Starting phenix.real_space_refine on Wed Mar 4 15:27:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk5_25173/03_2026/7sk5_25173_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk5_25173/03_2026/7sk5_25173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sk5_25173/03_2026/7sk5_25173_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk5_25173/03_2026/7sk5_25173_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sk5_25173/03_2026/7sk5_25173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk5_25173/03_2026/7sk5_25173.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.056 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 39 5.16 5 C 4713 2.51 5 N 1163 2.21 5 O 1317 1.98 5 H 6928 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14160 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4915 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain breaks: 1 Chain: "F" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3248 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Chain: "B" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1058 Classifications: {'peptide': 63} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "E" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3206 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain: "K" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1537 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 4 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.19 Number of scatterers: 14160 At special positions: 0 Unit cell: (59.4, 90.72, 160.92, 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 39 16.00 O 1317 8.00 N 1163 7.00 C 4713 6.00 H 6928 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 423.7 milliseconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1702 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 14 sheets defined 31.7% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 40 through 76 removed outlier: 3.911A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.826A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.723A pdb=" N GLN A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 removed outlier: 3.759A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix removed outlier: 3.827A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.589A pdb=" N VAL A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.835A pdb=" N GLU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 4.191A pdb=" N PHE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 316 removed outlier: 4.244A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'B' and resid 55 through 63 removed outlier: 3.509A pdb=" N GLN B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.935A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.578A pdb=" N GLU E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS E 190 " --> pdb=" O ASP E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 184 through 190' Processing helix chain 'K' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 5.908A pdb=" N ASP A 30 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN B 30 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 32 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.904A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.605A pdb=" N LYS A 184 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 197 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AA5, first strand: chain 'F' and resid 61 through 63 removed outlier: 3.771A pdb=" N SER F 53 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL F 102 " --> pdb=" O SER F 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.817A pdb=" N LYS F 160 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.817A pdb=" N LYS F 160 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 168 through 171 removed outlier: 4.859A pdb=" N TYR F 211 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F 228 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS F 213 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS F 226 " --> pdb=" O CYS F 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.256A pdb=" N LEU E 12 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN E 90 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 35 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.195A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.442A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 