Starting phenix.real_space_refine on Thu Mar 5 01:04:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g01_29641/03_2026/8g01_29641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g01_29641/03_2026/8g01_29641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g01_29641/03_2026/8g01_29641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g01_29641/03_2026/8g01_29641.map" model { file = "/net/cci-nas-00/data/ceres_data/8g01_29641/03_2026/8g01_29641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g01_29641/03_2026/8g01_29641.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5890 2.51 5 N 1472 2.21 5 O 1532 1.98 5 H 9214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18152 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 345} Chain: "B" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1088 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "G" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1088 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "E" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 5758 Classifications: {'peptide': 360} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 345} Chain: "D" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "C" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2230 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Time building chain proxies: 2.95, per 1000 atoms: 0.16 Number of scatterers: 18152 At special positions: 0 Unit cell: (86.528, 106.496, 102.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1532 8.00 N 1472 7.00 C 5890 6.00 H 9214 1.00 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 - 3.00 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: 1.73 Conformation dependent library (CDL) restraints added in 562.5 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 63.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 4.180A pdb=" N LYS A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 20 removed outlier: 6.926A pdb=" N GLY A 15 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.687A pdb=" N TRP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 153 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.673A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 201 through 220 removed outlier: 3.696A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.675A pdb=" N GLY A 237 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 266 through 285 removed outlier: 3.824A pdb=" N SER A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 334 through 360 removed outlier: 3.533A pdb=" N ARG A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'G' and resid 5 through 25 removed outlier: 4.336A pdb=" N LEU G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA G 11 " --> pdb=" O SER G 7 " (cutoff:3.500A) Proline residue: G 21 - end of helix Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 50 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 11 through 12 No H-bonds generated for 'chain 'E' and resid 11 through 12' Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 54 Proline residue: E 42 - end of helix Processing helix chain 'E' and resid 75 through 91 removed outlier: 4.126A pdb=" N ILE E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 174 through 194 removed outlier: 3.660A pdb=" N LEU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 201 through 221 removed outlier: 3.623A pdb=" N ASN E 221 " --> pdb=" O TRP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 229 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.766A pdb=" N GLY E 237 " --> pdb=" O ARG E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 258 removed outlier: 3.783A pdb=" N VAL E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 256 " --> pdb=" O GLY E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 284 removed outlier: 3.937A pdb=" N SER E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'E' and resid 323 through 332 Processing helix chain 'E' and resid 334 through 360 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 143 through 149 removed outlier: 3.866A pdb=" N LEU D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 143 through 149 Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.460A pdb=" N VAL D 118 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL D 112 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58 removed outlier: 6.951A pdb=" N VAL C 118 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL C 112 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 25 removed outlier: 6.736A pdb=" N LEU D 22 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR D 17 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 24 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 7 " --> pdb=" O HIS D 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 25 removed outlier: 6.736A pdb=" N LEU D 22 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR D 17 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 24 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA D 12 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL D 136 