Starting phenix.real_space_refine on Fri Jul 19 08:49:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umc_42375/07_2024/8umc_42375_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umc_42375/07_2024/8umc_42375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umc_42375/07_2024/8umc_42375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umc_42375/07_2024/8umc_42375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umc_42375/07_2024/8umc_42375_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umc_42375/07_2024/8umc_42375_neut.cif" } resolution = 2.5 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 54 5.16 5 C 4564 2.51 5 N 1270 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2630 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 307} Chain: "B" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 968 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2630 Classifications: {'peptide': 322} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 968 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.45, per 1000 atoms: 0.62 Number of scatterers: 7198 At special positions: 0 Unit cell: (107.06, 80.8, 82.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 54 16.00 O 1308 8.00 N 1270 7.00 C 4564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 43.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.563A pdb=" N GLU A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.770A pdb=" N ARG A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.860A pdb=" N THR A 180 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.030A pdb=" N LEU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 309 through 325 Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 65 through 69 removed outlier: 4.367A pdb=" N ASP B 68 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.658A pdb=" N TYR C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 111 removed outlier: 3.659A pdb=" N ASP C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.685A pdb=" N SER C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.996A pdb=" N LEU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 removed outlier: 3.526A pdb=" N GLU C 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 309 through 325 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.093A pdb=" N ILE A 115 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU A 143 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 117 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 114 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 75 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ARG A 116 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS A 77 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE A 41 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS A 77 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER A 43 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 40 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS A 7 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER A 294 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY A 9 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N TYR A 296 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N SER A 11 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 258 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 295 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA A 260 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48 removed outlier: 4.707A pdb=" N VAL B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 94 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.707A pdb=" N LEU C 140 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 173 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C 142 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 115 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C 143 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL C 117 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 41 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N HIS C 77 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER C 43 " --> pdb=" O HIS C 77 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 40 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 7 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER C 294 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 9 " --> pdb=" O SER C 294 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N TYR C 296 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER C 11 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.543A pdb=" N THR D 84 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 32 Processing sheet with id=AA9, first strand: chain 'D' and resid 46 through 47 removed outlier: 3.529A pdb=" N GLU D 46 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 43 " --> pdb=" O GLU D 46 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 834 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: 2.00 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2438 1.34 - 1.46: 1331 1.46 - 1.57: 3499 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 7368 Sorted by residual: bond pdb=" N VAL A 101 " pdb=" CA VAL A 101 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.76e+00 bond pdb=" N ASP A 266 " pdb=" CA ASP A 266 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.34e-02 5.57e+03 7.07e+00 bond pdb=" N GLN C 268 " pdb=" CA GLN C 268 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.18e-02 7.18e+03 6.98e+00 bond