Starting phenix.real_space_refine on Sat Aug 23 01:34:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnm_34916/08_2025/8hnm_34916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnm_34916/08_2025/8hnm_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_34916/08_2025/8hnm_34916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnm_34916/08_2025/8hnm_34916.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnm_34916/08_2025/8hnm_34916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnm_34916/08_2025/8hnm_34916.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.76, per 1000 atoms: 0.20 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: 0.90 Conformation dependent library (CDL) restraints added in 255.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.35 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: 1.35 Time building geometry restraints manager: 1.12 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: 0.010 Normalize map: mean=0, sd=1: 1.480 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.870 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- 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 8970 Z= 0.166 Angle : 0.600 9.611 12167 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 : 8.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 197 TYR 0.019 0.001 TYR S 235 PHE 0.030 0.001 PHE R 207 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8967) covalent geometry : angle 0.59961 (12161) SS BOND : bond 0.00464 ( 3) SS BOND : angle 1.29303 ( 6) hydrogen bonds : bond 0.11363 ( 454) hydrogen bonds : angle 5.21862 ( 1293) *********************** 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 : 0.257 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: 0.6291 time to fit residues: 80.1482 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 : 0.337 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096603 restraints weight = 12059.489| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.00 r_work: 0.3043 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8970 Z= 0.176 Angle : 0.615 9.738 12167 Z= 0.307 Chirality : 0.044 0.242 1391 Planarity : 0.004 0.047 1523 Dihedral : 6.191 46.293 1390 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.61 % Allowed : 18.56 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1101 helix: 1.92 (0.27), residues: 380 sheet: 0.25 (0.32), residues: 261 loop : -1.27 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.030 0.001 TYR S 235 PHE 0.012 0.001 PHE R 207 TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8967) covalent geometry : angle 0.61395 (12161) SS BOND : bond 0.00592 ( 3) SS BOND : angle 1.35826 ( 6) hydrogen bonds : bond 0.04092 ( 454) hydrogen bonds : angle 4.54807 ( 1293) *********************** 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 149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.363 Fit side-chains REVERT: G 21 MET cc_start: 0.8894 (mmm) cc_final: 0.8014 (tmt) REVERT: R 158 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7913 (tp40) REVERT: R 309 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7852 (ptm) REVERT: S 235 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7176 (t80) outliers start: 34 outliers final: 15 residues processed: 134 average time/residue: 0.6540 time to fit residues: 92.7888 Evaluate side-chains 124 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 B residue 35 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE 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 251 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098102 restraints weight = 11941.762| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.99 r_work: 0.3072 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8970 Z= 0.123 Angle : 0.566 9.651 12167 Z= 0.283 Chirality : 0.042 0.210 1391 Planarity : 0.004 0.045 1523 Dihedral : 5.571 40.861 1384 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.29 % Allowed : 19.19 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1101 helix: 2.11 (0.27), residues: 379 sheet: 0.40 (0.32), residues: 256 loop : -1.35 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.025 0.001 TYR S 235 PHE 0.010 0.001 PHE R 187 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8967) covalent geometry : angle 0.56571 (12161) SS BOND : bond 0.00515 ( 3) SS BOND : angle 1.04756 ( 6) hydrogen bonds : bond 0.03603 ( 454) hydrogen bonds : angle 4.36385 ( 1293) *********************** 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 145 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.250 Fit side-chains REVERT: A 186 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7725 (tm-30) REVERT: A 276 GLU cc_start: 0.7321 (mp0) cc_final: 0.7049 (mp0) REVERT: A 305 CYS cc_start: 0.7745 (p) cc_final: 0.7243 (p) REVERT: B 234 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8910 (m-80) REVERT: G 21 MET cc_start: 0.8890 (mmm) cc_final: 0.8014 (tmt) REVERT: R 124 CYS cc_start: 0.6289 (OUTLIER) cc_final: 0.6024 (t) REVERT: R 158 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: R 309 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7917 (ptm) REVERT: S 235 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6976 (t80) outliers start: 31 outliers final: 14 residues processed: 131 average time/residue: 0.6476 time to fit residues: 90.0191 Evaluate side-chains 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 262 MET 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 124 CYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.098385 restraints weight = 12159.494| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.00 r_work: 0.3080 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8970 Z= 0.121 Angle : 0.553 9.302 12167 Z= 0.277 Chirality : 0.042 0.203 1391 Planarity : 0.004 0.044 1523 Dihedral : 5.102 39.547 1380 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.67 % Allowed : 18.56 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.26), residues: 