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLN D 14 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL D 134 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ARG D 16 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE D 132 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.587A pdb=" N LEU C 22 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 17 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 24 " --> pdb=" O VAL C 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.587A pdb=" N LEU C 22 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR C 17 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 24 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 138 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA C 12 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL C 136 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLN C 14 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL C 134 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ARG C 16 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE C 132 " --> pdb=" O ARG C 16 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1584 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: 4.82 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9210 1.03 - 1.23: 4 1.23 - 1.42: 3794 1.42 - 1.62: 5280 1.62 - 1.81: 84 Bond restraints: 18372 Sorted by residual: bond pdb=" CA VAL B 54 " pdb=" CB VAL B 54 " ideal model delta sigma weight residual 1.530 1.541 -0.010 1.05e-02 9.07e+03 9.62e-01 bond pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta sigma weight residual 1.468 1.481 -0.013 1.70e-02 3.46e+03 5.64e-01 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.443 1.452 -0.009 1.38e-02 5.25e+03 4.17e-01 bond pdb=" N SER C 26 " pdb=" CA SER C 26 " ideal model delta sigma weight residual 1.463 1.457 0.007 1.08e-02 8.57e+03 3.87e-01 bond pdb=" CG PRO A 204 " pdb=" CD PRO A 204 " ideal model delta sigma weight residual 1.512 1.496 0.016 2.70e-02 1.37e+03 3.44e-01 ... (remaining 18367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 32721 1.37 - 2.75: 567 2.75 - 4.12: 48 4.12 - 5.50: 7 5.50 - 6.87: 1 Bond angle restraints: 33344 Sorted by residual: angle pdb=" N PRO A 204 " pdb=" CA PRO A 204 " pdb=" C PRO A 204 " ideal model delta sigma weight residual 112.10 118.97 -6.87 2.60e+00 1.48e-01 6.99e+00 angle pdb=" N TYR C 68 " pdb=" CA TYR C 68 " pdb=" CB TYR C 68 " ideal model delta sigma weight residual 113.65 110.24 3.41 1.47e+00 4.63e-01 5.39e+00 angle pdb=" N TYR D 68 " pdb=" CA TYR D 68 " pdb=" CB TYR D 68 " ideal model delta sigma weight residual 113.65 110.41 3.24 1.47e+00 4.63e-01 4.86e+00 angle pdb=" N ASP C 6 " pdb=" CA ASP C 6 " pdb=" CB ASP C 6 " ideal model delta sigma weight residual 114.27 110.94 3.33 1.64e+00 3.72e-01 4.12e+00 angle pdb=" C MET A 203 " pdb=" N PRO A 204 " pdb=" CA PRO A 204 " ideal model delta sigma weight residual 127.00 131.54 -4.54 2.40e+00 1.74e-01 3.58e+00 ... (remaining 33339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 7878 17.14 - 34.28: 446 34.28 - 51.42: 142 51.42 - 68.56: 88 68.56 - 85.69: 4 Dihedral angle restraints: 8558 sinusoidal: 4590 harmonic: 3968 Sorted by residual: dihedral pdb=" CA SER C 10 " pdb=" C SER C 10 " pdb=" N LEU C 11 " pdb=" CA LEU C 11 " ideal model delta harmonic sigma weight residual 180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP C 24 " pdb=" CB ASP C 24 " pdb=" CG ASP C 24 " pdb=" OD1 ASP C 24 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP E 267 " pdb=" CB ASP E 267 " pdb=" CG ASP E 267 " pdb=" OD1 ASP E 267 " ideal model delta sinusoidal sigma weight residual -30.00 -88.73 58.73 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 8555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 977 0.029 - 0.058: 283 0.058 - 0.086: 120 0.086 - 0.115: 65 0.115 - 0.144: 13 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL E 162 " pdb=" N VAL E 162 " pdb=" C VAL E 162 " pdb=" CB VAL E 162 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1455 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 155 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO A 156 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 105 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO D 106 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 106 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 106 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 103 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.25e-01 pdb=" N PRO D 104 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " -0.013 5.00e-02 4.00e+02 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 932 2.21 - 2.81: 38664 2.81 - 3.40: 50958 3.40 - 4.00: 65217 4.00 - 4.60: 102059 Nonbonded interactions: 257830 Sorted by model distance: nonbonded pdb="HE22 GLN A 307 " pdb=" O PHE A 319 " model vdw 1.612 2.450 nonbonded pdb=" HG SER D 10 " pdb=" OD1 ASP D 33 " model vdw 1.621 2.450 nonbonded pdb=" HD1 HIS D 52 " pdb=" OD2 ASP D 56 " model vdw 1.623 2.450 nonbonded pdb=" O PHE A 253 " pdb=" H ASN A 257 " model vdw 1.627 2.450 nonbonded pdb=" O