pdb=" N HIS A 145 " pdb=" CA HIS A 145 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.18e-02 7.18e+03 6.86e+00 ... (remaining 7363 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.34: 147 104.34 - 111.75: 3278 111.75 - 119.16: 2671 119.16 - 126.56: 3748 126.56 - 133.97: 110 Bond angle restraints: 9954 Sorted by residual: angle pdb=" N PRO A 147 " pdb=" CA PRO A 147 " pdb=" CB PRO A 147 " ideal model delta sigma weight residual 103.25 96.93 6.32 1.05e+00 9.07e-01 3.62e+01 angle pdb=" CA ILE A 302 " pdb=" C ILE A 302 " pdb=" O ILE A 302 " ideal model delta sigma weight residual 122.63 118.54 4.09 8.70e-01 1.32e+00 2.21e+01 angle pdb=" N MET C 320 " pdb=" CA MET C 320 " pdb=" C MET C 320 " ideal model delta sigma weight residual 111.14 106.07 5.07 1.08e+00 8.57e-01 2.20e+01 angle pdb=" CA ASP C 266 " pdb=" C ASP C 266 " pdb=" O ASP C 266 " ideal model delta sigma weight residual 122.01 118.23 3.78 1.05e+00 9.07e-01 1.30e+01 angle pdb=" CA ASP A 266 " pdb=" C ASP A 266 " pdb=" O ASP A 266 " ideal model delta sigma weight residual 122.01 118.28 3.73 1.05e+00 9.07e-01 1.26e+01 ... (remaining 9949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.28: 4078 26.28 - 52.56: 288 52.56 - 78.84: 47 78.84 - 105.12: 10 105.12 - 131.40: 1 Dihedral angle restraints: 4424 sinusoidal: 1862 harmonic: 2562 Sorted by residual: dihedral pdb=" CA ALA A 146 " pdb=" C ALA A 146 " pdb=" N PRO A 147 " pdb=" CA PRO A 147 " ideal model delta harmonic sigma weight residual 180.00 48.60 131.40 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CA ARG C 193 " pdb=" C ARG C 193 " pdb=" N GLN C 194 " pdb=" CA GLN C 194 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ARG C 105 " pdb=" C ARG C 105 " pdb=" N HIS C 106 " pdb=" CA HIS C 106 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 4421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 801 0.049 - 0.098: 192 0.098 - 0.147: 55 0.147 - 0.197: 6 0.197 - 0.246: 2 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA MET C 320 " pdb=" N MET C 320 " pdb=" C MET C 320 " pdb=" CB MET C 320 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL B 15 " pdb=" N VAL B 15 " pdb=" C VAL B 15 " pdb=" CB VAL B 15 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 1053 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 210 " 0.313 9.50e-02 1.11e+02 1.40e-01 1.21e+01 pdb=" NE ARG A 210 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 210 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 210 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 210 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 254 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.56e+00 pdb=" NE ARG A 254 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 254 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 254 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 254 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " 0.178 9.50e-02 1.11e+02 7.99e-02 4.29e+00 pdb=" NE ARG A 270 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " 0.003 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 113 2.62 - 3.19: 6478 3.19 - 3.76: 11573 3.76 - 4.33: 17203 4.33 - 4.90: 27913 Nonbonded interactions: 63280 Sorted by model distance: nonbonded pdb=" OH TYR B 27 " pdb=" OH TYR B 108 " model vdw 2.045 2.440 nonbonded pdb=" OH TYR D 28 " pdb=" OH TYR D 108 " model vdw 2.048 2.440 nonbonded pdb=" OE1 GLU A 295 " pdb="MN MN A 401 " model vdw 2.101 2.320 nonbonded pdb=" OE1 GLU C 295 " pdb="MN MN C 401 " model vdw 2.115 2.320 nonbonded pdb=" O LYS C 261 " pdb=" OH TYR C 276 " model vdw 2.133 2.440 ... (remaining 63275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.400 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.005 0.039 7368 Z= 0.334 Angle : 0.683 6.318 9954 Z= 0.420 Chirality : 0.048 0.246 1056 Planarity : 0.007 0.140 1310 Dihedral : 17.532 131.399 2780 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % Rotamer: Outliers : 1.16 % Allowed : 19.51 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.80 (0.28), residues: 882 helix: 0.14 (0.28), residues: 344 sheet: -1.05 (0.42), residues: 154 loop : -0.79 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 242 HIS 0.006 0.001 HIS C 257 PHE 0.012 0.002 PHE C 20 TYR 0.014 0.001 TYR A 13 ARG 0.011 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 241 ASN cc_start: 0.8181 (p0) cc_final: 0.7918 (p0) outliers start: 9 outliers final: 5 residues processed: 221 average time/residue: 1.3677 time to fit residues: 316.2670 Evaluate side-chains 214 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain D residue 62 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7368 Z= 0.356 Angle : 0.610 6.054 9954 Z= 0.317 Chirality : 0.046 0.168 1056 Planarity : 0.005 0.055 1310 Dihedral : 5.839 67.913 1004 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.01 % Allowed : 20.67 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.36 (0.28), residues: 882 helix: 0.54 (0.28), residues: 334 sheet: -0.77 (0.49), residues: 112 loop : -0.62 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 242 HIS 0.005 0.001 HIS A 149 PHE 0.016 0.002 PHE C 20 TYR 0.012 0.002 TYR A 13 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7063 (p0) cc_final: 0.6499 (p0) REVERT: A 61 ASP cc_start: 0.7449 (m-30) cc_final: 0.7192 (m-30) REVERT: C 278 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: C 284 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8714 (mttp) outliers start: 31 outliers final: 14 residues processed: 