20 through 22 removed outlier: 3.747A pdb=" N THR K 69 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.435A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET K 34 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR K 95 " --> pdb=" O PHE K 37 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL K 93 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE K 98 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.65 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: 6918 1.03 - 1.23: 43 1.23 - 1.43: 3101 1.43 - 1.62: 4245 1.62 - 1.82: 52 Bond restraints: 14359 Sorted by residual: bond pdb=" C6 CLR A 401 " pdb=" C7 CLR A 401 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C6 CLR A 406 " pdb=" C7 CLR A 406 " ideal model delta sigma weight residual 1.492 1.541 -0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" C6 CLR F 301 " pdb=" C7 CLR F 301 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C6 CLR A 405 " pdb=" C7 CLR A 405 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C6 CLR A 403 " pdb=" C7 CLR A 403 " ideal model delta sigma weight residual 1.492 1.540 -0.048 2.00e-02 2.50e+03 5.66e+00 ... (remaining 14354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 25366 1.56 - 3.13: 342 3.13 - 4.69: 55 4.69 - 6.26: 20 6.26 - 7.82: 8 Bond angle restraints: 25791 Sorted by residual: angle pdb=" C22 CLR A 405 " pdb=" C23 CLR A 405 " pdb=" C24 CLR A 405 " ideal model delta sigma weight residual 111.95 104.13 7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" C22 CLR A 401 " pdb=" C23 CLR A 401 " pdb=" C24 CLR A 401 " ideal model delta sigma weight residual 111.95 104.19 7.76 3.00e+00 1.11e-01 6.70e+00 angle pdb=" C22 CLR A 406 " pdb=" C23 CLR A 406 " pdb=" C24 CLR A 406 " ideal model delta sigma weight residual 111.95 104.35 7.60 3.00e+00 1.11e-01 6.42e+00 angle pdb=" C22 CLR A 404 " pdb=" C23 CLR A 404 " pdb=" C24 CLR A 404 " ideal model delta sigma weight residual 111.95 104.50 7.45 3.00e+00 1.11e-01 6.17e+00 angle pdb=" C22 CLR F 301 " pdb=" C23 CLR F 301 " pdb=" C24 CLR F 301 " ideal model delta sigma weight residual 111.95 104.68 7.27 3.00e+00 1.11e-01 5.87e+00 ... (remaining 25786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6574 17.15 - 34.29: 490 34.29 - 51.44: 127 51.44 - 68.59: 36 68.59 - 85.74: 11 Dihedral angle restraints: 7238 sinusoidal: 4023 harmonic: 3215 Sorted by residual: dihedral pdb=" CB CYS E 24 " pdb=" SG CYS E 24 " pdb=" SG CYS E 89 " pdb=" CB CYS E 89 " ideal model delta sinusoidal sigma weight residual 93.00 62.15 30.85 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CA ARG E 62 " pdb=" CB ARG E 62 " pdb=" CG ARG E 62 " pdb=" CD ARG E 62 " ideal model delta sinusoidal sigma weight residual 180.00 129.14 50.86 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA PHE K 103 " pdb=" C PHE K 103 " pdb=" N TYR K 104 " pdb=" CA TYR K 104 " ideal model delta harmonic sigma weight residual 180.00 165.16 14.84 0 5.00e+00 4.00e-02 8.81e+00 ... (remaining 7235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1049 0.075 - 0.150: 98 0.150 - 0.225: 0 0.225 - 0.300: 10 0.300 - 0.375: 18 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C17 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C16 CLR A 405 " pdb=" C20 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.37 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C17 CLR F 301 " pdb=" C13 CLR F 301 " pdb=" C16 CLR F 301 " pdb=" C20 CLR F 301 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1172 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 141 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO E 142 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 142 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 142 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 120 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO E 121 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 9 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO B 10 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.017 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 639 2.19 - 2.79: 27346 2.79 - 3.39: 36634 3.39 - 4.00: 47129 4.00 - 4.60: 71595 Nonbonded interactions: 183343 Sorted by model distance: nonbonded pdb=" OE1 GLU A 202 " pdb=" H GLU A 202 " model vdw 1.583 2.450 nonbonded pdb=" HD1 HIS F 217 " pdb=" OG SER F 220 " model vdw 1.621 