PRO G 35 " pdb=" HG SER G 38 " model vdw 1.635 2.450 ... (remaining 257825 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' 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=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: 1.490 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: 0.080 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.450 Find NCS groups from input model: 0.200 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 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 : 0.002 0.022 9158 Z= 0.088 Angle : 0.437 6.874 12462 Z= 0.232 Chirality : 0.038 0.144 1458 Planarity : 0.003 0.029 1540 Dihedral : 11.408 85.694 3226 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1136 helix: 2.17 (0.21), residues: 629 sheet: -0.15 (0.48), residues: 106 loop : 0.54 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 337 TYR 0.005 0.001 TYR A 328 PHE 0.011 0.001 PHE E 66 TRP 0.007 0.001 TRP A 90 HIS 0.004 0.000 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 9158) covalent geometry : angle 0.43706 (12462) hydrogen bonds : bond 0.15725 ( 551) hydrogen bonds : angle 6.10572 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.8411 (mt) cc_final: 0.8114 (mt) REVERT: A 63 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6818 (mt-10) REVERT: A 113 PHE cc_start: 0.7887 (t80) cc_final: 0.7685 (t80) REVERT: A 161 VAL cc_start: 0.8357 (t) cc_final: 0.7981 (m) REVERT: A 244 THR cc_start: 0.6857 (p) cc_final: 0.6559 (p) REVERT: A 300 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6406 (mm-30) REVERT: A 307 GLN cc_start: 0.7197 (tp40) cc_final: 0.6846 (tp40) REVERT: A 313 LEU cc_start: 0.8428 (mt) cc_final: 0.7060 (mm) REVERT: B 23 LEU cc_start: 0.8495 (tp) cc_final: 0.8230 (tp) REVERT: B 24 LEU cc_start: 0.8722 (mt) cc_final: 0.8301 (mt) REVERT: G 44 LEU cc_start: 0.8280 (tp) cc_final: 0.8064 (tp) REVERT: E 63 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6388 (mt-10) REVERT: E 94 SER cc_start: 0.8315 (t) cc_final: 0.8086 (p) REVERT: E 102 LEU cc_start: 0.8297 (mt) cc_final: 0.8025 (mp) REVERT: E 113 PHE cc_start: 0.7823 (t80) cc_final: 0.7576 (t80) REVERT: E 131 ARG cc_start: 0.7464 (mtt-85) cc_final: 0.7222 (mtt-85) REVERT: E 174 LEU cc_start: 0.7912 (mt) cc_final: 0.7636 (mm) REVERT: E 176 TYR cc_start: 0.8541 (t80) cc_final: 0.8182 (t80) REVERT: E 227 TYR cc_start: 0.7947 (t80) cc_final: 0.7727 (t80) REVERT: E 283 LEU cc_start: 0.8370 (mt) cc_final: 0.8076 (mp) REVERT: E 293 MET cc_start: 0.7667 (mtt) cc_final: 0.7462 (mtp) REVERT: E 303 SER cc_start: 0.8029 (t) cc_final: 0.7795 (t) REVERT: E 348 MET cc_start: 0.8093 (mmm) cc_final: 0.7854 (mmm) REVERT: E 350 VAL cc_start: 0.7897 (t) cc_final: 0.7635 (p) REVERT: D 66 ASP cc_start: 0.6847 (t0) cc_final: 0.6560 (t0) REVERT: D 105 VAL cc_start: 0.8415 (p) cc_final: 0.8018 (m) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2113 time to fit residues: 112.2753 Evaluate side-chains 358 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0010 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123509 restraints weight = 40094.651| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.48 r_work: 0.3408 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9158 Z= 0.150 Angle : 0.529 7.195 12462 Z= 0.282 Chirality : 0.040 0.159 1458 Planarity : 0.004 0.039 1540 Dihedral : 4.143 19.115 1230 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.15 % Allowed : 10.90 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.25), residues: 1136 helix: 1.89 (0.21), residues: 647 sheet: -0.29 (0.56), residues: 90 loop : 0.38 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.010 0.001 TYR D 34 PHE 0.015 0.001 PHE A 264 TRP 0.007 0.001 TRP E 39 HIS 0.004 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9158) covalent geometry : angle 0.52874 (12462) hydrogen bonds : bond 0.04544 ( 551) hydrogen bonds : angle 4.91543 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 360 time to evaluate : 0.429 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 113 PHE cc_start: 0.8178 (t80) cc_final: 0.7949 (t80) REVERT: A 161 VAL cc_start: 0.8332 (t) cc_final: 0.7978 (m) REVERT: A 244 THR cc_start: 0.7451 (p) cc_final: 0.7153 (p) REVERT: A 288 PHE cc_start: 0.8083 (m-80) cc_final: 0.7866 (m-80) REVERT: A 307 GLN cc_start: 0.7917 (tp40) cc_final: 0.7443 (tp40) REVERT: A 313 LEU cc_start: 0.8374 (mt) cc_final: 0.8157 (mm) REVERT: A 356 THR cc_start: 0.8508 (p) cc_final: 0.8241 (t) REVERT: B 24 LEU cc_start: 0.8942 (mt) cc_final: 0.8612 (mt) REVERT: G 44 LEU cc_start: 0.8571 (tp) cc_final: 0.8344 (tp) REVERT: E 63 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6784 (mt-10) REVERT: E 94 SER cc_start: 0.8562 (t) cc_final: 0.8340 (p) REVERT: E 116 ASP cc_start: 0.7340 (m-30) cc_final: 0.7071 (m-30) REVERT: E 131 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7864 (mtt-85) REVERT: E 174 LEU cc_start: 0.8088 (mt) cc_final: 0.7841 (mm) REVERT: E 227 TYR cc_start: 0.8457 (t80) cc_final: 0.8189 (t80) REVERT: E 253 PHE cc_start: 0.7888 (t80) cc_final: 0.7642 (t80) REVERT: E 283 LEU cc_start: 0.8591 (mt) cc_final: 0.8364 (mp) REVERT: E 348 MET cc_start: 0.8468 (mmm) cc_final: 0.8246 (mmm) REVERT: D 14 GLN cc_start: 0.8418 (tt0) cc_final: 0.8207 (tt0) REVERT: D 66 ASP cc_start: 0.7756 (t0) cc_final: 0.7301 (t70) REVERT: D 95 ARG cc_start: 0.6939 (mtt180) cc_final: 0.6141 (mtt180) REVERT: D 99 GLU cc_start: 0.6971 (mp0) cc_final: 0.6405 (mp0) REVERT: D 108 GLU cc_start: 0.6898 (tt0) cc_final: 0.6428 (tt0) REVERT: C 94 MET cc_start: 0.7186 (ttm) cc_final: 0.6755 (ttp) REVERT: C 108 GLU cc_start: 0.7435 (tt0) cc_final: 0.7203 (mt-10) outliers start: 11 outliers final: 8 residues processed: 360 average time/residue: 0.2219 time to fit residues: 106.4891 Evaluate side-chains 360 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 352 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 HIS ** D 102 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 = 0.3956 r_free = 0.3956 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122984 restraints weight = 40207.414| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.48 r_work: 0.3399 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9158 Z= 0.118 Angle : 0.491 6.277 12462 Z= 0.258 Chirality : 0.040 0.140 1458 Planarity : 0.004 0.044 1540 Dihedral : 4.088 18.752 1230 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.78 % Allowed : 12.68 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.26), residues: 1136 helix: 2.04 (0.21), residues: 636 sheet: -0.33 (0.55), residues: 100 loop : 0.36 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 55 TYR 0.014 0.001 TYR A 149 PHE 0.016 0.001 PHE A 264 TRP 0.007 0.001 TRP E 99 HIS 0.003 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9158) covalent geometry : angle 0.49134 (12462) hydrogen bonds : bond 0.04129 ( 551) hydrogen bonds : angle 4.65394 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 360 time to evaluate : 0.441 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 69 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7507 (mtt180) REVERT: A 113 PHE cc_start: 0.8168 (t80) cc_final: 0.7939 (t80) REVERT: A 149 TYR cc_start: 0.8726 (t80) cc_final: 0.8287 (t80) REVERT: A 161 VAL cc_start: 0.8310 (t) cc_final: 0.7952 (m) REVERT: A 244 THR cc_start: 0.7513 (p) cc_final: 0.7216 (p) REVERT: A 307 GLN cc_start: 0.7877 (tp40) cc_final: 0.7390 (tp40) REVERT: A 313 LEU cc_start: 0.8486 (mt) cc_final: 0.8183 (mm) REVERT: A 356 THR cc_start: 0.8476 (p) cc_final: 0.8222 (t) REVERT: B 24 LEU cc_start: 0.8913 (mt) cc_final: 0.8579 (mt) REVERT: B 40 LYS cc_start: 0.7967 (mttm) cc_final: 0.7738 (mtmm) REVERT: G 55 ARG cc_start: 0.7527 (mtm180) cc_final: 0.7292 (mtm110) REVERT: E 94 SER cc_start: 0.8611 (t) cc_final: 0.8364 (p) REVERT: E 116 ASP cc_start: 0.7356 (m-30) cc_final: 0.7126 (m-30) REVERT: E 131 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7819 (mtt-85) REVERT: E 176 TYR cc_start: 0.8667 (t80) cc_final: 0.8457 (t80) REVERT: E 227 TYR cc_start: 0.8435 (t80) cc_final: 0.8168 (t80) REVERT: E 253 PHE cc_start: 0.7961 (t80) cc_final: 0.7726 (t80) REVERT: E 283 LEU cc_start: 0.8653 (mt) cc_final: 0.8384 (mp) REVERT: E 348 MET cc_start: 0.8466 (mmm) cc_final: 0.8154 (mmm) REVERT: E 350 VAL cc_start: 0.8127 (t) cc_final: 0.7906 (p) REVERT: D 1 MET cc_start: 0.0743 (ttp) cc_final: -0.2928 (mmm) REVERT: D 66 ASP cc_start: 0.7858 (t0) cc_final: 0.7371 (t70) REVERT: D 73 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 95 ARG cc_start: 0.7028 (mtt180) cc_final: 0.6094 (mtt180) REVERT: D 99 GLU cc_start: 0.6970 (mp0) cc_final: 0.6411 (mp0) REVERT: D 108 GLU cc_start: 0.6951 (tt0) cc_final: 0.6375 (tt0) REVERT: D 117 VAL cc_start: 0.7776 (m) cc_final: 0.7370 (m) REVERT: C 94 MET cc_start: 0.7053 (ttm) cc_final: 0.6365 (ttm) REVERT: C 95 ARG cc_start: 0.7736 (ttm170) cc_final: 0.7497 (ttm-80) REVERT: C 128 GLN cc_start: 0.6426 (mt0) cc_final: 0.6140 (mt0) outliers start: 17 outliers final: 12 residues processed: 364 average time/residue: 0.2264 time to fit residues: 110.5580 Evaluate side-chains 363 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 351 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 HIS E 257 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.148833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119768 restraints weight = 40217.659| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.44 r_work: 0.3347 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9158 Z= 0.152 Angle : 0.507 6.151 12462 Z= 0.270 Chirality : 0.040 0.158 1458 Planarity : 0.004 0.045 1540 Dihedral : 4.172 19.477 1230 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.57 % Allowed : 14.05 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1136 helix: 1.89 (0.20), residues: 637 sheet: -0.52 (0.52), residues: 108 loop : 0.13 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.011 0.001 TYR E 149 PHE 0.012 0.001 PHE A 264 TRP 0.006 0.001 TRP E 39 HIS 0.002 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9158) covalent geometry : angle 0.50689 (12462) hydrogen bonds : bond 0.04201 ( 551) hydrogen bonds : angle 4.60910 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 