Starting phenix.real_space_refine on Sun Jun 15 22:52:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g01_29641/06_2025/8g01_29641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g01_29641/06_2025/8g01_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_29641/06_2025/8g01_29641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g01_29641/06_2025/8g01_29641.map" model { file = "/net/cci-nas-00/data/ceres_data/8g01_29641/06_2025/8g01_29641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g01_29641/06_2025/8g01_29641.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.48, per 1000 atoms: 0.47 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: 4.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.46 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: 5.96 Time building geometry restraints manager: 5.64 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: 0.01 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: 0.690 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: 0.300 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.330 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP A 90 HIS 0.004 0.000 HIS D 38 PHE 0.011 0.001 PHE E 66 TYR 0.005 0.001 TYR A 328 ARG 0.004 0.000 ARG E 337 Details of bonding type rmsd hydrogen bonds : bond 0.15725 ( 551) hydrogen bonds : angle 6.10572 ( 1584) covalent geometry : bond 0.00170 ( 9158) covalent geometry : angle 0.43706 (12462) *********************** 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 : 1.284 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: 0.8113 (mt) REVERT: A 63 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 113 PHE cc_start: 0.7887 (t80) cc_final: 0.7684 (t80) REVERT: A 161 VAL cc_start: 0.8357 (t) cc_final: 0.7980 (m) REVERT: A 244 THR cc_start: 0.6857 (p) cc_final: 0.6557 (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: 0.6840 (tp40) REVERT: A 312 LYS cc_start: 0.8212 (tptt) cc_final: 0.8010 (tppt) REVERT: A 313 LEU cc_start: 0.8428 (mt) cc_final: 0.8189 (mm) REVERT: B 23 LEU cc_start: 0.8495 (tp) cc_final: 0.8232 (tp) REVERT: B 24 LEU cc_start: 0.8722 (mt) cc_final: 0.8299 (mt) REVERT: G 44 LEU cc_start: 0.8280 (tp) cc_final: 0.8062 (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: 0.8085 (p) REVERT: E 102 LEU cc_start: 0.8297 (mt) cc_final: 0.8024 (mp) REVERT: E 113 PHE cc_start: 0.7823 (t80) cc_final: 0.7577 (t80) REVERT: E 131 ARG cc_start: 0.7464 (mtt-85) cc_final: 0.7224 (mtt-85) REVERT: E 174 LEU cc_start: 0.7912 (mt) cc_final: 0.7635 (mm) REVERT: E 176 TYR cc_start: 0.8541 (t80) cc_final: 0.8183 (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: 0.8074 (mp) REVERT: E 293 MET cc_start: 0.7668 (mtt) cc_final: 0.7461 (mtp) REVERT: E 303 SER cc_start: 0.8029 (t) cc_final: 0.7797 (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: 0.6559 (t0) REVERT: D 105 VAL cc_start: 0.8415 (p) cc_final: 0.8020 (m) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.4820 time to fit residues: 257.0275 Evaluate side-chains 359 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.148778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119592 restraints weight = 39954.006| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.47 r_work: 0.3385 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9158 Z= 0.175 Angle : 0.546 7.219 12462 Z= 0.293 Chirality : 0.041 0.154 1458 Planarity : 0.004 0.040 1540 Dihedral : 4.256 19.684 1230 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.68 % Allowed : 10.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1136 helix: 1.81 (0.21), residues: 648 sheet: -0.28 (0.56), residues: 91 loop : 0.31 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.004 0.001 HIS D 36 PHE 0.018 0.001 PHE A 264 TYR 0.011 0.001 TYR D 34 ARG 0.004 0.001 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 551) hydrogen bonds : angle 4.91177 ( 1584) covalent geometry : bond 0.00361 ( 9158) covalent geometry : angle 0.54589 (12462) *********************** 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 383 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 367 time to evaluate : 1.423 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: 0.7882 (ttm) cc_final: 0.7637 (ttm) REVERT: A 63 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 113 PHE cc_start: 0.8204 (t80) cc_final: 0.7975 (t80) REVERT: A 140 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8286 (tp) REVERT: A 161 VAL cc_start: 0.8343 (t) cc_final: 