Starting phenix.real_space_refine on Sat Dec 28 19:20:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnm_34916/12_2024/8hnm_34916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnm_34916/12_2024/8hnm_34916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnm_34916/12_2024/8hnm_34916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnm_34916/12_2024/8hnm_34916.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnm_34916/12_2024/8hnm_34916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnm_34916/12_2024/8hnm_34916.cif" } resolution = 2.94 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= 0.000 sd= 1.000 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 Br 1 7.06 5 S 63 5.16 5 C 5604 2.51 5 N 1504 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "R" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2159 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'4IE': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.64, per 1000 atoms: 0.64 Number of scatterers: 8784 At special positions: 0 Unit cell: (90.95, 120.7, 129.2, 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) Br 1 34.99 S 63 16.00 O 1612 8.00 N 1504 7.00 C 5604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.3% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.656A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.231A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.646A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.229A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.786A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.543A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 81 removed outlier: 4.036A pdb=" N ARG R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 115 Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 121 through 155 removed outlier: 3.614A pdb=" N ALA R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU R 142 " --> pdb=" O GLY R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 163 removed outlier: 3.624A pdb=" N ARG R 161 " --> pdb=" O THR R 157 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG R 162 " --> pdb=" O GLN R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 184 Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 208 through 245 removed outlier: 3.836A pdb=" N GLY R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 248 through 282 removed outlier: 4.229A pdb=" N ARG R 252 " --> pdb=" O GLN R 248 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR R 269 " --> pdb=" O ALA R 265 " (cutoff:3.500A) Proline residue: R 270 - end of helix Processing helix chain 'R' and resid 289 through 319 Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 322 through 335 removed outlier: 3.679A pdb=" N ARG R 335 " --> pdb=" O MET R 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.106A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.062A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.617A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.430A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.537A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.122A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.502A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.034A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.684A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 190 through 193 removed outlier: 3.738A pdb=" N HIS R 202 " --> pdb=" O HIS R 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.088A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.088A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.040A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1293 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: 2.63 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2868 1.36 - 1.50: 2319 1.50 - 1.63: 3689 1.63 - 1.77: 0 1.77 - 1.90: 91 Bond restraints: 8967 Sorted by residual: bond pdb=" N THR A 181 " pdb=" CA THR A 181 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.17e+00 bond pdb=" N GLU B 130 " pdb=" CA GLU B 130 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.31e-02 5.83e+03 6.01e+00 bond pdb=" N GLU G 42 " pdb=" CA GLU G 42 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.30e-02 5.92e+03 5.90e+00 bond pdb=" N LEU R 286 " pdb=" CA LEU R 286 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.32e-02 5.74e+03 5.75e+00 bond pdb=" N LEU R 273 " pdb=" CA LEU R 273 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.30e-02 5.92e+03 4.81e+00 ... (remaining 8962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11935 1.92 - 3.84: 199 3.84 - 5.77: 20 5.77 - 7.69: 3 7.69 - 9.61: 4 Bond angle restraints: 12161 Sorted by residual: angle pdb=" CA GLU S 246 " pdb=" C GLU S 246 " pdb=" O GLU S 246 " ideal model delta sigma weight residual 121.40 117.91 3.49 1.11e+00 8.12e-01 9.88e+00 angle pdb=" CA LEU R 283 " pdb=" C LEU R 283 " pdb=" O LEU R 283 " ideal model delta sigma weight residual 121.02 118.20 2.82 9.00e-01 1.23e+00 9.80e+00 angle pdb=" C LEU R 286 " pdb=" N ALA R 287 " pdb=" CA ALA R 287 " ideal model delta sigma weight residual 120.94 116.30 4.64 1.57e+00 4.06e-01 8.74e+00 angle pdb=" C PHE R 207 " pdb=" CA PHE R 207 " pdb=" CB PHE R 207 " ideal model delta sigma weight residual 109.51 114.92 -5.41 1.85e+00 2.92e-01 8.56e+00 angle pdb=" N LEU R 283 " pdb=" CA LEU R 283 " pdb=" C LEU R 283 " ideal model delta sigma weight residual 110.41 107.00 3.41 1.18e+00 7.18e-01 8.36e+00 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4732 