Starting phenix.real_space_refine on Tue Dec 31 02:07:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk5_25173/12_2024/7sk5_25173_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk5_25173/12_2024/7sk5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk5_25173/12_2024/7sk5_25173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk5_25173/12_2024/7sk5_25173.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk5_25173/12_2024/7sk5_25173_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk5_25173/12_2024/7sk5_25173_trim.cif" } resolution = 4.0 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= 0.056 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.98, per 1000 atoms: 0.56 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: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.30 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: 5.31 Time building geometry restraints manager: 4.56 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: 1.210 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: 0.280 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- 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 7431 Z= 0.285 Angle : 0.628 7.824 10157 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 (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: 0.50 (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 TRP 0.008 0.001 TRP K 36 HIS 0.003 0.001 HIS A 121 PHE 0.008 0.001 PHE F 139 TYR 0.007 0.001 TYR E 50 ARG 0.002 0.000 ARG B 20 *********************** 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 : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8451 (mt) cc_final: 0.8244 (mm) REVERT: A 212 MET cc_start: 0.8754 (mmp) cc_final: 0.8519 (tpp) 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: 0.8248 (p0) REVERT: B 10 PRO cc_start: 0.9230 (Cg_exo) cc_final: 0.8964 (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: 0.8443 (tp) REVERT: K 98 ILE cc_start: 0.8375 (tp) cc_final: 0.8048 (tp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.4099 time to fit residues: 91.1936 Evaluate side-chains 142 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7431 Z= 0.187 Angle : 0.546 5.289 10157 Z= 0.297 Chirality : 0.041 0.144 1175 Planarity : 0.004 0.035 1219 Dihedral : 5.372 47.199 1426 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.88 % Allowed : 7.69 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.37 (0.30), residues: 875 helix: 2.10 (0.33), residues: 239 sheet: 0.09 (0.33), residues: 267 loop : -0.85 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 36 HIS 0.005 0.001 HIS A 121 PHE 0.016 0.001 PHE F 71 TYR 0.014 0.001 TYR F 162 ARG 0.005 0.000 ARG B 20 *********************** 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: 7 poor density : 152 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.8776 (t0) cc_final: 0.8567 (t0) REVERT: A 205 ILE cc_start: 0.8183 (mt) cc_final: 0.7941 (mm) REVERT: F 9 GLU cc_start: 0.8062 (mp0) cc_final: 0.7826 (mp0) REVERT: F 65 ASP cc_start: 0.8451 (p0) cc_final: 0.8229 (p0) REVERT: F 171 TRP cc_start: 0.8513 (m100) cc_final: 0.8050 (m100) REVERT: F 212 ILE cc_start: 0.8428 (tt) cc_final: 0.8147 (tt) REVERT: B 10 PRO cc_start: 0.9161 (Cg_exo) cc_final: 0.8916 (Cg_endo) REVERT: E 5 MET cc_start: 0.8298 (mmm) cc_final: 0.8069 (mmm) REVERT: K 6 GLU cc_start: 0.7563 (mp0) cc_final: 0.6883 (mp0) REVERT: K 36 TRP cc_start: 0.8212 (m100) cc_final: 0.7690 (m100) REVERT: K 39 GLN cc_start: 0.6722 (tt0) cc_final: 0.5893 (tm-30) outliers start: 7 outliers final: 7 residues processed: 153 average time/residue: 0.3712 time to fit residues: 78.3708 Evaluate side-chains 148 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 57 TRP 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 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7431 Z= 0.314 Angle : 0.577 5.186 10157 Z= 0.312 Chirality : 0.041 0.161 1175 Planarity : 0.004 0.033 1219 Dihedral : 5.525 47.872 1426 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.77 % Allowed : 10.