2.450 nonbonded pdb=" OH TYR F 63 " pdb=" H ILE F 73 " model vdw 1.634 2.450 nonbonded pdb=" O ALA F 27 " pdb="HD22 ASN F 80 " model vdw 1.636 2.450 nonbonded pdb=" OD1 ASN F 31 " pdb=" H SER F 33 " model vdw 1.647 2.450 ... (remaining 183338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.004 0.050 7439 Z= 0.208 Angle : 0.628 7.824 10173 Z= 0.265 Chirality : 0.063 0.375 1175 Planarity : 0.003 0.036 1219 Dihedral : 13.452 85.737 2992 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.29), residues: 875 helix: 2.24 (0.33), residues: 235 sheet: 0.24 (0.34), residues: 252 loop : -0.79 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.007 0.001 TYR E 50 PHE 0.008 0.001 PHE F 139 TRP 0.008 0.001 TRP K 36 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 7431) covalent geometry : angle 0.62789 (10157) SS BOND : bond 0.00196 ( 8) SS BOND : angle 0.87092 ( 16) hydrogen bonds : bond 0.24246 ( 321) hydrogen bonds : angle 8.83943 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8452 (mt) cc_final: 0.8250 (mm) REVERT: A 212 MET cc_start: 0.8754 (mmp) cc_final: 0.8518 (tpp) REVERT: A 275 ASP cc_start: 0.8500 (t70) cc_final: 0.8283 (t70) REVERT: A 322 TYR cc_start: 0.9268 (t80) cc_final: 0.9063 (t80) REVERT: F 65 ASP cc_start: 0.8472 (p0) cc_final: 0.8249 (p0) REVERT: B 10 PRO cc_start: 0.9230 (Cg_exo) cc_final: 0.8965 (Cg_endo) REVERT: K 34 MET cc_start: 0.7539 (mmm) cc_final: 0.7212 (mmm) REVERT: K 36 TRP cc_start: 0.8174 (m100) cc_final: 0.7474 (m100) REVERT: K 47 PHE cc_start: 0.9155 (t80) cc_final: 0.8905 (t80) REVERT: K 81 LEU cc_start: 0.8650 (tp) cc_final: 0.8442 (tp) REVERT: K 98 ILE cc_start: 0.8375 (tp) cc_final: 0.8049 (tp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1680 time to fit residues: 37.4079 Evaluate side-chains 144 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.135544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100410 restraints weight = 37202.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104841 restraints weight = 15506.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107502 restraints weight = 9134.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108737 restraints weight = 6757.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109769 restraints weight = 5830.481| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7439 Z= 0.141 Angle : 0.545 5.352 10173 Z= 0.294 Chirality : 0.041 0.143 1175 Planarity : 0.004 0.037 1219 Dihedral : 5.391 47.096 1426 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.01 % Allowed : 7.19 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.30), residues: 875 helix: 2.11 (0.33), residues: 239 sheet: 0.06 (0.33), residues: 267 loop : -0.83 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 12 TYR 0.013 0.001 TYR F 162 PHE 0.011 0.001 PHE F 139 TRP 0.006 0.001 TRP K 36 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7431) covalent geometry : angle 0.54398 (10157) SS BOND : bond 0.00688 ( 8) SS BOND : angle 0.98009 ( 16) hydrogen bonds : bond 0.06706 ( 321) hydrogen bonds : angle 6.47836 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.377 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: A 205 ILE cc_start: 0.8168 (mt) cc_final: 0.7921 (mm) REVERT: F 9 GLU cc_start: 0.8046 (mp0) cc_final: 0.7836 (mp0) REVERT: F 65 ASP cc_start: 0.8478 (p0) cc_final: 0.8265 (p0) REVERT: F 171 TRP cc_start: 0.8523 (m100) cc_final: 0.8146 (m100) REVERT: F 212 ILE cc_start: 0.8425 (tt) cc_final: 0.8127 (tt) REVERT: B 10 PRO cc_start: 0.9159 (Cg_exo) cc_final: 0.8913 (Cg_endo) REVERT: E 5 MET cc_start: 0.8304 (mmm) cc_final: 0.8068 (mmm) REVERT: K 6 GLU cc_start: 0.7539 (mp0) cc_final: 0.6875 (mp0) REVERT: K 36 TRP cc_start: 0.8230 (m100) cc_final: 0.7701 (m100) REVERT: K 39 GLN cc_start: 0.6720 (tt0) cc_final: 0.5884 (tm-30) outliers start: 8 outliers final: 8 residues processed: 152 average time/residue: 0.1614 time to fit residues: 34.1216 Evaluate side-chains 149 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 103 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099759 restraints weight = 36663.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104019 restraints weight = 15059.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106588 restraints weight = 8831.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108156 restraints weight = 6504.