0.7960 (m) REVERT: A 244 THR cc_start: 0.7512 (p) cc_final: 0.7210 (p) REVERT: A 307 GLN cc_start: 0.7930 (tp40) cc_final: 0.7457 (tp40) REVERT: A 312 LYS cc_start: 0.8568 (tptt) cc_final: 0.8303 (tppt) REVERT: A 313 LEU cc_start: 0.8568 (mt) cc_final: 0.8309 (mm) REVERT: B 24 LEU cc_start: 0.8947 (mt) cc_final: 0.8623 (mt) REVERT: B 40 LYS cc_start: 0.7963 (mttm) cc_final: 0.7740 (mtmm) REVERT: G 44 LEU cc_start: 0.8591 (tp) cc_final: 0.8376 (tp) REVERT: E 94 SER cc_start: 0.8584 (t) cc_final: 0.8358 (p) REVERT: E 116 ASP cc_start: 0.7366 (m-30) cc_final: 0.7090 (m-30) REVERT: E 131 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7959 (mtt-85) REVERT: E 174 LEU cc_start: 0.8119 (mt) cc_final: 0.7859 (mm) REVERT: E 227 TYR cc_start: 0.8457 (t80) cc_final: 0.8193 (t80) REVERT: E 283 LEU cc_start: 0.8618 (mt) cc_final: 0.8386 (mp) REVERT: E 348 MET cc_start: 0.8489 (mmm) cc_final: 0.8170 (mmm) REVERT: D 14 GLN cc_start: 0.8416 (tt0) cc_final: 0.8214 (tt0) REVERT: D 66 ASP cc_start: 0.7867 (t0) cc_final: 0.7364 (t70) REVERT: D 95 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6157 (mtt180) REVERT: D 99 GLU cc_start: 0.6962 (mp0) cc_final: 0.6451 (mp0) REVERT: D 108 GLU cc_start: 0.7033 (tt0) cc_final: 0.6590 (tt0) REVERT: C 95 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7584 (ttm-80) REVERT: C 112 VAL cc_start: 0.8433 (p) cc_final: 0.8211 (t) REVERT: C 128 GLN cc_start: 0.6403 (mt0) cc_final: 0.6106 (mt0) outliers start: 16 outliers final: 10 residues processed: 369 average time/residue: 0.5452 time to fit residues: 271.1791 Evaluate side-chains 369 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 358 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain A residue 226 SER 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 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 26 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.142206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112949 restraints weight = 40022.612| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.39 r_work: 0.3270 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9158 Z= 0.306 Angle : 0.624 5.868 12462 Z= 0.347 Chirality : 0.044 0.153 1458 Planarity : 0.005 0.058 1540 Dihedral : 4.854 21.280 1230 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 12.37 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1136 helix: 1.14 (0.20), residues: 642 sheet: -0.42 (0.55), residues: 97 loop : -0.18 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 217 HIS 0.007 0.001 HIS E 325 PHE 0.022 0.002 PHE A 264 TYR 0.019 0.002 TYR C 71 ARG 0.008 0.001 ARG E 285 Details of bonding type rmsd hydrogen bonds : bond 0.05706 ( 551) hydrogen bonds : angle 5.21886 ( 1584) covalent geometry : bond 0.00620 ( 9158) covalent geometry : angle 0.62371 (12462) *********************** 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 436 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 413 time to evaluate : 2.091 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: A 40 MET cc_start: 0.8097 (ttm) cc_final: 0.7829 (ttm) REVERT: A 63 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 67 SER cc_start: 0.9017 (m) cc_final: 0.8813 (t) REVERT: A 69 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7778 (mtt180) REVERT: A 113 PHE cc_start: 0.8313 (t80) cc_final: 0.8001 (t80) REVERT: A 140 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 162 VAL cc_start: 0.8539 (t) cc_final: 0.8096 (m) REVERT: A 307 GLN cc_start: 0.7914 (tp40) cc_final: 0.7497 (tp40) REVERT: A 312 LYS cc_start: 0.8601 (tptt) cc_final: 0.8324 (tppt) REVERT: A 313 LEU cc_start: 0.8608 (mt) cc_final: 0.8264 (mt) REVERT: B 24 LEU cc_start: 0.8964 (mt) cc_final: 0.8706 (mt) REVERT: B 31 THR cc_start: 0.8494 (t) cc_final: 0.8214 (m) REVERT: B 40 LYS cc_start: 0.8402 (mttm) cc_final: 0.8100 (mtmm) REVERT: G 44 LEU cc_start: 0.8673 (tp) cc_final: 0.8390 (tt) REVERT: G 53 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8051 (p) REVERT: E 44 MET cc_start: 0.8242 (tmm) cc_final: 0.7843 (tmm) REVERT: E 131 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7963 (mtt-85) REVERT: E 162 VAL cc_start: 0.8738 (t) cc_final: 0.8421 (m) REVERT: E 227 TYR cc_start: 0.8440 (t80) cc_final: 0.8113 (t80) REVERT: E 283 LEU cc_start: 0.8675 (mt) cc_final: 0.8449 (mp) REVERT: E 348 MET cc_start: 0.8513 (mmm) cc_final: 0.8218 (mmm) REVERT: D 66 ASP cc_start: 0.7934 (t0) cc_final: 0.7448 (t0) REVERT: D 73 