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.29), residues: 875 helix: 1.84 (0.33), residues: 240 sheet: -0.05 (0.33), residues: 261 loop : -1.04 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 171 HIS 0.007 0.001 HIS A 121 PHE 0.016 0.001 PHE K 47 TYR 0.011 0.001 TYR E 50 ARG 0.002 0.000 ARG K 38 *********************** 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 159 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 TYR cc_start: 0.9332 (t80) cc_final: 0.9048 (t80) REVERT: F 9 GLU cc_start: 0.8188 (mp0) cc_final: 0.7902 (mp0) REVERT: F 65 ASP cc_start: 0.8518 (p0) cc_final: 0.8305 (p0) REVERT: F 171 TRP cc_start: 0.8551 (m100) cc_final: 0.8131 (m100) REVERT: B 10 PRO cc_start: 0.9250 (Cg_exo) cc_final: 0.9009 (Cg_endo) REVERT: E 5 MET cc_start: 0.8357 (mmm) cc_final: 0.8121 (mmm) REVERT: K 6 GLU cc_start: 0.7529 (mp0) cc_final: 0.6712 (mp0) REVERT: K 36 TRP cc_start: 0.8334 (m100) cc_final: 0.7837 (m100) REVERT: K 39 GLN cc_start: 0.6762 (tt0) cc_final: 0.5961 (tm-30) REVERT: K 83 MET cc_start: 0.7767 (tmm) cc_final: 0.7544 (tmm) outliers start: 14 outliers final: 12 residues processed: 151 average time/residue: 0.3682 time to fit residues: 77.0482 Evaluate side-chains 149 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 120 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 F residue 214 ASN 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 103 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7431 Z= 0.211 Angle : 0.524 5.400 10157 Z= 0.280 Chirality : 0.040 0.159 1175 Planarity : 0.003 0.031 1219 Dihedral : 5.462 51.883 1426 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.13 % Allowed : 12.48 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.11 (0.29), residues: 875 helix: 1.98 (0.33), residues: 240 sheet: -0.05 (0.33), residues: 263 loop : -1.11 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 149 HIS 0.005 0.001 HIS A 121 PHE 0.009 0.001 PHE A 231 TYR 0.012 0.001 TYR E 50 ARG 0.002 0.000 ARG B 20 *********************** 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 154 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.264 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 205 ILE cc_start: 0.8155 (mt) cc_final: 0.7931 (mm) REVERT: A 213 GLU cc_start: 0.9007 (tp30) cc_final: 0.8656 (mm-30) REVERT: A 322 TYR cc_start: 0.9339 (t80) cc_final: 0.9050 (t80) REVERT: F 65 ASP cc_start: 0.8472 (p0) cc_final: 0.8254 (p0) REVERT: F 171 TRP cc_start: 0.8612 (m100) cc_final: 0.8217 (m100) REVERT: B 10 PRO cc_start: 0.9170 (Cg_exo) cc_final: 0.8941 (Cg_endo) REVERT: E 5 MET cc_start: 0.8368 (mmm) cc_final: 0.8112 (mmm) REVERT: E 149 TRP cc_start: 0.8790 (m100) cc_final: 0.8582 (m100) REVERT: K 6 GLU cc_start: 0.7551 (mp0) cc_final: 0.6745 (mp0) REVERT: K 36 TRP cc_start: 0.8352 (m100) cc_final: 0.7792 (m100) REVERT: K 39 GLN cc_start: 0.6771 (tt0) cc_final: 0.5972 (tm-30) REVERT: K 103 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8343 (t80) outliers start: 9 outliers final: 8 residues processed: 148 average time/residue: 0.3661 time to fit residues: 75.3417 Evaluate side-chains 151 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 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 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7431 Z= 0.201 Angle : 0.510 5.841 10157 Z= 0.272 Chirality : 0.041 0.179 1175 Planarity : 0.003 0.030 1219 Dihedral : 5.398 52.029 1426 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.26 % Allowed : 14.00 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.12 (0.29), residues: 875 helix: 2.10 (0.33), residues: 240 sheet: -0.10 (0.32), residues: 272 loop : -1.16 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 149 HIS 0.005 0.001 HIS A 121 PHE 0.010 0.001 PHE F 139 TYR 0.011 0.001 TYR E 50 ARG 0.002 0.000 ARG B 20 *********************** 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 159 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.230 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: A 205 ILE cc_start: 0.8169 (mt) cc_final: 0.7924 (mm) REVERT: F 65 ASP cc_start: 0.8459 (p0) cc_final: 0.8232 (p0) REVERT: F 171 TRP cc_start: 0.8583 (m100) cc_final: 0.8183 (m100) REVERT: B 10 PRO cc_start: 0.9144 (Cg_exo) cc_final: 0.8858 (Cg_endo) REVERT: E 5 MET cc_start: 0.8448 (mmm) cc_final: 0.8238 (mmm) REVERT: K 6 GLU cc_start: 0.7569 (mp0) cc_final: 0.6801 (mp0) REVERT: K 36 TRP cc_start: 0.8377 (m100) cc_final: 0.7872 (m100) REVERT: K 39 GLN cc_start: 0.6762 (tt0) cc_final: 0.5938 (tm-30) REVERT: K 103 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8359 (t80) outliers start: 10 outliers final: 9 residues processed: 153 average time/residue: 0.3827 time to fit residues: 81.3922 Evaluate side-chains 154 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 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 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7431 Z= 0.162 Angle : 0.495 6.344 10157 Z= 0.261 Chirality : 0.041 0.189 1175 Planarity : 0.003 0.031 1219 