364 time to evaluate : 0.522 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7971 (ttm) cc_final: 0.7695 (ttm) REVERT: A 63 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 113 PHE cc_start: 0.8180 (t80) cc_final: 0.7910 (t80) REVERT: A 161 VAL cc_start: 0.8347 (t) cc_final: 0.7964 (m) REVERT: A 244 THR cc_start: 0.7659 (p) cc_final: 0.7386 (p) REVERT: A 356 THR cc_start: 0.8466 (p) cc_final: 0.8208 (t) REVERT: B 24 LEU cc_start: 0.8930 (mt) cc_final: 0.8636 (mt) REVERT: B 40 LYS cc_start: 0.8106 (mttm) cc_final: 0.7848 (mtmm) REVERT: E 116 ASP cc_start: 0.7325 (m-30) cc_final: 0.7057 (m-30) REVERT: E 131 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7923 (mtt-85) REVERT: E 162 VAL cc_start: 0.8741 (t) cc_final: 0.8409 (m) REVERT: E 174 LEU cc_start: 0.8065 (mp) cc_final: 0.7825 (mm) REVERT: E 176 TYR cc_start: 0.8666 (t80) cc_final: 0.7792 (t80) REVERT: E 227 TYR cc_start: 0.8472 (t80) cc_final: 0.8181 (t80) REVERT: E 253 PHE cc_start: 0.8073 (t80) cc_final: 0.7687 (t80) REVERT: E 283 LEU cc_start: 0.8672 (mt) cc_final: 0.8401 (mp) REVERT: E 348 MET cc_start: 0.8464 (mmm) cc_final: 0.8237 (mmm) REVERT: E 350 VAL cc_start: 0.8140 (t) cc_final: 0.7902 (p) REVERT: D 1 MET cc_start: 0.0846 (ttp) cc_final: -0.2868 (mmm) REVERT: D 14 GLN cc_start: 0.8449 (tt0) cc_final: 0.8243 (tt0) REVERT: D 66 ASP cc_start: 0.7951 (t0) cc_final: 0.7456 (t0) REVERT: D 73 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8054 (mm-30) REVERT: D 95 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6355 (mtt180) REVERT: D 99 GLU cc_start: 0.7001 (mp0) cc_final: 0.6394 (mp0) REVERT: D 108 GLU cc_start: 0.7065 (tt0) cc_final: 0.6581 (tt0) REVERT: C 16 ARG cc_start: 0.7460 (mtt180) cc_final: 0.7165 (mtt180) REVERT: C 128 GLN cc_start: 0.6604 (mt0) cc_final: 0.6304 (mt0) outliers start: 15 outliers final: 13 residues processed: 369 average time/residue: 0.2207 time to fit residues: 109.3708 Evaluate side-chains 373 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 360 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 ASN E 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119088 restraints weight = 39925.362| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.41 r_work: 0.3354 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9158 Z= 0.131 Angle : 0.497 5.992 12462 Z= 0.261 Chirality : 0.039 0.133 1458 Planarity : 0.004 0.046 1540 Dihedral : 4.100 19.098 1230 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.26 % Allowed : 15.51 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1136 helix: 1.93 (0.20), residues: 638 sheet: -0.60 (0.51), residues: 108 loop : 0.02 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 55 TYR 0.013 0.001 TYR A 149 PHE 0.008 0.001 PHE A 264 TRP 0.006 0.001 TRP E 39 HIS 0.002 0.000 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9158) covalent geometry : angle 0.49679 (12462) hydrogen bonds : bond 0.04017 ( 551) hydrogen bonds : angle 4.51788 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 371 time to evaluate : 0.433 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7944 (ttm) cc_final: 0.7702 (ttm) REVERT: A 63 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 113 PHE cc_start: 0.8184 (t80) cc_final: 0.7923 (t80) REVERT: A 149 TYR cc_start: 0.8749 (t80) cc_final: 0.8328 (t80) REVERT: A 161 VAL cc_start: 0.8354 (t) cc_final: 0.7961 (m) REVERT: A 244 THR cc_start: 0.7719 (p) cc_final: 0.7446 (p) REVERT: A 314 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7871 (mmm160) REVERT: B 24 LEU cc_start: 0.8917 (mt) cc_final: 0.8623 (mt) REVERT: B 40 LYS cc_start: 0.8156 (mttm) cc_final: 0.7901 (mtmm) REVERT: G 44 LEU cc_start: 0.8545 (tp) cc_final: 0.8344 (tt) REVERT: E 116 ASP cc_start: 0.7295 (m-30) cc_final: 0.7028 (m-30) REVERT: E 131 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7914 (mtt-85) REVERT: E 174 LEU cc_start: 0.7971 (mp) cc_final: 0.7714 (mm) REVERT: E 176 TYR cc_start: 0.8661 (t80) cc_final: 0.7734 (t80) REVERT: E 227 TYR cc_start: 0.8462 (t80) cc_final: 0.8192 (t80) REVERT: E 253 PHE cc_start: 0.8108 (t80) cc_final: 0.7705 (t80) REVERT: E 283 LEU cc_start: 0.8657 (mt) cc_final: 0.8396 (mp) REVERT: E 348 MET cc_start: 0.8482 (mmm) cc_final: 0.8169 (mmm) REVERT: D 1 MET cc_start: 0.0693 (ttp) cc_final: -0.2937 (mmm) REVERT: D 16 ARG cc_start: 0.6676 (mtm-85) cc_final: 0.6470 (mtm-85) REVERT: D 66 ASP cc_start: 0.7960 (t0) cc_final: 0.7521 (t70) REVERT: D 73 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8020 (mm-30) REVERT: D 99 GLU cc_start: 0.7010 (mp0) cc_final: 0.6391 (mp0) REVERT: C 16 ARG cc_start: 0.7394 (mtt180) cc_final: 0.7106 (mtt180) REVERT: C 128 GLN cc_start: 0.6658 (mt0) cc_final: 0.6341 (mt0) outliers start: 12 outliers final: 9 residues processed: 374 average time/residue: 0.2217 time to fit residues: 111.4272 Evaluate side-chains 375 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 366 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 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 = 0.3834 r_free = 0.3834 target = 