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108842 restraints weight = 5458.889| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7439 Z= 0.166 Angle : 0.543 5.596 10173 Z= 0.291 Chirality : 0.041 0.160 1175 Planarity : 0.004 0.032 1219 Dihedral : 5.356 46.914 1426 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.26 % Allowed : 11.10 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.29), residues: 875 helix: 1.97 (0.32), residues: 246 sheet: -0.04 (0.33), residues: 261 loop : -1.08 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 143 TYR 0.010 0.001 TYR E 50 PHE 0.018 0.001 PHE K 47 TRP 0.006 0.001 TRP E 149 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7431) covalent geometry : angle 0.54232 (10157) SS BOND : bond 0.00454 ( 8) SS BOND : angle 0.93961 ( 16) hydrogen bonds : bond 0.06002 ( 321) hydrogen bonds : angle 5.91867 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.387 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: A 205 ILE cc_start: 0.8175 (mt) cc_final: 0.7924 (mm) REVERT: A 213 GLU cc_start: 0.9055 (tp30) cc_final: 0.8786 (mm-30) REVERT: A 322 TYR cc_start: 0.9394 (t80) cc_final: 0.9130 (t80) REVERT: F 65 ASP cc_start: 0.8491 (p0) cc_final: 0.8266 (p0) REVERT: F 160 LYS cc_start: 0.8779 (ptmm) cc_final: 0.8451 (ptmm) REVERT: F 171 TRP cc_start: 0.8559 (m100) cc_final: 0.8124 (m100) REVERT: B 10 PRO cc_start: 0.9272 (Cg_exo) cc_final: 0.9050 (Cg_endo) REVERT: E 5 MET cc_start: 0.8329 (mmm) cc_final: 0.8076 (mmm) REVERT: E 149 TRP cc_start: 0.8845 (m100) cc_final: 0.8446 (m100) REVERT: K 6 GLU cc_start: 0.7517 (mp0) cc_final: 0.7046 (mp0) REVERT: K 36 TRP cc_start: 0.8345 (m100) cc_final: 0.7850 (m100) REVERT: K 39 GLN cc_start: 0.6729 (tt0) cc_final: 0.5924 (tm-30) outliers start: 10 outliers final: 8 residues processed: 152 average time/residue: 0.1586 time to fit residues: 33.7818 Evaluate side-chains 147 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 103 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.099086 restraints weight = 36394.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103355 restraints weight = 15097.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.105946 restraints weight = 8783.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107410 restraints weight = 6419.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108291 restraints weight = 5406.449| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7439 Z= 0.186 Angle : 0.550 5.212 10173 Z= 0.295 Chirality : 0.041 0.171 1175 Planarity : 0.004 0.032 1219 Dihedral : 5.573 51.358 1426 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.64 % Allowed : 12.74 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.29), residues: 875 helix: 1.90 (0.33), residues: 240 sheet: -0.07 (0.32), residues: 268 loop : -1.18 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.012 0.001 TYR E 50 PHE 0.009 0.001 PHE F 139 TRP 0.005 0.001 TRP E 149 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7431) covalent geometry : angle 0.54887 (10157) SS BOND : bond 0.00345 ( 8) SS BOND : angle 1.03829 ( 16) hydrogen bonds : bond 0.05676 ( 321) hydrogen bonds : angle 5.65475 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.386 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: A 213 GLU cc_start: 0.9073 (tp30) cc_final: 0.8826 (mm-30) REVERT: F 65 ASP cc_start: 0.8524 (p0) cc_final: 0.8313 (p0) REVERT: F 160 LYS cc_start: 0.8795 (ptmm) cc_final: 0.8466 (ptmm) REVERT: F 171 TRP cc_start: 0.8617 (m100) cc_final: 0.8164 (m100) REVERT: B 10 PRO cc_start: 0.9163 (Cg_exo) cc_final: 0.8914 (Cg_endo) REVERT: E 5 MET cc_start: 0.8472 (mmm) cc_final: 0.8251 (mmm) REVERT: K 6 GLU cc_start: 0.7528 (mp0) cc_final: 0.6747 (mp0) REVERT: K 36 TRP cc_start: 0.8355 (m100) cc_final: 0.7836 (m100) REVERT: K 39 GLN cc_start: 0.6771 (tt0) cc_final: 0.5937 (tm-30) REVERT: K 103 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8384 (t80) outliers start: 13 outliers final: 12 residues processed: 153 average time/residue: 0.1607 time to fit residues: 34.6552 Evaluate side-chains 154 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.133214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098954 restraints weight = 36704.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103190 restraints weight = 15135.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105815 restraints weight = 8853.