Dihedral : 5.272 52.598 1426 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.39 % Allowed : 15.01 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.21 (0.29), residues: 875 helix: 2.23 (0.33), residues: 241 sheet: -0.06 (0.32), residues: 267 loop : -1.12 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 149 HIS 0.003 0.001 HIS F 38 PHE 0.010 0.001 PHE E 119 TYR 0.010 0.001 TYR E 50 ARG 0.002 0.000 ARG A 320 *********************** 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 164 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.140 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 205 ILE cc_start: 0.8165 (mt) cc_final: 0.7916 (mm) REVERT: F 65 ASP cc_start: 0.8435 (p0) cc_final: 0.8223 (p0) REVERT: F 171 TRP cc_start: 0.8603 (m100) cc_final: 0.8171 (m100) REVERT: B 10 PRO cc_start: 0.9147 (Cg_exo) cc_final: 0.8888 (Cg_endo) REVERT: E 148 GLN cc_start: 0.7998 (pm20) cc_final: 0.7632 (pm20) REVERT: K 6 GLU cc_start: 0.7565 (mp0) cc_final: 0.6809 (mp0) REVERT: K 36 TRP cc_start: 0.8340 (m100) cc_final: 0.7799 (m100) REVERT: K 39 GLN cc_start: 0.6774 (tt0) cc_final: 0.5954 (tm-30) REVERT: K 103 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8330 (t80) outliers start: 11 outliers final: 7 residues processed: 159 average time/residue: 0.3636 time to fit residues: 80.2247 Evaluate side-chains 154 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 6 SER Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain K residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7431 Z= 0.171 Angle : 0.500 8.796 10157 Z= 0.262 Chirality : 0.040 0.175 1175 Planarity : 0.003 0.031 1219 Dihedral : 5.162 50.803 1426 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.13 % Allowed : 15.76 % 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 (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: 0.22 (0.29), residues: 875 helix: 2.24 (0.33), residues: 241 sheet: -0.06 (0.32), residues: 267 loop : -1.11 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 149 HIS 0.004 0.001 HIS A 121 PHE 0.012 0.001 PHE F 139 TYR 0.011 0.001 TYR A 322 ARG 0.001 0.000 ARG E 212 *********************** 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 158 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.119 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 193 GLU cc_start: 0.8182 (pm20) cc_final: 0.7939 (pm20) REVERT: A 205 ILE cc_start: 0.8125 (mt) cc_final: 0.7883 (mm) REVERT: A 322 TYR cc_start: 0.9218 (t80) cc_final: 0.8836 (t80) REVERT: F 9 GLU cc_start: 0.8301 (mp0) cc_final: 0.8100 (mp0) REVERT: F 65 ASP cc_start: 0.8424 (p0) cc_final: 0.8193 (p0) REVERT: F 171 TRP cc_start: 0.8614 (m100) cc_final: 0.8172 (m100) REVERT: K 6 GLU cc_start: 0.7518 (mp0) cc_final: 0.6825 (mp0) REVERT: K 36 TRP cc_start: 0.8312 (m100) cc_final: 0.7826 (m100) REVERT: K 103 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8304 (t80) outliers start: 9 outliers final: 7 residues processed: 152 average time/residue: 0.3859 time to fit residues: 81.0572 Evaluate side-chains 152 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7431 Z= 0.235 Angle : 0.525 8.818 10157 Z= 0.278 Chirality : 0.040 0.186 1175 Planarity : 0.004 0.051 1219 Dihedral : 5.330 50.238 1426 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.02 % Allowed : 15.64 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.15 (0.29), residues: 875 helix: 2.15 (0.33), residues: 241 sheet: -0.09 (0.32), residues: 267 loop : -1.15 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 39 HIS 0.007 0.001 HIS A 121 PHE 0.009 0.001 PHE B 14 TYR 0.011 0.001 TYR E 50 ARG 0.002 0.000 ARG E 212 *********************** 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 160 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.178 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: 0.8140 (mt) cc_final: 0.7904 (mm) REVERT: A 322 TYR cc_start: 0.9226 (t80) cc_final: 0.8805 (t80) REVERT: F 65 ASP cc_start: 0.8447 (p0) cc_final: 0.8203 (p0) REVERT: F 171 TRP cc_start: 0.8663 (m100) cc_final: 0.8210 (m100) REVERT: B 37 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: E 148 GLN cc_start: 0.8059 (pm20) cc_final: 0.7678 (pm20) REVERT: K 6 GLU cc_start: 0.7585 (mp0) cc_final: 0.6938 (mp0) REVERT: K 36 TRP cc_start: 0.8305 (m100) cc_final: 0.7809 (m100) REVERT: K 103 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8303 (t80) outliers start: 16 outliers final: 11 residues processed: 150 average time/residue: 0.3687 time to fit residues: 76.3947 Evaluate