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7987 (mm-30) REVERT: D 95 ARG cc_start: 0.6917 (mtt180) cc_final: 0.6212 (mtt180) REVERT: D 99 GLU cc_start: 0.7034 (mp0) cc_final: 0.6436 (mp0) REVERT: D 108 GLU cc_start: 0.7252 (tt0) cc_final: 0.6613 (tt0) REVERT: C 81 LYS cc_start: 0.8542 (tttt) cc_final: 0.8290 (tttt) REVERT: C 89 GLU cc_start: 0.7371 (tt0) cc_final: 0.7083 (tt0) REVERT: C 112 VAL cc_start: 0.8952 (p) cc_final: 0.8708 (t) REVERT: C 128 GLN cc_start: 0.7018 (mt0) cc_final: 0.6697 (mt0) outliers start: 23 outliers final: 14 residues processed: 419 average time/residue: 0.5197 time to fit residues: 298.1653 Evaluate side-chains 422 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 406 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 MET 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 62 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115311 restraints weight = 39717.242| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.40 r_work: 0.3315 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3981 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= 0.147 Angle : 0.526 6.027 12462 Z= 0.279 Chirality : 0.040 0.145 1458 Planarity : 0.004 0.052 1540 Dihedral : 4.465 20.985 1230 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.89 % Allowed : 16.56 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1136 helix: 1.42 (0.20), residues: 640 sheet: -0.41 (0.54), residues: 102 loop : -0.25 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 99 HIS 0.003 0.001 HIS E 327 PHE 0.013 0.001 PHE C 84 TYR 0.013 0.001 TYR E 149 ARG 0.003 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 551) hydrogen bonds : angle 4.80590 ( 1584) covalent geometry : bond 0.00302 ( 9158) covalent geometry : angle 0.52588 (12462) *********************** 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 415 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 397 time to evaluate : 1.371 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: A 40 MET cc_start: 0.8091 (ttm) cc_final: 0.7836 (ttm) REVERT: A 44 MET cc_start: 0.7740 (ttp) cc_final: 0.7329 (ttp) REVERT: A 63 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 113 PHE cc_start: 0.8222 (t80) cc_final: 0.7906 (t80) REVERT: A 140 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 162 VAL cc_start: 0.8487 (t) cc_final: 0.8008 (m) REVERT: A 227 TYR cc_start: 0.8535 (t80) cc_final: 0.8249 (t80) REVERT: A 312 LYS cc_start: 0.8505 (tptt) cc_final: 0.8193 (tppt) REVERT: B 24 LEU cc_start: 0.8898 (mt) cc_final: 0.8617 (mt) REVERT: B 31 THR cc_start: 0.8338 (t) cc_final: 0.8064 (m) REVERT: B 40 LYS cc_start: 0.8305 (mttm) cc_final: 0.7988 (mtmm) REVERT: E 44 MET cc_start: 0.8145 (tmm) cc_final: 0.7696 (tmm) REVERT: E 81 THR cc_start: 0.8694 (t) cc_final: 0.8365 (p) REVERT: E 131 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7834 (mtt-85) REVERT: E 138 SER cc_start: 0.8534 (m) cc_final: 0.8226 (p) REVERT: E 162 VAL cc_start: 0.8684 (t) cc_final: 0.8441 (m) REVERT: E 174 LEU cc_start: 0.8025 (mp) cc_final: 0.7763 (mm) REVERT: E 227 TYR cc_start: 0.8385 (t80) cc_final: 0.8072 (t80) REVERT: E 283 LEU cc_start: 0.8678 (mt) cc_final: 0.8446 (mp) REVERT: E 302 LEU cc_start: 0.8582 (tp) cc_final: 0.8302 (tt) REVERT: E 348 MET cc_start: 0.8459 (mmm) cc_final: 0.8169 (mmm) REVERT: D 1 MET cc_start: 0.1530 (ptm) cc_final: -0.3973 (mmm) REVERT: D 66 ASP cc_start: 0.7940 (t0) cc_final: 0.7553 (t70) REVERT: D 73 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7950 (mm-30) REVERT: D 95 ARG cc_start: 0.6937 (mtt180) cc_final: 0.6307 (mtt180) REVERT: D 99 GLU cc_start: 0.7003 (mp0) cc_final: 0.6389 (mp0) REVERT: D 108 GLU cc_start: 0.7259 (tt0) cc_final: 0.6642 (tt0) REVERT: C 81 LYS cc_start: 0.8452 (tttt) cc_final: 0.8182 (tttt) REVERT: C 89 GLU cc_start: 0.7268 (tt0) cc_final: 0.7019 (tt0) REVERT: C 112 VAL cc_start: 0.8926 (p) cc_final: 0.8681 (t) REVERT: C 128 GLN cc_start: 0.6947 (mt0) cc_final: 0.6620 (mt0) outliers start: 18 outliers final: 11 residues processed: 401 average time/residue: 0.5227 time to fit residues: 285.3892 Evaluate side-chains 406 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 394 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 117 TYR 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 79 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 77 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.142951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114875 restraints