236 average time/residue: 1.2873 time to fit residues: 318.7619 Evaluate side-chains 228 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.0060 chunk 86 optimal weight: 0.5980 chunk 71 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7368 Z= 0.202 Angle : 0.536 5.584 9954 Z= 0.277 Chirality : 0.043 0.163 1056 Planarity : 0.005 0.101 1310 Dihedral : 5.248 57.121 999 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.62 % Allowed : 21.58 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.12 (0.29), residues: 882 helix: 0.84 (0.29), residues: 334 sheet: -1.02 (0.41), residues: 172 loop : -0.29 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS C 199 PHE 0.011 0.001 PHE C 20 TYR 0.018 0.001 TYR A 13 ARG 0.006 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7012 (p0) cc_final: 0.6798 (p0) REVERT: A 252 MET cc_start: 0.8415 (mmp) cc_final: 0.7992 (mmp) REVERT: C 236 MET cc_start: 0.8863 (mtt) cc_final: 0.8528 (mtt) REVERT: C 241 ASN cc_start: 0.8135 (p0) cc_final: 0.7911 (p0) REVERT: C 278 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: C 297 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: C 300 ARG cc_start: 0.8044 (ptp-170) cc_final: 0.7580 (ptp-170) outliers start: 28 outliers final: 13 residues processed: 224 average time/residue: 1.3260 time to fit residues: 311.1661 Evaluate side-chains 223 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 40 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 303 GLN C 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7368 Z= 0.355 Angle : 0.605 5.784 9954 Z= 0.311 Chirality : 0.046 0.156 1056 Planarity : 0.006 0.110 1310 Dihedral : 5.447 57.167 998 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.52 % Allowed : 22.35 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.15 (0.29), residues: 882 helix: 0.75 (0.28), residues: 334 sheet: -1.02 (0.43), residues: 150 loop : -0.31 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 63 HIS 0.003 0.001 HIS A 149 PHE 0.019 0.002 PHE C 20 TYR 0.010 0.001 TYR A 288 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7768 (mtm180) REVERT: C 232 ARG cc_start: 0.8270 (ttp80) cc_final: 0.8070 (ttm110) REVERT: C 278 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: C 297 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6654 (tm-30) outliers start: 35 outliers final: 21 residues processed: 234 average time/residue: 1.3077 time to fit residues: 320.7696 Evaluate side-chains 235 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7368 Z= 0.266 Angle : 0.569 5.893 9954 Z= 0.293 Chirality : 0.044 0.157 1056 Planarity : 0.005 0.107 1310 Dihedral : 5.290 54.145 998 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.75 % Allowed : 23.39 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 (0.29), residues: 882 helix: 0.84 (0.29), residues: 334 sheet: -1.03 (0.43), residues: 152 loop : -0.27 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.003 0.001 HIS A 182 PHE 0.015 0.002 PHE C 20 TYR 0.018 0.001 TYR A 13 ARG 0.006 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 205 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7769 (mtm180) REVERT: C 241 ASN cc_start: 0.8151 (p0) cc_final: 0.7926 (p0) REVERT: C 278 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7261 (mm-30) outliers start: 29 outliers final: 18 residues processed: 230 average time/residue: 1.3119 time to fit residues: 316.1631 Evaluate side-chains 229 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.0370 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 241 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7368 Z= 0.235 Angle : 0.561 6.442 9954 Z= 0.288 Chirality : 0.043 0.158 1056 Planarity : 0.005 0.111 1310 Dihedral : 5.161 49.706 998 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.88 % Allowed : 24.42 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 (0.29), residues: 882 helix: 0.93 (0.29), residues: 334 sheet: -0.94 (0.43), residues: 152 loop : -0.20 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.003 0.001 HIS A 182 PHE 0.014 0.002 PHE C 20 TYR 0.011 0.001 TYR B 27 ARG 0.007 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.8012 (mtt) cc_final: 0.7786 (mtp) REVERT: C 187 MET cc_start: 0.8152 (mtt) cc_final: 0.7807 (mtm) REVERT: C 203 TYR cc_start: 0.8132 (t80) cc_final: 0.7832 (t80) REVERT: C 205 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7757 (mtm180) REVERT: C 241 ASN cc_start: 0.8134 (p0) cc_final: 0.7920 (p0) REVERT: C 278 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7252 (mm-30) outliers start: 30 outliers final: 22 residues processed: 229 average time/residue: 1.3583 time to fit residues: 325.4963 Evaluate side-chains 234 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 241 ASN C 303 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7368 Z= 0.343 Angle : 0.613 6.990 9954 Z= 0.316 Chirality : 0.046 0.171 1056 Planarity : 0.005 0.102 1310 Dihedral : 5.348 50.525 998 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.52 % Allowed : 23.90 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 (0.29), residues: 882 helix: 0.88 (0.29), residues: 334 sheet: -0.92 (0.44), residues: 152 loop : -0.25 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 63 HIS 0.005 0.001 HIS C 145 PHE 0.018 0.002 PHE C 20 TYR 0.018 0.002 TYR A 13 ARG 0.007 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 252 MET cc_start: 0.8513 (mmp) cc_final: 0.7936 (mmp) REVERT: C 205 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7740 (mtm180) REVERT: C 232 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8148 (ttm110) REVERT: C 278 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: C 297 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7322 (tt0) outliers start: 35 outliers final: 27 residues processed: 228 average time/residue: 1.3485 time to fit residues: 321.9877 Evaluate side-chains 237 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 74 optimal weight: 0.3980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 241 ASN C 313 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7368 Z= 0.212 Angle : 0.566 7.282 9954 Z= 0.292 Chirality : 0.043 0.188 1056 Planarity : 0.005 0.096 1310 Dihedral : 5.102 45.079 998 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.13 % Allowed : 24.55 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.08 (0.29), residues: 882 helix: 0.99 (0.29), residues: 334 sheet: -1.06 (0.42), residues: 164 loop : -0.11 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.005 0.001 HIS C 145 PHE 0.016 0.002 PHE A 80 TYR 0.014 0.001 TYR B 27 ARG 0.009 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 213 time to evaluate : 0.838 Fit side-chains REVERT: A 28 ASP cc_start: 0.8055 (m-30) cc_final: 0.7804 (m-30) REVERT: A 203 TYR cc_start: 0.8308 (t80) cc_final: 0.8098 (t80) REVERT: C 48 MET cc_start: 0.8563 (mtt) cc_final: 0.8244 (mtt) REVERT: C 203 TYR cc_start: 0.8138 (t80) cc_final: 0.7882 (t80) REVERT: C 205 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7746 (mtm180) REVERT: C 232 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8116 (ttm110) REVERT: C 297 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7254 (tt0) outliers start: 32 outliers final: 25 residues processed: 231 average time/residue: 1.3069 time to fit residues: 315.9891 Evaluate side-chains 236 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 244 ASN C 303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7368 Z= 0.279 Angle : 0.596 7.708 9954 Z= 0.308 Chirality : 0.045 0.202 1056 Planarity : 0.005 0.093 1310 Dihedral : 5.193 46.215 998 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.13 % Allowed : 25.06 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 (0.29), residues: 882 helix: 0.95 (0.29), residues: 334 sheet: -1.02 (0.43), residues: 164 loop : -0.16 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 63 HIS 0.006 0.001 HIS A 301 PHE 0.018 0.002 PHE A 80 TYR 0.017 0.002 TYR A 13 ARG 0.009 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8090 (m-30) cc_final: 0.7835 (m-30) REVERT: A 203 TYR cc_start: 0.8310 (t80) cc_final: 0.8090 (t80) REVERT: B 35 MET cc_start: 0.7674 (mtp) cc_final: 0.7370 (mtp) REVERT: C 48 MET cc_start: 0.8552 (mtt) cc_final: 0.8238 (mtt) REVERT: C 203 TYR cc_start: 0.8164 (t80) cc_final: 0.7919 (t80) REVERT: C 205 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7744 (mtm180) REVERT: C 232 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8131 (ttm110) REVERT: C 297 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: D 1 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6660 (mtt) outliers start: 32 outliers final: 27 residues processed: 224 average time/residue: 1.3884 time to fit residues: 325.4877 Evaluate side-chains 232 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 0.0570 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7368 Z= 0.221 Angle : 0.587 8.037 9954 Z= 0.301 Chirality : 0.044 0.193 1056 Planarity : 0.005 0.092 1310 Dihedral : 5.064 44.434 998 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.23 % Allowed : 25.97 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 (0.30), residues: 882 helix: 1.01 (0.29), residues: 334 sheet: -0.95 (0.43), residues: 164 loop : -0.15 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 63 HIS 0.004 0.001 HIS C 145 PHE 0.019 0.002 PHE A 80 TYR 0.013 0.001 TYR D 108 ARG 0.009 0.001 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8108 (m-30) cc_final: 0.7877 (m-30) REVERT: B 35 MET cc_start: 0.7608 (mtp) cc_final: 0.7331 (mtp) REVERT: C 48 MET cc_start: 0.8543 (mtt) cc_final: 0.8227 (mtt) REVERT: C 189 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7124 (mp0) REVERT: C 203 TYR cc_start: 0.8114 (t80) cc_final: 0.7885 (t80) REVERT: C 205 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7742 (mtm180) REVERT: C 232 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8131 (ttm110) outliers start: 25 outliers final: 23 residues processed: 222 average time/residue: 1.3730 time to fit residues: 318.7294 Evaluate side-chains 230 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 71 optimal weight: 0.0270 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125653 restraints weight = 8985.592| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.30 r_work: 0.3596 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7368 Z= 0.242 Angle : 0.598 7.730 9954 Z= 0.307 Chirality : 0.044 0.191 1056 Planarity : 0.005 0.088 1310 Dihedral : 5.061 44.167 998 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.49 % Allowed : 25.71 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: 0.13 (0.29), residues: 882 helix: 1.05 (0.29), residues: 332 sheet: -0.92 (0.43), residues: 164 loop : -0.17 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 63 HIS 0.005 0.001 HIS C 145 PHE 0.020 0.002 PHE A 80 TYR 0.018 0.001 TYR A 13 ARG 0.009 0.001 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4679.75 seconds wall clock time: 81 minutes 51.85 seconds (4911.85 seconds total)