side-chains 155 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 138 VAL Chi-restraints excluded: chain F residue 214 ASN Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 37 GLN 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 46 GLU Chi-restraints excluded: chain K residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7431 Z= 0.302 Angle : 0.567 9.476 10157 Z= 0.301 Chirality : 0.041 0.187 1175 Planarity : 0.004 0.040 1219 Dihedral : 5.554 51.447 1426 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.89 % Allowed : 16.02 % 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 (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: 0.04 (0.29), residues: 875 helix: 2.02 (0.33), residues: 241 sheet: -0.14 (0.32), residues: 267 loop : -1.20 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 39 HIS 0.007 0.001 HIS A 121 PHE 0.009 0.001 PHE A 149 TYR 0.019 0.001 TYR F 162 ARG 0.002 0.000 ARG F 22 *********************** 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 157 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8237 (mt) cc_final: 0.8000 (mm) REVERT: A 322 TYR cc_start: 0.9249 (t80) cc_final: 0.8829 (t80) REVERT: F 65 ASP cc_start: 0.8494 (p0) cc_final: 0.8266 (p0) REVERT: F 171 TRP cc_start: 0.8673 (m100) cc_final: 0.8210 (m100) REVERT: B 37 GLN cc_start: 0.7559 (tp40) cc_final: 0.7124 (tm-30) REVERT: E 148 GLN cc_start: 0.8097 (pm20) cc_final: 0.7706 (pm20) REVERT: K 6 GLU cc_start: 0.7624 (mp0) cc_final: 0.6987 (mp0) REVERT: K 36 TRP cc_start: 0.8319 (m100) cc_final: 0.7771 (m100) REVERT: K 103 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8292 (t80) outliers start: 15 outliers final: 13 residues processed: 147 average time/residue: 0.3933 time to fit residues: 80.5475 Evaluate side-chains 153 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 138 VAL Chi-restraints excluded: chain F residue 214 ASN 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 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 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 88 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7431 Z= 0.182 Angle : 0.516 9.226 10157 Z= 0.270 Chirality : 0.040 0.175 1175 Planarity : 0.004 0.035 1219 Dihedral : 5.406 52.948 1426 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.26 % Allowed : 16.90 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.20 (0.29), residues: 875 helix: 2.24 (0.33), residues: 241 sheet: -0.08 (0.32), residues: 267 loop : -1.14 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 149 HIS 0.005 0.001 HIS A 121 PHE 0.012 0.001 PHE E 119 TYR 0.016 0.001 TYR F 162 ARG 0.002 0.000 ARG F 101 ********************** 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 154 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.208 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: 0.8148 (mt) cc_final: 0.7895 (mm) REVERT: A 322 TYR cc_start: 0.9235 (t80) cc_final: 0.8818 (t80) REVERT: F 65 ASP cc_start: 0.8422 (p0) cc_final: 0.8186 (p0) REVERT: B 37 GLN cc_start: 0.7412 (tp40) cc_final: 0.7015 (tm-30) REVERT: K 6 GLU cc_start: 0.7586 (mp0) cc_final: 0.6973 (mp0) REVERT: K 36 TRP cc_start: 0.8315 (m100) cc_final: 0.7851 (m100) REVERT: K 103 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8274 (t80) outliers start: 10 outliers final: 8 residues processed: 149 average time/residue: 0.3792 time to fit residues: 79.6145 Evaluate side-chains 151 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.135985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101799 restraints weight = 36156.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106039 restraints weight = 14739.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108707 restraints weight = 8614.073| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7431 Z= 0.206 Angle : 0.532 10.862 10157 Z= 0.278 Chirality : 0.040 0.170 1175 Planarity : 0.003 0.035 1219 Dihedral : 5.392 51.580 1426 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.39 % Allowed : 16.90 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.63 % 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: 0.18 (0.29), residues: 875 helix: 2.25 (0.33), residues: 241 sheet: -0.07 (0.32), residues: 267 loop : -1.18 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 50 HIS 0.005 0.001 HIS A 121 PHE 0.017 0.001 PHE F 139 TYR 0.014 0.001 TYR F 162 ARG 0.001 0.000 ARG E 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3699.28 seconds wall clock time: 67 minutes 4.53 seconds (4024.53 seconds total)