weight = 40098.886| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.35 r_work: 0.3319 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4155 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= 0.141 Angle : 0.520 6.370 12462 Z= 0.273 Chirality : 0.039 0.136 1458 Planarity : 0.004 0.055 1540 Dihedral : 4.327 20.932 1230 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 17.19 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1136 helix: 1.53 (0.20), residues: 640 sheet: -0.40 (0.54), residues: 102 loop : -0.26 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 99 HIS 0.003 0.001 HIS A 325 PHE 0.016 0.001 PHE E 182 TYR 0.013 0.001 TYR E 232 ARG 0.005 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 551) hydrogen bonds : angle 4.72852 ( 1584) covalent geometry : bond 0.00292 ( 9158) covalent geometry : angle 0.51987 (12462) *********************** 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 407 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 388 time to evaluate : 1.288 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: 0.8093 (ttm) cc_final: 0.7813 (ttm) REVERT: A 48 LEU cc_start: 0.8562 (mt) cc_final: 0.8310 (mp) REVERT: A 63 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 113 PHE cc_start: 0.8234 (t80) cc_final: 0.7937 (t80) REVERT: A 140 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 227 TYR cc_start: 0.8524 (t80) cc_final: 0.8229 (t80) REVERT: A 312 LYS cc_start: 0.8504 (tptt) cc_final: 0.8186 (tppt) REVERT: A 317 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6621 (ptt-90) REVERT: B 24 LEU cc_start: 0.8876 (mt) cc_final: 0.8599 (mt) REVERT: B 31 THR cc_start: 0.8342 (t) cc_final: 0.8091 (m) REVERT: B 40 LYS cc_start: 0.8330 (mttm) cc_final: 0.8002 (mtmm) REVERT: E 81 THR cc_start: 0.8718 (t) cc_final: 0.8396 (p) REVERT: E 131 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7782 (mtt-85) REVERT: E 162 VAL cc_start: 0.8679 (t) cc_final: 0.8428 (m) REVERT: E 174 LEU cc_start: 0.8000 (mp) cc_final: 0.7740 (mm) REVERT: E 227 TYR cc_start: 0.8391 (t80) cc_final: 0.8083 (t80) REVERT: E 302 LEU cc_start: 0.8614 (tp) cc_final: 0.8332 (tt) REVERT: D 1 MET cc_start: 0.1740 (ptm) cc_final: -0.3847 (mmm) REVERT: D 16 ARG cc_start: 0.6569 (mtm-85) cc_final: 0.6073 (mtm-85) REVERT: D 66 ASP cc_start: 0.7942 (t0) cc_final: 0.7557 (t70) REVERT: D 73 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7952 (mm-30) REVERT: D 95 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6424 (mtt180) REVERT: D 99 GLU cc_start: 0.7040 (mp0) cc_final: 0.6401 (mp0) REVERT: D 108 GLU cc_start: 0.7192 (tt0) cc_final: 0.6682 (tt0) REVERT: C 81 LYS cc_start: 0.8448 (tttt) cc_final: 0.8180 (tttt) REVERT: C 89 GLU cc_start: 0.7355 (tt0) cc_final: 0.7091 (tt0) REVERT: C 112 VAL cc_start: 0.8934 (p) cc_final: 0.8688 (t) REVERT: C 128 GLN cc_start: 0.6978 (mt0) cc_final: 0.6450 (mt0) outliers start: 19 outliers final: 15 residues processed: 394 average time/residue: 0.5278 time to fit residues: 281.8984 Evaluate side-chains 401 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 384 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 85 MET 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 60 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114074 restraints weight = 40227.893| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.36 r_work: 0.3289 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9158 Z= 0.210 Angle : 0.547 5.810 12462 Z= 0.294 Chirality : 0.040 0.137 1458 Planarity : 0.004 0.054 1540 Dihedral : 4.425 21.116 1230 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.35 % Allowed : 16.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1136 helix: 1.40 (0.20), residues: 636 sheet: -0.49 (0.50), residues: 111 loop : -0.31 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 4 HIS 0.004 0.001 HIS E 235 PHE 0.018 0.001 PHE A 264 TYR 0.017 0.001 TYR E 232 ARG 0.003 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 551) hydrogen bonds : angle 4.82762 ( 1584) covalent geometry : bond 0.00431 ( 9158) covalent geometry : angle 0.54686 (12462) *********************** 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 435 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 403 time to evaluate : 1.281 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: A 40 MET cc_start: 0.8087 (ttm) cc_final: 0.7812 (ttm) REVERT: A 63 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 113 PHE cc_start: 0.8258 (t80) cc_final: 0.7956 (t80) REVERT: A 140 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8381 (tp) REVERT: A 227 TYR cc_start: 0.8551 (t80) cc_final: 0.8235 (t80) REVERT: A 312 LYS cc_start: 0.8569 (tptt) cc_final: 0.8246 (tppt) REVERT: A 317 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6601 (ptt-90) REVERT: B 24 LEU cc_start: 0.8905 (mt) cc_final: 0.8630 (mt) REVERT: B 31 THR cc_start: 0.8373 (t) cc_final: 0.8145 (m) REVERT: B 40 LYS cc_start: 0.8406 (mttm) cc_final: 0.8057 (mtmm) REVERT: G 53 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7889 (p) REVERT: E 81 THR cc_start: 0.8766 (t) cc_final: 0.8419 (p) REVERT: E 131 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7762 (mtt-85) REVERT: E 138 SER cc_start: 0.8536 (m) cc_final: 0.8239 (p) REVERT: E 162 VAL cc_start: 0.8689 (t) cc_final: 0.8445 (m) REVERT: E 174 LEU cc_start: 0.8086 (mp) cc_final: 0.7825 (mm) REVERT: E 227 TYR cc_start: 0.8385 (t80) cc_final: 0.8076 (t80) REVERT: E 283 LEU cc_start: 0.8646 (mt) cc_final: 0.8433 (mp) REVERT: D 1 MET cc_start: 0.1746 (ptm) cc_final: -0.3880 (mmm) REVERT: D 66 ASP cc_start: 0.7965 (t0) cc_final: 0.7563 (t70) REVERT: D 73 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7937 (mm-30) REVERT: D 77 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7399 (mm-40) REVERT: D 95 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6744 (mtt180) REVERT: D 99 GLU cc_start: 0.7082 (mp0) cc_final: 0.6474 (mp0) REVERT: D 108 GLU cc_start: 0.7278 (tt0) cc_final: 0.6833 (tt0) REVERT: C 81 LYS cc_start: 0.8532 (tttt) cc_final: 0.8244 (tttt) REVERT: C 89 GLU cc_start: 0.7421 (tt0) cc_final: 0.7166 (tt0) REVERT: C 112 VAL cc_start: 0.8986 (p) cc_final: 0.8750 (t) REVERT: C 128 GLN cc_start: 0.7140 (mt0) cc_final: 0.6581 (mt0) REVERT: C 149 HIS cc_start: 0.6554 (m-70) cc_final: 0.5945 (m-70) outliers start: 32 outliers final: 24 residues processed: 411 average time/residue: 0.5150 time to fit residues: 286.6592 Evaluate side-chains 423 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 396 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR 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 76 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain C residue 22 LEU 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 108 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113777 restraints weight = 40182.491| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.34 r_work: 0.3296 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9158 Z= 0.162 Angle : 0.537 5.858 12462 Z= 0.283 Chirality : 0.040 0.134 1458 Planarity : 0.004 0.052 1540 Dihedral : 4.342 21.141 1230 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.83 % Allowed : 17.61 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1136 helix: 1.47 (0.20), residues: 636 sheet: -0.48 (0.50), residues: 111 loop : -0.28 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 136 HIS 0.003 0.001 HIS A 325 PHE 0.018 0.001 PHE E 182 TYR 0.017 0.001 TYR E 232 ARG 0.002 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 551) hydrogen bonds : angle 4.73000 ( 1584) covalent geometry : bond 0.00338 ( 9158) covalent geometry : angle 0.53735 (12462) *********************** 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 411 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 384 time to evaluate : 1.474 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 40 MET cc_start: 0.8088 (ttm) cc_final: 0.7821 (ttm) REVERT: A 63 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 113 PHE cc_start: 0.8245 (t80) cc_final: 0.7952 (t80) REVERT: A 140 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8359 (tp) REVERT: A 227 TYR cc_start: 0.8576 (t80) cc_final: 0.8277 (t80) REVERT: A 312 LYS cc_start: 0.8559 (tptt) cc_final: 0.8226 (tppt) REVERT: A 317 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6587 (ptt-90) REVERT: B 24 LEU cc_start: 0.8869 (mt) cc_final: 0.8605 (mt) REVERT: B 31 THR cc_start: 0.8374 (t) cc_final: 0.8160 (m) REVERT: B 40 LYS cc_start: 0.8399 (mttm) cc_final: 0.8049 (mtmm) REVERT: G 53 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.7878 (p) REVERT: E 81 THR cc_start: 0.8753 (t) cc_final: 0.8421 (p) REVERT: E 131 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7757 (mtt-85) REVERT: E 162 VAL cc_start: 0.8687 (t) cc_final: 0.8478 (m) REVERT: E 174 LEU cc_start: 0.8040 (mp) cc_final: 0.7786 (mm) REVERT: E 227 TYR cc_start: 0.8381 (t80) cc_final: 0.8072 (t80) REVERT: E 