17.13 - 34.27: 523 34.27 - 51.40: 147 51.40 - 68.53: 23 68.53 - 85.66: 12 Dihedral angle restraints: 5437 sinusoidal: 2210 harmonic: 3227 Sorted by residual: dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA PHE R 207 " pdb=" C PHE R 207 " pdb=" N PRO R 208 " pdb=" CA PRO R 208 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 920 0.034 - 0.068: 335 0.068 - 0.102: 88 0.102 - 0.136: 43 0.136 - 0.170: 5 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA MET A 53 " pdb=" N MET A 53 " pdb=" C MET A 53 " pdb=" CB MET A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA LEU R 106 " pdb=" N LEU R 106 " pdb=" C LEU R 106 " pdb=" CB LEU R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1388 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 285 " -0.013 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C ALA R 285 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA R 285 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 286 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO S 75 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 272 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C HIS R 272 " 0.031 2.00e-02 2.50e+03 pdb=" O HIS R 272 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU R 273 " -0.011 2.00e-02 2.50e+03 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1356 2.76 - 3.29: 8068 3.29 - 3.83: 14269 3.83 - 4.36: 16866 4.36 - 4.90: 30410 Nonbonded interactions: 70969 Sorted by model distance: nonbonded pdb=" NE2 GLN R 209 " pdb=" NH2 ARG R 212 " model vdw 2.223 3.200 nonbonded pdb=" O ARG R 167 " pdb=" OG1 THR R 171 " model vdw 2.238 3.040 nonbonded pdb=" NE2 GLN R 158 " pdb=" NH2 ARG R 162 " model vdw 2.255 3.200 nonbonded pdb=" NZ LYS R 125 " pdb=" O PHE R 187 " model vdw 2.298 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.298 3.040 ... (remaining 70964 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.003 0.064 8967 Z= 0.206 Angle : 0.600 9.611 12161 Z= 0.328 Chirality : 0.042 0.170 1391 Planarity : 0.004 0.047 1523 Dihedral : 15.735 85.662 3348 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.53 % Allowed : 19.72 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.26), residues: 1101 helix: 1.94 (0.27), residues: 378 sheet: 0.30 (0.32), residues: 257 loop : -1.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 272 PHE 0.030 0.001 PHE R 207 TYR 0.019 0.001 TYR S 235 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.027 Fit side-chains REVERT: R 271 TYR cc_start: 0.8080 (t80) cc_final: 0.7786 (t80) outliers start: 5 outliers final: 5 residues processed: 120 average time/residue: 1.3664 time to fit residues: 174.5118 Evaluate side-chains 109 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 191 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.0670 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 294 ASN R 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8967 Z= 0.193 Angle : 0.575 9.691 12161 Z= 0.286 Chirality : 0.042 0.211 1391 Planarity : 0.004 0.045 1523 Dihedral : 6.000 48.399 1390 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.29 % Allowed : 18.66 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.26), residues: 1101 helix: 2.06 (0.27), residues: 379 sheet: 0.34 (0.32), residues: 258 loop : -1.28 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 272 PHE 0.011 0.001 PHE R 207 TYR 0.026 0.001 TYR S 235 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.982 Fit side-chains REVERT: A 195 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7654 (t-170) REVERT: B 130 GLU cc_start: 0.8833 (mp0) cc_final: 0.8621 (mp0) REVERT: G 21 MET cc_start: 0.8674 (mmm) cc_final: 0.7898 (tmt) REVERT: R 158 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7652 (tp40) REVERT: R 309 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7758 (ptm) REVERT: S 235 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7111 (t80) outliers start: 31 outliers final: 14 residues processed: 136 average time/residue: 1.2701 time to fit residues: 184.1472 Evaluate side-chains 126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8967 Z= 0.237 Angle : 0.589 9.014 12161 Z= 0.295 Chirality : 0.043 0.230 1391 Planarity : 0.004 0.045 1523 Dihedral : 5.448 39.772 1380 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.71 % Allowed : 18.66 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.25), residues: 1101 helix: 2.06 (0.27), residues: 379 sheet: 0.29 (0.32), residues: 261 loop : -1.31 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE R 187 TYR 0.027 0.001 TYR S 235 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.918 Fit side-chains REVERT: A 276 GLU cc_start: 0.7309 (mp0) cc_final: 0.7015 (mp0) REVERT: A 305 CYS cc_start: 0.7634 (p) cc_final: 0.7112 (p) REVERT: B 130 GLU cc_start: 0.8859 (mp0) cc_final: 0.8634 (mp0) REVERT: B 234 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: G 21 MET cc_start: 0.8665 (mmm) cc_final: 0.7871 (tmt) REVERT: R 158 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7626 (tp40) REVERT: R 309 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7781 (ptm) REVERT: S 191 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7586 (mpt-90) REVERT: S 235 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7141 (t80) outliers start: 35 outliers final: 15 residues processed: 132 average time/residue: 1.3480 time to fit residues: 188.8874 Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 0.0040 