033 0.002 PHE R 435 TYR 0.012 0.001 TYR A 235 ARG 0.003 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7565 (pmm) cc_final: 0.6336 (mpp) REVERT: R 83 MET cc_start: 0.8190 (mmm) cc_final: 0.7963 (mmt) REVERT: R 93 TRP cc_start: 0.6077 (t-100) cc_final: 0.5645 (t-100) REVERT: R 130 GLN cc_start: 0.8173 (tp40) cc_final: 0.7775 (tm-30) REVERT: R 179 LYS cc_start: 0.5817 (pttm) cc_final: 0.4903 (mttp) REVERT: R 181 GLU cc_start: 0.4939 (OUTLIER) cc_final: 0.4695 (tp30) REVERT: R 436 MET cc_start: 0.8403 (tpp) cc_final: 0.8171 (mmp) REVERT: R 481 ARG cc_start: 0.8870 (mtt90) cc_final: 0.7842 (tpt90) REVERT: B 6 GLN cc_start: 0.8861 (pp30) cc_final: 0.8625 (pp30) REVERT: B 20 ASP cc_start: 0.8204 (m-30) cc_final: 0.7996 (m-30) REVERT: B 32 GLN cc_start: 0.7887 (tt0) cc_final: 0.7248 (tm-30) REVERT: B 42 ARG cc_start: 0.7297 (tpp80) cc_final: 0.7018 (tpp80) REVERT: B 44 GLN cc_start: 0.7463 (mp10) cc_final: 0.7104 (mp10) REVERT: B 57 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8044 (mtpt) REVERT: B 137 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6685 (mmm-85) REVERT: B 160 SER cc_start: 0.8943 (m) cc_final: 0.8116 (p) REVERT: B 228 ASP cc_start: 0.7367 (m-30) cc_final: 0.6924 (m-30) REVERT: B 234 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: B 254 ASP cc_start: 0.7981 (t70) cc_final: 0.7477 (t70) REVERT: B 293 ASN cc_start: 0.7102 (m-40) cc_final: 0.6552 (p0) REVERT: B 297 TRP cc_start: 0.7595 (m100) cc_final: 0.7106 (m100) REVERT: G 32 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8026 (ttpp) REVERT: A 9 ASP cc_start: 0.8449 (m-30) cc_final: 0.8175 (m-30) REVERT: A 57 LYS cc_start: 0.8368 (tttt) cc_final: 0.8096 (mttp) REVERT: A 265 GLN cc_start: 0.8197 (mt0) cc_final: 0.7799 (mt0) REVERT: A 275 LYS cc_start: 0.8159 (tttp) cc_final: 0.7726 (tttp) REVERT: A 280 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: A 311 LYS cc_start: 0.8219 (tptm) cc_final: 0.7939 (tptm) REVERT: A 315 ASP cc_start: 0.8870 (m-30) cc_final: 0.8407 (m-30) REVERT: A 333 ASP cc_start: 0.2963 (OUTLIER) cc_final: 0.1879 (t70) REVERT: A 346 ASP cc_start: 0.8084 (m-30) cc_final: 0.7527 (t70) REVERT: A 350 GLN cc_start: 0.7293 (tp40) cc_final: 0.6488 (mm110) REVERT: C 73 ASP cc_start: 0.6954 (t0) cc_final: 0.6522 (t0) REVERT: C 82 GLN cc_start: 0.7399 (mt0) cc_final: 0.7055 (mt0) REVERT: C 113 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8302 (tp40) REVERT: C 153 GLU cc_start: 0.8528 (tp30) cc_final: 0.8187 (tp30) REVERT: C 160 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7705 (ttm-80) REVERT: C 195 LEU cc_start: 0.7045 (mp) cc_final: 0.6717 (mt) REVERT: C 202 ARG cc_start: 0.7368 (mpp80) cc_final: 0.6839 (mtm-85) REVERT: C 218 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.7896 (mpp80) REVERT: C 230 MET cc_start: 0.8069 (ttp) cc_final: 0.7641 (ttp) REVERT: C 234 GLU cc_start: 0.7644 (pt0) cc_final: 0.6987 (pm20) outliers start: 37 outliers final: 29 residues processed: 259 average time/residue: 0.2173 time to fit residues: 76.3952 Evaluate side-chains 253 