283 LEU cc_start: 0.8637 (mt) cc_final: 0.8402 (mp) REVERT: D 1 MET cc_start: 0.1794 (ptm) cc_final: -0.3801 (mmm) REVERT: D 66 ASP cc_start: 0.7964 (t0) cc_final: 0.7580 (t70) REVERT: D 73 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 77 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7415 (mm-40) REVERT: D 95 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6834 (mtt180) REVERT: D 99 GLU cc_start: 0.7096 (mp0) cc_final: 0.6479 (mp0) REVERT: D 108 GLU cc_start: 0.7323 (tt0) cc_final: 0.6872 (tt0) REVERT: C 81 LYS cc_start: 0.8572 (tttt) cc_final: 0.8269 (tttt) REVERT: C 89 GLU cc_start: 0.7520 (tt0) cc_final: 0.7215 (tt0) REVERT: C 112 VAL cc_start: 0.8996 (p) cc_final: 0.8755 (t) REVERT: C 128 GLN cc_start: 0.7211 (mt0) cc_final: 0.6634 (mt0) REVERT: C 149 HIS cc_start: 0.6562 (m-70) cc_final: 0.5945 (m-70) outliers start: 27 outliers final: 23 residues processed: 392 average time/residue: 0.5048 time to fit residues: 264.9929 Evaluate side-chains 408 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 382 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 189 ASN 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 14 GLN Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 85 MET 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 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114885 restraints weight = 40166.258| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.41 r_work: 0.3306 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9158 Z= 0.130 Angle : 0.518 5.915 12462 Z= 0.270 Chirality : 0.039 0.133 1458 Planarity : 0.004 0.051 1540 Dihedral : 4.214 20.975 1230 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.94 % Allowed : 17.82 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1136 helix: 1.61 (0.20), residues: 636 sheet: -0.53 (0.50), residues: 111 loop : -0.20 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 136 HIS 0.003 0.001 HIS A 325 PHE 0.018 0.001 PHE E 182 TYR 0.016 0.001 TYR E 232 ARG 0.002 0.000 ARG E 360 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 551) hydrogen bonds : angle 4.60316 ( 1584) covalent geometry : bond 0.00272 ( 9158) covalent geometry : angle 0.51814 (12462) *********************** 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 411 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 383 time to evaluate : 1.262 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 48 LEU cc_start: 0.8556 (mt) cc_final: 0.8305 (mp) REVERT: A 63 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 113 PHE cc_start: 0.8219 (t80) cc_final: 0.7936 (t80) REVERT: A 140 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8334 (tp) REVERT: A 227 TYR cc_start: 0.8547 (t80) cc_final: 0.8253 (t80) REVERT: A 312 LYS cc_start: 0.8533 (tptt) cc_final: 0.8197 (tppt) REVERT: A 317 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6568 (ptt-90) REVERT: B 24 LEU cc_start: 0.8851 (mt) cc_final: 0.8583 (mt) REVERT: B 40 LYS cc_start: 0.8346 (mttm) cc_final: 0.7984 (mtmm) REVERT: E 44 MET cc_start: 0.8177 (tmm) cc_final: 0.7705 (tmm) REVERT: E 81 THR cc_start: 0.8731 (t) cc_final: 0.8367 (p) REVERT: E 131 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7696 (mtt-85) REVERT: E 162 VAL cc_start: 0.8686 (t) cc_final: 0.8411 (m) REVERT: E 174 LEU cc_start: 0.7971 (mp) cc_final: 0.7729 (mm) REVERT: E 176 TYR cc_start: 0.8703 (t80) cc_final: 0.7926 (t80) REVERT: E 227 TYR cc_start: 0.8350 (t80) cc_final: 0.8075 (t80) REVERT: E 283 LEU cc_start: 0.8637 (mt) cc_final: 0.8358 (mp) REVERT: E 317 ARG cc_start: 0.7829 (mtt180) cc_final: 0.7562 (mtt180) REVERT: D 1 MET cc_start: 0.1914 (ptm) cc_final: -0.3608 (mmm) REVERT: D 66 ASP cc_start: 0.8003 (t0) cc_final: 0.7623 (t70) REVERT: D 73 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7953 (mm-30) REVERT: D 77 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7446 (mm-40) REVERT: D 95 ARG cc_start: 0.7287 (mtt180) cc_final: 0.6776 (mtt180) REVERT: D 99 GLU cc_start: 0.7062 (mp0) cc_final: 0.6423 (mp0) REVERT: D 108 GLU cc_start: 0.7343 (tt0) cc_final: 0.6965 (tt0) REVERT: C 89 GLU cc_start: 0.7515 (tt0) cc_final: 0.7205 (tt0) REVERT: C 112 VAL cc_start: 0.8995 (p) cc_final: 0.8759 (t) REVERT: C 128 GLN cc_start: 0.7162 (mt0) cc_final: 0.6600 (mt0) REVERT: C 149 HIS cc_start: 0.6544 (m-70) cc_final: 0.5970 (m-70) outliers start: 28 outliers final: 26 residues processed: 391 average time/residue: 0.5672 time to fit residues: 300.9385 Evaluate side-chains 