0.141205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113163 restraints weight = 40355.310| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.33 r_work: 0.3286 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9158 Z= 0.286 Angle : 0.582 5.699 12462 Z= 0.321 Chirality : 0.042 0.147 1458 Planarity : 0.004 0.053 1540 Dihedral : 4.464 19.991 1230 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.99 % Allowed : 15.72 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1136 helix: 1.42 (0.20), residues: 642 sheet: -0.52 (0.53), residues: 101 loop : -0.30 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 285 TYR 0.015 0.002 TYR C 71 PHE 0.014 0.002 PHE E 207 TRP 0.015 0.002 TRP A 217 HIS 0.004 0.001 HIS E 325 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9158) covalent geometry : angle 0.58201 (12462) hydrogen bonds : bond 0.04999 ( 551) hydrogen bonds : angle 4.91258 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 393 time to evaluate : 0.414 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8061 (ttm) cc_final: 0.7818 (ttm) REVERT: A 63 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 113 PHE cc_start: 0.8279 (t80) cc_final: 0.7998 (t80) REVERT: A 192 ASN cc_start: 0.8354 (t0) cc_final: 0.8068 (t0) REVERT: A 317 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6593 (ptt-90) REVERT: B 24 LEU cc_start: 0.8938 (mt) cc_final: 0.8677 (mt) REVERT: B 31 THR cc_start: 0.8506 (t) cc_final: 0.8249 (m) REVERT: B 40 LYS cc_start: 0.8412 (mttm) cc_final: 0.8087 (mtmm) REVERT: G 53 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7992 (p) REVERT: E 81 THR cc_start: 0.8760 (t) cc_final: 0.8434 (p) REVERT: E 116 ASP cc_start: 0.7251 (m-30) cc_final: 0.6980 (m-30) REVERT: E 131 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7921 (mtt-85) REVERT: E 162 VAL cc_start: 0.8744 (t) cc_final: 0.8382 (m) REVERT: E 174 LEU cc_start: 0.8105 (mp) cc_final: 0.7835 (mm) REVERT: E 176 TYR cc_start: 0.8690 (t80) cc_final: 0.7580 (t80) REVERT: E 222 MET cc_start: 0.7840 (mmm) cc_final: 0.7619 (mmt) REVERT: E 227 TYR cc_start: 0.8428 (t80) cc_final: 0.8126 (t80) REVERT: E 283 LEU cc_start: 0.8607 (mt) cc_final: 0.8398 (mp) REVERT: E 348 MET cc_start: 0.8482 (mmm) cc_final: 0.8165 (mmm) REVERT: D 66 ASP cc_start: 0.7998 (t0) cc_final: 0.7573 (t70) REVERT: D 73 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7970 (mm-30) REVERT: D 99 GLU cc_start: 0.7109 (mp0) cc_final: 0.6494 (mp0) REVERT: D 108 GLU cc_start: 0.7358 (tt0) cc_final: 0.6810 (tt0) REVERT: C 89 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6792 (pp20) REVERT: C 128 GLN cc_start: 0.7009 (mt0) cc_final: 0.6678 (mt0) outliers start: 19 outliers final: 12 residues processed: 396 average time/residue: 0.2221 time to fit residues: 117.8519 Evaluate side-chains 403 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 389 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS E 189 ASN ** C 91 GLN ** 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 = 0.3865 r_free = 0.3865 target = 0.144025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115881 restraints weight = 39998.969| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.37 r_work: 0.3313 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9158 Z= 0.145 Angle : 0.523 6.719 12462 Z= 0.278 Chirality : 0.039 0.133 1458 Planarity : 0.004 0.050 1540 Dihedral : 4.286 19.897 1230 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.26 % Allowed : 18.55 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1136 helix: 1.61 (0.20), residues: 640 sheet: -0.64 (0.51), residues: 107 loop : -0.24 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.013 0.001 TYR A 149 PHE 0.020 0.001 PHE C 84 TRP 0.007 0.001 TRP A 136 HIS 0.003 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9158) covalent geometry : angle 0.52333 (12462) hydrogen bonds : bond 0.04267 ( 551) hydrogen bonds : angle 4.67688 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 386 time to evaluate : 0.448 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8047 (ttm) cc_final: 0.7820 (ttm) REVERT: A 63 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 113 PHE cc_start: 0.8236 (t80) cc_final: 0.7952 (t80) REVERT: A 232 TYR cc_start: 0.8701 (t80) cc_final: 0.8495 (t80) REVERT: A 317 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6593 (ptt-90) REVERT: B 24 LEU cc_start: 0.8895 (mt) cc_final: 0.8620 (mt) REVERT: B 31 THR cc_start: 0.8400 (t) cc_final: 0.8132 (m) REVERT: B 40 LYS cc_start: 0.8301 (mttm) cc_final: 0.7980 (mtmm) REVERT: G 55 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7265 (mtm110) REVERT: E 44 MET cc_start: 0.8294 (tmm) cc_final: 0.7750 (tmm) REVERT: E 81 THR cc_start: 0.8710 (t) cc_final: 0.8399 (p) REVERT: E 116 ASP cc_start: 0.7229 (m-30) cc_final: 0.6966 (m-30) REVERT: E 131 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7889 (mtt-85) REVERT: E 174 LEU cc_start: 0.8004 (mp) cc_final: 0.7775 (mm) REVERT: E 176 TYR cc_start: 0.8681 (t80) cc_final: 0.7592 (t80) REVERT: E 227 TYR cc_start: 0.8393 (t80) cc_final: 0.8111 (t80) REVERT: E 283 LEU cc_start: 0.8679 (mt) cc_final: 0.8425 (mp) REVERT: E 348 MET cc_start: 0.8434 (mmm) cc_final: 0.8118 (mmm) REVERT: D 66 ASP cc_start: 0.8011 (t0) cc_final: 0.7637 (t70) REVERT: D 73 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 99 GLU cc_start: 0.7065 (mp0) cc_final: 0.6444 (mp0) REVERT: D 108 GLU cc_start: 0.7353 (tt0) cc_final: 0.6794 (tt0) REVERT: C 128 GLN cc_start: 0.7000 (mt0) cc_final: 0.6470 (mt0) outliers start: 12 outliers final: 11 residues processed: 390 average time/residue: 0.2283 time to fit residues: 118.7317 Evaluate side-chains 397 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 385 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116695 restraints weight = 39900.409| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.36 r_work: 0.3320 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9158 Z= 0.148 Angle : 0.534 9.069 12462 Z= 0.281 Chirality : 0.039 0.138 1458 Planarity : 0.004 0.048 1540 Dihedral : 4.237 19.632 1230 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.57 % Allowed : 18.55 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1136 helix: 1.65 (0.20), residues: 638 sheet: -0.70 (0.51), residues: 107 loop : -0.30 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 314 TYR 0.017 0.001 TYR E 232 PHE 0.017 0.001 PHE A 182 TRP 0.006 0.001 TRP A 136 HIS 0.003 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9158) covalent geometry : angle 0.53374 (12462) hydrogen bonds : bond 0.04203 ( 551) hydrogen bonds : angle 4.64866 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 386 time to evaluate : 0.526 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8019 (ttm) cc_final: 0.7804 (ttm) REVERT: A 63 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 113 PHE cc_start: 0.8242 (t80) cc_final: 0.7963 (t80) REVERT: A 232 TYR cc_start: 0.8724 (t80) cc_final: 0.8520 (t80) REVERT: A 317 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6570 (ptt-90) REVERT: B 24 LEU cc_start: 0.8856 (mt) cc_final: 0.8597 (mt) REVERT: B 31 THR cc_start: 0.8410 (t) cc_final: 0.8165 (m) REVERT: B 40 LYS cc_start: 0.8322 (mttm) cc_final: 0.7985 (mtmm) REVERT: E 44 MET cc_start: 0.8288 (tmm) cc_final: 0.7747 (tmm) REVERT: E 81 THR cc_start: 0.8719 (t) cc_final: 0.8386 (p) REVERT: E 116 ASP cc_start: 0.7255 (m-30) cc_final: 0.6977 (m-30) REVERT: E 131 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7863 (mtt-85) REVERT: E 174 LEU cc_start: 0.7993 (mp) cc_final: 0.7743 (mm) REVERT: E 176 TYR cc_start: 0.8687 (t80) cc_final: 0.7572 (t80) REVERT: E 227 TYR cc_start: 0.8388 (t80) cc_final: 0.8108 (t80) REVERT: E 283 LEU cc_start: 0.8696 (mt) cc_final: 0.8442 (mp) REVERT: E 317 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7410 (mtt180) REVERT: E 348 MET cc_start: 0.8456 (mmm) cc_final: 0.8131 (mmm) REVERT: D 1 MET cc_start: 0.2141 (ptm) cc_final: -0.3635 (mmm) REVERT: D 66 ASP cc_start: 0.8016 (t0) cc_final: 0.7655 (t70) REVERT: D 99 GLU cc_start: 0.7042 (mp0) cc_final: 0.6416 (mp0) REVERT: D 108 GLU cc_start: 0.7324 (tt0) cc_final: 0.6841 (tt0) REVERT: C 128 GLN cc_start: 0.7033 (mt0) cc_final: 0.6499 (mt0) outliers start: 15 outliers final: 13 residues processed: 390 average time/residue: 0.2305 time to fit residues: 119.5622 Evaluate side-chains 398 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 384 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 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 = 0.3850 r_free = 0.3850 target = 0.143853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115785 restraints weight = 39913.033| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.32 r_work: 0.3293 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9158 Z= 0.223 Angle : 0.566 8.139 12462 Z= 0.304 Chirality : 0.041 0.138 1458 Planarity : 0.004 0.053 1540 Dihedral : 4.349 19.777 1230 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 18.45 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1136 helix: 1.49 (0.20), residues: 635 sheet: -0.72 (0.50), residues: 109 loop : -0.35 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.017 0.002 TYR E 232 PHE 0.020 0.001 PHE A 182 TRP 0.010 0.001 TRP A 217 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9158) covalent geometry : angle 0.56556 (12462) hydrogen bonds : bond 0.04515 ( 551) hydrogen bonds : angle 4.75396 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 389 time to evaluate : 0.546 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8023 (ttm) cc_final: 0.7791 (ttm) REVERT: A 63 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 113 PHE cc_start: 0.8272 (t80) cc_final: 0.7997 (t80) REVERT: A 317 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6651 (ptt-90) REVERT: B 24 LEU cc_start: 0.8894 (mt) cc_final: 0.8635 (mt) REVERT: B 31 THR cc_start: 0.8455 (t) cc_final: 0.8221 (m) REVERT: B 40 LYS cc_start: 0.8391 (mttm) cc_final: 0.8041 (mtmm) REVERT: E 81 THR cc_start: 0.8757 (t) cc_final: 0.8431 (p) REVERT: E 116 ASP cc_start: 0.7288 (m-30) cc_final: 0.7008 (m-30) REVERT: E 131 ARG cc_start: 0.8134 (mtt-85) cc_final: 0.7875 (mtt-85) REVERT: E 162 VAL cc_start: 