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107104 restraints weight = 6478.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108092 restraints weight = 5525.803| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7439 Z= 0.190 Angle : 0.552 5.441 10173 Z= 0.296 Chirality : 0.041 0.156 1175 Planarity : 0.004 0.032 1219 Dihedral : 5.670 52.020 1426 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.77 % Allowed : 14.50 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.29), residues: 875 helix: 1.87 (0.33), residues: 241 sheet: -0.17 (0.32), residues: 272 loop : -1.27 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 22 TYR 0.013 0.001 TYR E 50 PHE 0.010 0.001 PHE F 139 TRP 0.018 0.001 TRP E 149 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 7431) covalent geometry : angle 0.55149 (10157) SS BOND : bond 0.00342 ( 8) SS BOND : angle 0.90661 ( 16) hydrogen bonds : bond 0.05639 ( 321) hydrogen bonds : angle 5.55948 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.371 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: A 322 TYR cc_start: 0.9357 (t80) cc_final: 0.9033 (t80) REVERT: F 65 ASP cc_start: 0.8523 (p0) cc_final: 0.8317 (p0) REVERT: F 171 TRP cc_start: 0.8638 (m100) cc_final: 0.8182 (m100) REVERT: B 10 PRO cc_start: 0.9209 (Cg_exo) cc_final: 0.8933 (Cg_endo) REVERT: K 6 GLU cc_start: 0.7537 (mp0) cc_final: 0.6831 (mp0) REVERT: K 36 TRP cc_start: 0.8324 (m100) cc_final: 0.7748 (m100) REVERT: K 39 GLN cc_start: 0.6783 (tt0) cc_final: 0.5944 (tm-30) REVERT: K 103 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8365 (t80) outliers start: 14 outliers final: 12 residues processed: 150 average time/residue: 0.1562 time to fit residues: 32.8933 Evaluate side-chains 154 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.0470 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100995 restraints weight = 36251.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105310 restraints weight = 14650.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107956 restraints weight = 8473.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109341 restraints weight = 6163.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110296 restraints weight = 5194.926| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7439 Z= 0.124 Angle : 0.510 5.992 10173 Z= 0.270 Chirality : 0.040 0.158 1175 Planarity : 0.003 0.031 1219 Dihedral : 5.513 53.707 1426 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.77 % Allowed : 15.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.29), residues: 875 helix: 2.12 (0.33), residues: 241 sheet: -0.14 (0.32), residues: 272 loop : -1.24 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 101 TYR 0.011 0.001 TYR E 50 PHE 0.009 0.001 PHE F 139 TRP 0.011 0.001 TRP E 149 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7431) covalent geometry : angle 0.50883 (10157) SS BOND : bond 0.00555 ( 8) SS BOND : angle 0.88665 ( 16) hydrogen bonds : bond 0.05135 ( 321) hydrogen bonds : angle 5.30255 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.535 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: A 205 ILE cc_start: 0.8124 (mt) cc_final: 0.7871 (mm) REVERT: F 65 ASP cc_start: 0.8454 (p0) cc_final: 0.8240 (p0) REVERT: F 160 LYS cc_start: 0.8802 (ptmm) cc_final: 0.8512 (ptmm) REVERT: F 171 TRP cc_start: 0.8633 (m100) cc_final: 0.8204 (m100) REVERT: B 10 PRO cc_start: 0.9144 (Cg_exo) cc_final: 0.8855 (Cg_endo) REVERT: K 6 GLU cc_start: 0.7499 (mp0) cc_final: 0.6829 (mp0) REVERT: K 36 TRP cc_start: 0.8336 (m100) cc_final: 0.7871 (m100) REVERT: K 39 GLN cc_start: 0.6742 (tt0) cc_final: 0.5923 (tm-30) outliers start: 14 outliers final: 11 residues processed: 158 average time/residue: 0.1535 time to fit residues: 34.3313 Evaluate side-chains 155 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102448 restraints weight = 36174.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106767 restraints weight = 14657.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109459 restraints weight = 8516.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110818 restraints weight = 6206.