410 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 382 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 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 B residue 30 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 189 ASN 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 76 VAL Chi-restraints excluded: chain C residue 22 LEU 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 108 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 ASN C 123 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113426 restraints weight = 40284.164| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.41 r_work: 0.3254 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9158 Z= 0.193 Angle : 0.548 5.843 12462 Z= 0.291 Chirality : 0.040 0.135 1458 Planarity : 0.004 0.066 1540 Dihedral : 4.309 20.920 1230 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.73 % Allowed : 18.66 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1136 helix: 1.47 (0.20), residues: 637 sheet: -0.65 (0.50), residues: 111 loop : -0.32 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 4 HIS 0.004 0.001 HIS A 325 PHE 0.021 0.001 PHE E 19 TYR 0.017 0.001 TYR E 232 ARG 0.003 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 551) hydrogen bonds : angle 4.70513 ( 1584) covalent geometry : bond 0.00399 ( 9158) covalent geometry : angle 0.54786 (12462) *********************** 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 415 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 389 time to evaluate : 1.350 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: A 40 MET cc_start: 0.8082 (ttm) cc_final: 0.7845 (ttm) REVERT: A 63 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 113 PHE cc_start: 0.8265 (t80) cc_final: 0.7962 (t80) REVERT: A 140 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8304 (tp) REVERT: A 312 LYS cc_start: 0.8567 (tptt) cc_final: 0.8214 (tppt) REVERT: A 317 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6597 (ptt-90) REVERT: B 24 LEU cc_start: 0.8855 (mt) cc_final: 0.8588 (mt) REVERT: B 40 LYS cc_start: 0.8417 (mttm) cc_final: 0.8048 (mtmm) REVERT: G 53 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7901 (p) REVERT: E 7 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7288 (mt-10) REVERT: E 81 THR cc_start: 0.8778 (t) cc_final: 0.8421 (p) REVERT: E 131 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7775 (mtt-85) REVERT: E 162 VAL cc_start: 0.8685 (t) cc_final: 0.8391 (m) REVERT: E 174 LEU cc_start: 0.8024 (mp) cc_final: 0.7762 (mm) REVERT: E 176 TYR cc_start: 0.8680 (t80) cc_final: 0.7836 (t80) REVERT: E 227 TYR cc_start: 0.8357 (t80) cc_final: 0.8086 (t80) REVERT: E 283 LEU cc_start: 0.8642 (mt) cc_final: 0.8397 (mp) REVERT: E 317 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7584 (mtt180) REVERT: D 1 MET cc_start: 0.2013 (ptm) cc_final: -0.3586 (mmm) REVERT: D 66 ASP cc_start: 0.8031 (t0) cc_final: 0.7651 (t70) REVERT: D 73 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7906 (mm-30) REVERT: D 77 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7459 (mm-40) REVERT: D 95 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6795 (mtt180) REVERT: D 97 LEU cc_start: 0.8045 (tp) cc_final: 0.7816 (tp) REVERT: D 99 GLU cc_start: 0.7052 (mp0) cc_final: 0.6427 (mp0) REVERT: D 108 GLU cc_start: 0.7330 (tt0) cc_final: 0.6979 (tt0) REVERT: C 89 GLU cc_start: 0.7557 (tt0) cc_final: 0.7246 (tt0) REVERT: C 112 VAL cc_start: 0.9018 (p) cc_final: 0.8772 (t) REVERT: C 128 GLN cc_start: 0.7290 (mt0) cc_final: 0.6735 (mt0) REVERT: C 149 HIS cc_start: 0.6611 (m-70) cc_final: 0.6020 (m-70) outliers start: 26 outliers final: 22 residues processed: 396 average time/residue: 0.5176 time to fit residues: 276.2860 Evaluate side-chains 407 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 382 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 189 ASN 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 76 VAL 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 78 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 257 ASN C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113721 restraints weight = 40181.060| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.36 r_work: 0.3293 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4818 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= 0.159 Angle : 0.538 5.906 12462 Z= 0.282 Chirality : 0.040 0.138 1458 Planarity : 0.004 0.057 1540 Dihedral : 4.277 20.664 