0.8773 (t) cc_final: 0.8412 (m) REVERT: E 174 LEU cc_start: 0.8047 (mp) cc_final: 0.7796 (mm) REVERT: E 176 TYR cc_start: 0.8682 (t80) cc_final: 0.7548 (t80) REVERT: E 227 TYR cc_start: 0.8385 (t80) cc_final: 0.8107 (t80) REVERT: E 283 LEU cc_start: 0.8663 (mt) cc_final: 0.8413 (mp) REVERT: E 317 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7440 (mtt180) REVERT: E 321 MET cc_start: 0.8166 (tpp) cc_final: 0.7864 (mmm) REVERT: E 348 MET cc_start: 0.8480 (mmm) cc_final: 0.8178 (mmm) REVERT: D 1 MET cc_start: 0.2106 (ptm) cc_final: -0.3658 (mmm) REVERT: D 66 ASP cc_start: 0.8081 (t0) cc_final: 0.7685 (t70) REVERT: D 77 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7414 (mm-40) REVERT: D 99 GLU cc_start: 0.7087 (mp0) cc_final: 0.6477 (mp0) REVERT: D 108 GLU cc_start: 0.7325 (tt0) cc_final: 0.6828 (tt0) REVERT: C 128 GLN cc_start: 0.7159 (mt0) cc_final: 0.6594 (mt0) outliers start: 16 outliers final: 14 residues processed: 392 average time/residue: 0.2252 time to fit residues: 118.9363 Evaluate side-chains 405 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 390 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 84 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN C 123 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116076 restraints weight = 40396.775| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.37 r_work: 0.3289 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9158 Z= 0.148 Angle : 0.539 7.924 12462 Z= 0.284 Chirality : 0.040 0.132 1458 Planarity : 0.004 0.050 1540 Dihedral : 4.262 19.799 1230 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.57 % Allowed : 19.29 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.25), residues: 1136 helix: 1.62 (0.20), residues: 633 sheet: -0.71 (0.50), residues: 109 loop : -0.32 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.017 0.001 TYR E 232 PHE 0.019 0.001 PHE E 182 TRP 0.007 0.001 TRP E 39 HIS 0.004 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9158) covalent geometry : angle 0.53906 (12462) hydrogen bonds : bond 0.04208 ( 551) hydrogen bonds : angle 4.64543 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 389 time to evaluate : 0.448 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 113 PHE cc_start: 0.8253 (t80) cc_final: 0.7964 (t80) REVERT: A 317 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6670 (ptt-90) REVERT: B 24 LEU cc_start: 0.8851 (mt) cc_final: 0.8587 (mt) REVERT: B 31 THR cc_start: 0.8423 (t) cc_final: 0.8202 (m) REVERT: B 40 LYS cc_start: 0.8362 (mttm) cc_final: 0.8020 (mtmm) REVERT: G 13 LEU cc_start: 0.8308 (mt) cc_final: 0.8049 (mm) REVERT: E 81 THR cc_start: 0.8739 (t) cc_final: 0.8400 (p) REVERT: E 116 ASP cc_start: 0.7262 (m-30) cc_final: 0.6995 (m-30) REVERT: E 131 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7829 (mtt-85) REVERT: E 174 LEU cc_start: 0.7967 (mp) cc_final: 0.7728 (mm) REVERT: E 176 TYR cc_start: 0.8687 (t80) cc_final: 0.7573 (t80) REVERT: E 227 TYR cc_start: 0.8375 (t80) cc_final: 0.8092 (t80) REVERT: E 283 LEU cc_start: 0.8685 (mt) cc_final: 0.8420 (mp) REVERT: E 317 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7449 (mtt180) REVERT: E 348 MET cc_start: 0.8445 (mmm) cc_final: 0.8141 (mmm) REVERT: D 1 MET cc_start: 0.2161 (ptm) cc_final: -0.3593 (mmm) REVERT: D 66 ASP cc_start: 0.8070 (t0) cc_final: 0.7689 (t70) REVERT: D 77 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7442 (mm-40) REVERT: D 99 GLU cc_start: 0.7006 (mp0) cc_final: 0.6398 (mp0) REVERT: D 108 GLU cc_start: 0.7296 (tt0) cc_final: 0.6756 (tt0) REVERT: C 128 GLN cc_start: 0.7134 (mt0) cc_final: 0.6589 (mt0) outliers start: 15 outliers final: 14 residues processed: 393 average time/residue: 0.2272 time to fit residues: 119.5276 Evaluate side-chains 401 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 386 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 116 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** 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 = 0.3852 r_free = 0.3852 target = 0.143087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114756 restraints weight = 40040.302| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.36 r_work: 0.3310 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.276 9158 Z= 0.248 Angle : 0.870 59.183 12462 Z= 0.511 Chirality : 0.039 0.133 1458 Planarity : 0.004 0.050 1540 Dihedral : 4.258 19.767 1230 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.57 % Allowed : 20.02 % Favored : 78.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.25), residues: 1136 helix: 1.62 (0.20), residues: 633 sheet: -0.71 (0.50), residues: 109 loop : -0.31 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 16 TYR 0.014 0.001 TYR E 232 PHE 0.032 0.001 PHE E 288 TRP 0.006 0.001 TRP E 39 HIS 0.003 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9158) covalent geometry : angle 0.87032 (12462) hydrogen bonds : bond 0.04201 ( 551) hydrogen bonds : angle 4.64552 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.63 seconds wall clock time: 86 minutes 35.28 seconds (5195.28 seconds total)