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111812 restraints weight = 5250.695| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7439 Z= 0.121 Angle : 0.510 7.609 10173 Z= 0.270 Chirality : 0.040 0.153 1175 Planarity : 0.003 0.032 1219 Dihedral : 5.427 52.905 1426 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.77 % Allowed : 16.14 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.29), residues: 875 helix: 2.24 (0.33), residues: 241 sheet: -0.14 (0.32), residues: 272 loop : -1.23 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 101 TYR 0.011 0.001 TYR E 50 PHE 0.010 0.001 PHE F 139 TRP 0.024 0.001 TRP E 149 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7431) covalent geometry : angle 0.50921 (10157) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.02863 ( 16) hydrogen bonds : bond 0.04890 ( 321) hydrogen bonds : angle 5.18696 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8069 (mt) cc_final: 0.7820 (mm) REVERT: F 65 ASP cc_start: 0.8440 (p0) cc_final: 0.8224 (p0) REVERT: F 160 LYS cc_start: 0.8768 (ptmm) cc_final: 0.8460 (ptmm) REVERT: F 171 TRP cc_start: 0.8631 (m100) cc_final: 0.8182 (m100) REVERT: K 6 GLU cc_start: 0.7493 (mp0) cc_final: 0.6824 (mp0) REVERT: K 36 TRP cc_start: 0.8318 (m100) cc_final: 0.7842 (m100) REVERT: K 39 GLN cc_start: 0.6771 (tt0) cc_final: 0.5950 (tm-30) outliers start: 14 outliers final: 13 residues processed: 153 average time/residue: 0.1602 time to fit residues: 34.3485 Evaluate side-chains 158 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 30 ASN B 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.134722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100788 restraints weight = 36307.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105054 restraints weight = 14856.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107690 restraints weight = 8653.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109197 restraints weight = 6308.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109800 restraints weight = 5301.904| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7439 Z= 0.148 Angle : 0.530 9.900 10173 Z= 0.279 Chirality : 0.040 0.152 1175 Planarity : 0.004 0.065 1219 Dihedral : 5.481 52.145 1426 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.89 % Allowed : 16.90 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.29), residues: 875 helix: 2.17 (0.33), residues: 241 sheet: -0.14 (0.32), residues: 272 loop : -1.25 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 212 TYR 0.011 0.001 TYR E 50 PHE 0.015 0.001 PHE F 139 TRP 0.011 0.001 TRP E 149 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7431) covalent geometry : angle 0.52790 (10157) SS BOND : bond 0.00315 ( 8) SS BOND : angle 1.17665 ( 16) hydrogen bonds : bond 0.04950 ( 321) hydrogen bonds : angle 5.20263 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8093 (mt) cc_final: 0.7846 (mm) REVERT: A 322 TYR cc_start: 0.9240 (t80) cc_final: 0.8835 (t80) REVERT: F 65 ASP cc_start: 0.8458 (p0) cc_final: 0.8224 (p0) REVERT: F 160 LYS cc_start: 0.8768 (ptmm) cc_final: 0.8436 (ptmm) REVERT: B 8 ARG cc_start: 0.7217 (mmm160) cc_final: 0.7015 (mmt180) REVERT: B 37 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: E 149 TRP cc_start: 0.8889 (m100) cc_final: 0.8339 (m100) REVERT: K 6 GLU cc_start: 0.7562 (mp0) cc_final: 0.6953 (mp0) REVERT: K 36 TRP cc_start: 0.8300 (m100) cc_final: 0.7837 (m100) REVERT: K 39 GLN cc_start: 0.6765 (tt0) cc_final: 0.5949 (tm-30) outliers start: 15 outliers final: 13 residues processed: 153 average time/residue: 0.1625 time to fit residues: 34.6308 Evaluate side-chains 159 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101801 restraints weight = 35915.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106219 restraints weight = 14374.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108865 restraints weight = 8248.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110361 restraints weight = 5994.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111197 restraints weight = 5043.368| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7439 Z= 0.111 Angle : 0.512 10.225 10173 Z= 0.268 Chirality : 0.041 0.169 1175 Planarity : 0.004 0.050 1219 Dihedral : 5.382 52.877 1426 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.77 % Allowed : 16.77 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.29), residues: 875 helix: 2.30 (0.33), residues: 241 sheet: -0.11 (0.32), residues: 267 loop : -1.15 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.010 0.001 TYR E 50 PHE 0.011 0.001 PHE B 14 TRP 0.012 0.001 TRP E 149 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7431) covalent