1230 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.73 % Allowed : 19.71 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1136 helix: 1.53 (0.20), residues: 636 sheet: -0.66 (0.50), residues: 111 loop : -0.34 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 136 HIS 0.003 0.001 HIS A 325 PHE 0.018 0.001 PHE A 182 TYR 0.019 0.001 TYR E 232 ARG 0.002 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 551) hydrogen bonds : angle 4.65010 ( 1584) covalent geometry : bond 0.00329 ( 9158) covalent geometry : angle 0.53758 (12462) ********************** 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 411 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 385 time to evaluate : 1.396 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: A 40 MET cc_start: 0.8125 (ttm) cc_final: 0.7880 (ttm) REVERT: A 48 LEU cc_start: 0.8589 (mt) cc_final: 0.8334 (mp) REVERT: A 63 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 113 PHE cc_start: 0.8247 (t80) cc_final: 0.7949 (t80) REVERT: A 140 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8344 (tp) REVERT: A 312 LYS cc_start: 0.8563 (tptt) cc_final: 0.8213 (tppt) REVERT: A 317 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6615 (ptt-90) REVERT: B 24 LEU cc_start: 0.8870 (mt) cc_final: 0.8604 (mt) REVERT: B 40 LYS cc_start: 0.8409 (mttm) cc_final: 0.8040 (mtmm) REVERT: E 7 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7264 (mt-10) REVERT: E 81 THR cc_start: 0.8761 (t) cc_final: 0.8411 (p) REVERT: E 131 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7777 (mtt-85) REVERT: E 162 VAL cc_start: 0.8695 (t) cc_final: 0.8383 (m) REVERT: E 174 LEU cc_start: 0.8000 (mp) cc_final: 0.7752 (mm) REVERT: E 176 TYR cc_start: 0.8693 (t80) cc_final: 0.7570 (t80) REVERT: E 227 TYR cc_start: 0.8367 (t80) cc_final: 0.8079 (t80) REVERT: E 283 LEU cc_start: 0.8657 (mt) cc_final: 0.8407 (mp) REVERT: E 317 ARG cc_start: 0.7873 (mtt180) cc_final: 0.7638 (mtt180) REVERT: D 1 MET cc_start: 0.2049 (ptm) cc_final: -0.3482 (mmm) REVERT: D 66 ASP cc_start: 0.8013 (t0) cc_final: 0.7640 (t70) REVERT: D 73 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7922 (mm-30) REVERT: D 95 ARG cc_start: 0.7386 (mtt180) cc_final: 0.6843 (mtt180) REVERT: D 97 LEU cc_start: 0.8049 (tp) cc_final: 0.7821 (tp) REVERT: D 99 GLU cc_start: 0.7053 (mp0) cc_final: 0.6421 (mp0) REVERT: D 102 GLN cc_start: 0.8033 (mp10) cc_final: 0.7460 (pp30) REVERT: D 108 GLU cc_start: 0.7335 (tt0) cc_final: 0.6952 (tt0) REVERT: C 70 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: C 89 GLU cc_start: 0.7520 (tt0) cc_final: 0.7232 (tt0) REVERT: C 112 VAL cc_start: 0.9016 (p) cc_final: 0.8771 (t) REVERT: C 115 ASP cc_start: 0.7086 (m-30) cc_final: 0.6824 (m-30) REVERT: C 128 GLN cc_start: 0.7310 (mt0) cc_final: 0.6754 (mt0) REVERT: C 149 HIS cc_start: 0.6735 (m-70) cc_final: 0.6122 (m-70) outliers start: 26 outliers final: 20 residues processed: 392 average time/residue: 0.5392 time to fit residues: 286.6675 Evaluate side-chains 408 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 385 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 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 B residue 30 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 189 ASN 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 76 VAL Chi-restraints excluded: chain C residue 70 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 1 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113591 restraints weight = 40051.017| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.35 r_work: 0.3288 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.253 9158 Z= 0.268 Angle : 0.882 59.001 12462 Z= 0.511 Chirality : 0.043 0.556 1458 Planarity : 0.004 0.057 1540 Dihedral : 4.292 20.640 1230 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.62 % Allowed : 20.02 % Favored : 77.36 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1136 helix: 1.53 (0.20), residues: 636 sheet: -0.67 (0.50), residues: 111 loop : -0.34 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 136 HIS 0.004 0.001 HIS A 325 PHE 0.018 0.001 PHE E 288 TYR 0.017 0.001 TYR E 232 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 551) hydrogen bonds : angle 4.64979 ( 1584) covalent geometry : bond 0.00537 ( 9158) covalent geometry : angle 0.88204 (12462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11917.07 seconds wall clock time: 204 minutes 7.99 seconds (12247.99 seconds total)