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 183 ASP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 450 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.147162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110653 restraints weight = 14678.791| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.92 r_work: 0.3354 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9181 Z= 0.218 Angle : 0.680 12.883 12427 Z= 0.343 Chirality : 0.044 0.214 1393 Planarity : 0.004 0.063 1568 Dihedral : 4.492 27.563 1239 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.36 % Allowed : 18.82 % Favored : 77.82 % 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: 0.01 (0.25), residues: 1115 helix: 1.26 (0.27), residues: 370 sheet: -0.71 (0.30), residues: 272 loop : -0.45 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 287 PHE 0.033 0.002 PHE R 435 TYR 0.028 0.002 TYR A 295 ARG 0.006 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 81 MET cc_start: 0.8179 (mtt) cc_final: 0.7664 (ptp) REVERT: R 83 MET cc_start: 0.8214 (mmm) cc_final: 0.8006 (mmt) REVERT: R 93 TRP cc_start: 0.6104 (t-100) cc_final: 0.5412 (t-100) REVERT: R 130 GLN cc_start: 0.8212 (tp40) cc_final: 0.7865 (tm-30) REVERT: R 179 LYS cc_start: 0.5860 (pttm) cc_final: 0.4999 (mttp) REVERT: R 181 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.4649 (tp30) REVERT: R 426 LEU cc_start: 0.8216 (tt) cc_final: 0.7778 (mt) REVERT: R 436 MET cc_start: 0.8527 (tpp) cc_final: 0.8308 (mmp) REVERT: R 481 ARG cc_start: 0.8790 (mtt90) cc_final: 0.7806 (tpt90) REVERT: B 6 GLN cc_start: 0.8888 (pp30) cc_final: 0.8645 (pp30) REVERT: B 20 ASP cc_start: 0.8237 (m-30) cc_final: 0.7962 (m-30) REVERT: B 32 GLN cc_start: 0.7949 (tt0) cc_final: 0.7308 (tm-30) REVERT: B 42 ARG cc_start: 0.7365 (tpp80) cc_final: 0.7098 (tpp80) REVERT: B 44 GLN cc_start: 0.7511 (mp10) cc_final: 0.7175 (mp10) REVERT: B 137 ARG cc_start: 0.7325 (mmt-90) cc_final: 0.6794 (mmm-85) REVERT: B 160 SER cc_start: 0.8943 (m) cc_final: 0.8184 (p) REVERT: B 228 ASP cc_start: 0.7498 (m-30) cc_final: 0.7058 (m-30) REVERT: B 234 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: B 254 ASP cc_start: 0.8053 (t70) cc_final: 0.7582 (t70) REVERT: B 293 ASN cc_start: 0.7226 (m-40) cc_final: 0.6671 (p0) REVERT: B 297 TRP cc_start: 0.7769 (m100) cc_final: 0.7323 (m100) REVERT: G 20 LYS cc_start: 0.8869 (ptpt) cc_final: 0.8649 (pttm) REVERT: G 32 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8064 (ttpp) REVERT: G 46 LYS cc_start: 0.9308 (mptt) cc_final: 0.8858 (mmmt) REVERT: A 9 ASP cc_start: 0.8470 (m-30) cc_final: 0.8197 (m-30) REVERT: A 57 LYS cc_start: 0.8398 (tttt) cc_final: 0.8131 (mttp) REVERT: A 237 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 265 GLN cc_start: 0.8248 (mt0) cc_final: 0.7867 (mt0) REVERT: A 275 LYS cc_start: 0.8271 (tttp) cc_final: 0.7824 (tttp) REVERT: A 280 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8255 (pp20) REVERT: A 311 LYS cc_start: 0.8235 (tptm) cc_final: 0.7944 (tptm) REVERT: A 315 ASP cc_start: 0.8958 (m-30) cc_final: 0.8465 (m-30) REVERT: A 333 ASP cc_start: 0.3001 (OUTLIER) cc_final: 0.1831 (t70) REVERT: A 350 GLN cc_start: 0.7356 (tp40) cc_final: 0.6542 (mm110) REVERT: C 73 ASP cc_start: 0.7152 (t0) cc_final: 0.6573 (t0) REVERT: C 82 GLN cc_start: 0.7412 (mt0) cc_final: 0.7069 (mt0) REVERT: C 113 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8370 (tp40) REVERT: C 153 GLU cc_start: 0.8526 (tp30) cc_final: 0.8169 (tp30) REVERT: C 160 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7779 (ttm-80) REVERT: C 195 LEU cc_start: 0.7146 (mp) cc_final: 0.6828 (mt) REVERT: C 202 ARG cc_start: 0.7409 (mpp80) cc_final: 0.6834 (mtm-85) REVERT: C 218 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.7896 (mpp80) REVERT: C 230 MET cc_start: 0.8035 (ttp) cc_final: 0.7652 (ttp) REVERT: C 231 GLN cc_start: 0.8626 (pp30) cc_final: 0.8121 (pp30) REVERT: C 234 GLU cc_start: 0.7631 (pt0) cc_final: 0.6977 (pm20) outliers start: 33 outliers final: 28 residues processed: 245 average time/residue: 0.2335 time to fit residues: 77.3101 Evaluate side-chains 252 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 183 ASP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 73 optimal weight: 0.0370 chunk 16 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.148624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.112304 restraints weight = 14636.219| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.93 r_work: 0.3382 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9181 Z= 0.190 Angle : 0.686 12.628 12427 Z= 0.347 Chirality : 0.043 0.203 1393 Planarity : 0.004 0.062 1568 Dihedral : 4.409 27.631 1239 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.95 % Allowed : 19.53 % Favored : 77.52 % 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: 0.03 (0.25), residues: 1115 helix: 1.30 (0.27), residues: 370 sheet: -0.69 (0.30), residues: 272 loop : -0.45 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 165 HIS 0.003 0.000 HIS C 35 PHE 0.032 0.001 PHE R 435 TYR 0.017 0.001 TYR C 228 ARG 0.005 0.000 ARG C 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 93 TRP cc_start: 0.6140 (t-100) cc_final: 0.5594 (t-100) REVERT: R 103 TRP cc_start: 0.7013 (t60) cc_final: 0.6782 (t60) REVERT: R 179 LYS cc_start: 0.5853 (pttm) cc_final: 0.5124 (ptmt) REVERT: R 181 GLU cc_start: 0.4993 (OUTLIER) cc_final: 0.4561 (tp30) REVERT: R 186 ASP cc_start: 0.6640 (p0) cc_final: 0.5841 (t0) REVERT: R 426 LEU cc_start: 0.8184 (tt) cc_final: 0.7822 (mt) REVERT: R 481 ARG cc_start: 0.8721 (mtt90) cc_final: 0.7817 (tpt90) REVERT: B 6 GLN cc_start: 0.8851 (pp30) cc_final: 0.8636 (pp30) REVERT: B 20 ASP cc_start: 0.8218 (m-30) cc_final: 0.8006 (m-30) REVERT: B 32 GLN cc_start: 0.7927 (tt0) cc_final: 0.7283 (tm-30) REVERT: B 44 GLN cc_start: 0.7531 (mp10) cc_final: 0.7231 (mp10) REVERT: B 57 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8501 (mtpt) REVERT: B 160 SER cc_start: 0.8838 (m) cc_final: 0.8093 (p) REVERT: B 228 ASP cc_start: 0.7463 (m-30) cc_final: 0.7049 (m-30) REVERT: B 234 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: B 254 ASP cc_start: 0.8023 (t70) cc_final: 0.7566 (t70) REVERT: B 293 ASN cc_start: 0.7154 (m-40) cc_final: 0.6684 (p0) REVERT: B 297 TRP cc_start: 0.7702 (m100) cc_final: 0.7114 (m100) REVERT: G 20 LYS cc_start: 0.8825 (ptpt) cc_final: 0.8595 (pttm) REVERT: G 32 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7979 (ttpp) REVERT: G 42 GLU cc_start: 0.8832 (tp30) cc_final: 0.8567 (tt0) REVERT: G 46 LYS cc_start: 0.9288 (mptt) cc_final: 0.8891 (mmmt) REVERT: A 9 ASP cc_start: 0.8446 (m-30) cc_final: 0.8174 (m-30) REVERT: A 57 LYS cc_start: 0.8403 (tttt) cc_final: 0.8132 (mttp) REVERT: A 203 MET cc_start: 0.7296 (mtp) cc_final: 0.6892 (ttt) REVERT: A 265 GLN cc_start: 0.8152 (mt0) cc_final: 0.7803 (mt0) REVERT: A 275 LYS cc_start: 0.8201 (tttp) cc_final: 0.7766 (tttp) REVERT: A 280 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8199 (pp20) REVERT: A 311 LYS cc_start: 0.8275 (tptm) cc_final: 0.7980 (tptm) REVERT: A 315 ASP cc_start: 0.8950 (m-30) cc_final: 0.8463 (m-30) REVERT: A 333 ASP cc_start: 0.2973 (OUTLIER) cc_final: 0.1879 (t0) REVERT: A 350 GLN cc_start: 0.7324 (tp40) cc_final: 0.6515 (mm110) REVERT: C 73 ASP cc_start: 0.7105 (t0) cc_final: 0.6504 (t0) REVERT: C 82 GLN cc_start: 0.7339 (mt0) cc_final: 0.6969 (mp10) REVERT: C 113 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8298 (tp40) REVERT: C 153 GLU cc_start: 0.8511 (tp30) cc_final: 0.8165 (tp30) REVERT: C 160 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7706 (ttm-80) REVERT: C 178 LEU cc_start: 0.9021 (tt) cc_final: 0.8639 (tp) REVERT: C 202 ARG cc_start: 0.7325 (mpp80) cc_final: 0.6687 (mtm-85) REVERT: C 218 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.7863 (mpp80) REVERT: C 230 MET cc_start: 0.8053 (ttp) cc_final: 0.7686 (ttp) REVERT: C 231 GLN cc_start: 0.8590 (pp30) cc_final: 0.7825 (pp30) REVERT: C 234 GLU cc_start: 0.7639 (pt0) cc_final: 0.7081 (pm20) outliers start: 29 outliers final: 25 residues processed: 253 average time/residue: 0.2211 time to fit residues: 75.5213 Evaluate side-chains 255 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 183 ASP Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 105 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.112029 restraints weight = 14659.887| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.96 r_work: 0.3376 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9181 Z= 0.207 Angle : 0.705 13.782 12427 Z= 0.358 Chirality : 0.043 0.213 1393 Planarity : 0.004 0.063 1568 Dihedral : 4.379 26.394 1239 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.95 % Allowed : 19.84 % Favored : 77.21 % 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: 0.07 (0.25), residues: 1115 helix: 1.36 (0.27), residues: 370 sheet: -0.62 (0.30), residues: 273 loop : -0.48 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 211 HIS 0.003 0.001 HIS C 35 PHE 0.032 0.001 PHE R 435 TYR 0.025 0.001 TYR C 228 ARG 0.006 0.000 ARG C 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4803.71 seconds wall clock time: 84 minutes 59.30 seconds (5099.30 seconds total)