geometry : angle 0.51042 (10157) SS BOND : bond 0.00295 ( 8) SS BOND : angle 1.06079 ( 16) hydrogen bonds : bond 0.04680 ( 321) hydrogen bonds : angle 5.02591 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8067 (mt) cc_final: 0.7803 (mm) REVERT: A 322 TYR cc_start: 0.9245 (t80) cc_final: 0.8850 (t80) REVERT: F 65 ASP cc_start: 0.8401 (p0) cc_final: 0.8184 (p0) REVERT: F 160 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8401 (ptmm) REVERT: B 8 ARG cc_start: 0.7168 (mmm160) cc_final: 0.6956 (mmt180) REVERT: B 37 GLN cc_start: 0.7470 (tp40) cc_final: 0.7199 (tm-30) REVERT: E 149 TRP cc_start: 0.8847 (m100) cc_final: 0.8362 (m100) REVERT: K 6 GLU cc_start: 0.7507 (mp0) cc_final: 0.6870 (mp0) REVERT: K 36 TRP cc_start: 0.8285 (m100) cc_final: 0.7848 (m100) outliers start: 14 outliers final: 14 residues processed: 152 average time/residue: 0.1539 time to fit residues: 32.9522 Evaluate side-chains 159 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 214 ASN B 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102807 restraints weight = 35841.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107137 restraints weight = 14545.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109830 restraints weight = 8440.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111154 restraints weight = 6156.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112150 restraints weight = 5235.492| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 7439 Z= 0.159 Angle : 0.904 59.196 10173 Z= 0.536 Chirality : 0.041 0.279 1175 Planarity : 0.004 0.048 1219 Dihedral : 5.380 52.898 1426 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.51 % Allowed : 17.28 % Favored : 81.21 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 875 helix: 2.30 (0.33), residues: 241 sheet: -0.12 (0.32), residues: 267 loop : -1.15 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 101 TYR 0.010 0.001 TYR E 50 PHE 0.009 0.001 PHE B 14 TRP 0.010 0.001 TRP E 149 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7431) covalent geometry : angle 0.90372 (10157) SS BOND : bond 0.00297 ( 8) SS BOND : angle 1.07413 ( 16) hydrogen bonds : bond 0.04723 ( 321) hydrogen bonds : angle 5.03728 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8074 (mt) cc_final: 0.7806 (mm) REVERT: A 322 TYR cc_start: 0.9246 (t80) cc_final: 0.8850 (t80) REVERT: F 65 ASP cc_start: 0.8408 (p0) cc_final: 0.8185 (p0) REVERT: F 160 LYS cc_start: 0.8741 (ptmm) cc_final: 0.8399 (ptmm) REVERT: B 8 ARG cc_start: 0.7179 (mmm160) cc_final: 0.6959 (mmt180) REVERT: B 37 GLN cc_start: 0.7448 (tp40) cc_final: 0.7166 (tm-30) REVERT: E 149 TRP cc_start: 0.8849 (m100) cc_final: 0.8335 (m100) REVERT: K 6 GLU cc_start: 0.7510 (mp0) cc_final: 0.6874 (mp0) REVERT: K 36 TRP cc_start: 0.8286 (m100) cc_final: 0.7851 (m100) outliers start: 12 outliers final: 11 residues processed: 149 average time/residue: 0.1579 time to fit residues: 33.0421 Evaluate side-chains 156 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102444 restraints weight = 36978.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106855 restraints weight = 15069.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109633 restraints weight = 8802.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111084 restraints weight = 6431.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112118 restraints weight = 5436.241| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 7439 Z= 0.159 Angle : 0.904 59.196 10173 Z= 0.536 Chirality : 0.041 0.279 1175 Planarity : 0.004 0.048 1219 Dihedral : 5.380 52.898 1426 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.39 % Allowed : 17.28 % Favored : 81.34 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 14.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.29), residues: 875 helix: 2.30 (0.33), residues: 241 sheet: -0.12 (0.32), residues: 267 loop : -1.15 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 101 TYR 0.010 0.001 TYR E 50 PHE 0.009 0.001 PHE B 14 TRP 0.010 0.001 TRP E 149 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7431) covalent geometry : angle 0.90372 (10157) SS BOND : bond 0.00297 ( 8) SS BOND : angle 1.07413 ( 16) hydrogen bonds : bond 0.04723 ( 321) hydrogen bonds : angle 5.03728 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.11 seconds wall clock time: 43 minutes 30.18 seconds (2610.18 seconds total)