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8967 Z= 0.271 Angle : 0.598 9.488 12161 Z= 0.301 Chirality : 0.044 0.242 1391 Planarity : 0.004 0.045 1523 Dihedral : 5.480 41.834 1378 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.14 % Allowed : 19.41 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.25), residues: 1101 helix: 1.99 (0.27), residues: 380 sheet: 0.34 (0.32), residues: 260 loop : -1.33 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS A 195 PHE 0.013 0.001 PHE R 187 TYR 0.029 0.001 TYR S 235 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.964 Fit side-chains REVERT: A 186 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 276 GLU cc_start: 0.7318 (mp0) cc_final: 0.6944 (mp0) REVERT: A 305 CYS cc_start: 0.7688 (p) cc_final: 0.7122 (p) REVERT: B 130 GLU cc_start: 0.8877 (mp0) cc_final: 0.8623 (mp0) REVERT: B 261 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8156 (mp) REVERT: G 21 MET cc_start: 0.8668 (mmm) cc_final: 0.7853 (tmt) REVERT: G 42 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: R 158 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7641 (tp40) REVERT: R 309 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7771 (ptm) REVERT: S 191 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7609 (mpt-90) REVERT: S 235 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.7223 (t80) outliers start: 39 outliers final: 15 residues processed: 137 average time/residue: 1.2412 time to fit residues: 181.1447 Evaluate side-chains 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8967 Z= 0.182 Angle : 0.557 9.603 12161 Z= 0.278 Chirality : 0.042 0.205 1391 Planarity : 0.004 0.044 1523 Dihedral : 5.135 42.521 1378 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.56 % Allowed : 19.30 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.26), residues: 1101 helix: 2.12 (0.27), residues: 380 sheet: 0.45 (0.32), residues: 256 loop : -1.32 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.011 0.001 PHE R 187 TYR 0.024 0.001 TYR S 235 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.051 Fit side-chains REVERT: A 186 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: A 276 GLU cc_start: 0.7331 (mp0) cc_final: 0.7004 (mp0) REVERT: A 305 CYS cc_start: 0.7690 (p) cc_final: 0.7122 (p) REVERT: B 130 GLU cc_start: 0.8904 (mp0) cc_final: 0.8601 (mp0) REVERT: G 21 MET cc_start: 0.8684 (mmm) cc_final: 0.7819 (tmt) REVERT: R 158 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7607 (tp40) REVERT: R 309 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7807 (ptm) REVERT: S 63 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8935 (t) REVERT: S 82 GLN cc_start: 0.8731 (tp40) cc_final: 0.8432 (tp40) REVERT: S 235 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.7013 (t80) outliers start: 43 outliers final: 13 residues processed: 142 average time/residue: 1.2159 time to fit residues: 185.4728 Evaluate side-chains 123 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8967 Z= 0.276 Angle : 0.612 9.844 12161 Z= 0.304 Chirality : 0.044 0.240 1391 Planarity : 0.004 0.046 1523 Dihedral : 5.412 44.648 1378 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.67 % Allowed : 19.09 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.26), residues: 1101 helix: 2.00 (0.27), residues: 381 sheet: 0.34 (0.32), residues: 260 loop : -1.32 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE R 187 TYR 0.028 0.001 TYR S 235 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 1.002 Fit side-chains REVERT: A 186 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: A 276 GLU cc_start: 0.7401 (mp0) cc_final: 0.7057 (mp0) REVERT: A 305 CYS cc_start: 0.7797 (p) cc_final: 0.7196 (p) REVERT: B 130 GLU cc_start: 0.8941 (mp0) cc_final: 0.8739 (mp0) REVERT: B 261 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8149 (mp) REVERT: G 21 MET cc_start: 0.8702 (mmm) cc_final: 0.7833 (tmt) REVERT: R 158 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7676 (tp40) REVERT: R 309 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7805 (ptm) REVERT: S 63 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8917 (t) REVERT: S 191 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7995 (mpt-90) REVERT: S 235 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.7262 (t80) outliers start: 44 outliers final: 21 residues processed: 134 average time/residue: 1.2531 time to fit residues: 179.2286 Evaluate side-chains 130 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8967 Z= 0.341 Angle : 0.660 10.696 12161 Z= 0.327 Chirality : 0.045 0.268 1391 Planarity : 0.004 0.046 1523 Dihedral : 5.736 47.268 1378 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.67 % Allowed : 19.72 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.26), residues: 1101 helix: 1.83 (0.27), residues: 381 sheet: 0.29 (0.32), residues: 266 loop : -1.38 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 47 HIS 0.006 0.001 HIS A 195 PHE 0.015 0.002 PHE R 187 TYR 0.032 0.002 TYR S 235 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.982 Fit side-chains REVERT: A 276 GLU cc_start: 0.7425 (mp0) cc_final: 0.7092 (mp0) REVERT: A 305 CYS cc_start: 0.7819 (p) cc_final: 0.7240 (p) REVERT: B 130 GLU cc_start: 0.8936 (mp0) cc_final: 0.8732 (mp0) REVERT: B 261 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8127 (mp) REVERT: G 21 MET cc_start: 0.8740 (mmm) cc_final: 0.7885 (tmt) REVERT: R 158 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7653 (tp40) REVERT: R 309 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7821 (ptm) REVERT: S 191 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7715 (mpt-90) REVERT: S 235 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7319 (t80) outliers start: 44 outliers final: 20 residues processed: 136 average time/residue: 1.2448 time to fit residues: 180.9054 Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 191 ARG Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8967 Z= 0.198 Angle : 0.605 11.014 12161 Z= 0.298 Chirality : 0.043 0.213 1391 Planarity : 0.004 0.044 1523 Dihedral : 5.310 47.695 1378 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.24 % Allowed : 20.78 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.26), residues: 1101 helix: 2.00 (0.27), residues: 381 sheet: 0.44 (0.32), residues: 256 loop : -1.39 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 272 PHE 0.013 0.001 PHE R 187 TYR 0.025 0.001 TYR S 235 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 1.005 Fit side-chains REVERT: A 276 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 305 CYS cc_start: 0.7792 (p) cc_final: 0.7221 (p) REVERT: B 130 GLU cc_start: 0.8906 (mp0) cc_final: 0.8587 (mp0) REVERT: G 21 MET cc_start: 0.8722 (mmm) cc_final: 0.7874 (tmt) REVERT: R 158 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7625 (tp40) REVERT: R 309 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7880 (ptm) REVERT: S 63 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8910 (t) REVERT: S 235 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7073 (t80) outliers start: 40 outliers final: 19 residues processed: 126 average time/residue: 1.2076 time to fit residues: 162.7962 Evaluate side-chains 121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8967 Z= 0.184 Angle : 0.595 12.127 12161 Z= 0.293 Chirality : 0.043 0.201 1391 Planarity : 0.004 0.044 1523 Dihedral : 5.089 47.358 1378 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.61 % Allowed : 21.00 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.26), residues: 1101 helix: 2.06 (0.27), residues: 381 sheet: 0.37 (0.32), residues: 259 loop : -1.33 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 272 PHE 0.015 0.001 PHE R 187 TYR 0.023 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.043 Fit side-chains REVERT: A 276 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: A 305 CYS cc_start: 0.7785 (p) cc_final: 0.7208 (p) REVERT: B 130 GLU cc_start: 0.8899 (mp0) cc_final: 0.8569 (mp0) REVERT: B 261 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8089 (mp) REVERT: G 21 MET cc_start: 0.8725 (mmm) cc_final: 0.7898 (tmt) REVERT: G 22 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: R 158 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7635 (tp40) REVERT: R 309 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7964 (ptm) REVERT: S 63 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8910 (t) REVERT: S 235 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6999 (t80) outliers start: 34 outliers final: 21 residues processed: 126 average time/residue: 1.2781 time to fit residues: 171.8858 Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 0.0670 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN B 35 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8967 Z= 0.154 Angle : 0.594 12.933 12161 Z= 0.288 Chirality : 0.042 0.196 1391 Planarity : 0.004 0.044 1523 Dihedral : 4.784 46.001 1378 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.76 % Allowed : 22.48 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.26), residues: 1101 helix: 2.29 (0.27), residues: 375 sheet: 0.37 (0.32), residues: 248 loop : -1.25 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 272 PHE 0.014 0.001 PHE R 187 TYR 0.019 0.001 TYR S 235 ARG 0.004 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.985 Fit side-chains REVERT: A 276 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: A 305 CYS cc_start: 0.7716 (p) cc_final: 0.7158 (p) REVERT: B 130 GLU cc_start: 0.8910 (mp0) cc_final: 0.8650 (mp0) REVERT: G 21 MET cc_start: 0.8723 (mmm) cc_final: 0.7851 (tmt) REVERT: R 158 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7611 (tp40) REVERT: R 309 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8017 (ptm) REVERT: S 235 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6814 (t80) outliers start: 26 outliers final: 16 residues processed: 128 average time/residue: 1.2053 time to fit residues: 165.4476 Evaluate side-chains 121 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN B 35 ASN B 237 ASN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100084 restraints weight = 11587.009| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.97 r_work: 0.3108 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8967 Z= 0.173 Angle : 0.609 13.188 12161 Z= 0.293 Chirality : 0.042 0.187 1391 Planarity : 0.004 0.044 1523 Dihedral : 4.756 44.716 1378 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.55 % Allowed : 23.12 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.25), residues: 1101 helix: 2.10 (0.27), residues: 381 sheet: 0.34 (0.32), residues: 248 loop : -1.24 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 117 HIS 0.005 0.001 HIS R 272 PHE 0.014 0.001 PHE R 187 TYR 0.021 0.001 TYR S 235 ARG 0.002 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.33 seconds wall clock time: 62 minutes 16.94 seconds (3736.94 seconds total)