1101 helix: 2.18 (0.27), residues: 379 sheet: 0.36 (0.32), residues: 258 loop : -1.31 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.023 0.001 TYR S 235 PHE 0.010 0.001 PHE R 187 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8967) covalent geometry : angle 0.55247 (12161) SS BOND : bond 0.00506 ( 3) SS BOND : angle 1.11159 ( 6) hydrogen bonds : bond 0.03456 ( 454) hydrogen bonds : angle 4.28515 ( 1293) *********************** 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 155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.338 Fit side-chains REVERT: A 186 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: A 276 GLU cc_start: 0.7426 (mp0) cc_final: 0.7065 (mp0) REVERT: A 305 CYS cc_start: 0.7920 (p) cc_final: 0.7438 (p) REVERT: G 21 MET cc_start: 0.8881 (mmm) cc_final: 0.8013 (tmt) REVERT: G 42 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: R 124 CYS cc_start: 0.6272 (OUTLIER) cc_final: 0.6002 (t) REVERT: R 158 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7951 (tp40) REVERT: R 309 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7968 (ptm) REVERT: S 235 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7020 (t80) outliers start: 44 outliers final: 13 residues processed: 139 average time/residue: 0.6014 time to fit residues: 88.9624 Evaluate side-chains 123 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 245 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 25 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 124 CYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 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 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098459 restraints weight = 11991.397| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.02 r_work: 0.3077 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8970 Z= 0.123 Angle : 0.552 9.640 12167 Z= 0.276 Chirality : 0.042 0.204 1391 Planarity : 0.004 0.044 1523 Dihedral : 5.000 39.966 1378 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.67 % Allowed : 19.30 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.26), residues: 1101 helix: 2.21 (0.27), residues: 379 sheet: 0.40 (0.32), residues: 259 loop : -1.30 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.024 0.001 TYR S 235 PHE 0.011 0.001 PHE R 187 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8967) covalent geometry : angle 0.55164 (12161) SS BOND : bond 0.00509 ( 3) SS BOND : angle 1.12917 ( 6) hydrogen bonds : bond 0.03422 ( 454) hydrogen bonds : angle 4.27253 ( 1293) *********************** 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: 44 poor density : 110 time to evaluate : 0.329 Fit side-chains REVERT: A 186 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 276 GLU cc_start: 0.7352 (mp0) cc_final: 0.7037 (mp0) REVERT: A 305 CYS cc_start: 0.7849 (p) cc_final: 0.7340 (p) REVERT: B 261 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (mp) REVERT: G 21 MET cc_start: 0.8891 (mmm) cc_final: 0.7951 (tmt) REVERT: R 124 CYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5953 (t) REVERT: R 158 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7898 (tp40) REVERT: R 309 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8033 (ptm) REVERT: S 82 GLN cc_start: 0.8783 (tp40) cc_final: 0.8508 (tp40) REVERT: S 235 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6915 (t80) outliers start: 44 outliers final: 18 residues processed: 141 average time/residue: 0.5903 time to fit residues: 88.7677 Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 124 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099392 restraints weight = 11902.628| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.01 r_work: 0.3088 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8970 Z= 0.115 Angle : 0.561 9.842 12167 Z= 0.279 Chirality : 0.042 0.192 1391 Planarity : 0.004 0.045 1523 Dihedral : 4.880 39.424 1378 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.45 % Allowed : 19.51 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1101 helix: 2.25 (0.27), residues: 380 sheet: 0.38 (0.32), residues: 248 loop : -1.26 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.022 0.001 TYR S 235 PHE 0.011 0.001 PHE R 187 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8967) covalent geometry : angle 0.56059 (12161) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.10441 ( 6) hydrogen bonds : bond 0.03283 ( 454) hydrogen bonds : angle 4.24581 ( 1293) *********************** 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: 42 poor density : 107 time to evaluate : 0.367 Fit side-chains REVERT: A 276 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 305 CYS cc_start: 0.7837 (p) cc_final: 0.7306 (p) REVERT: G 21 MET cc_start: 0.8896 (mmm) cc_final: 0.7940 (tmt) REVERT: R 124 CYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5964 (t) REVERT: R 158 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7892 (tp40) REVERT: R 309 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8057 (ptm) REVERT: S 235 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6829 (t80) outliers start: 42 outliers final: 20 residues processed: 134 average time/residue: 0.5936 time to fit residues: 84.8442 Evaluate side-chains 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 70 LEU 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 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 274 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 35 ASN ** R 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102350 restraints weight = 11725.372| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.97 r_work: 0.3154 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8970 Z= 0.100 Angle : 0.552 10.691 12167 Z= 0.270 Chirality : 0.041 0.187 1391 Planarity : 0.003 0.043 1523 Dihedral : 4.517 36.024 1378 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.39 % Allowed : 21.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1101 helix: 2.30 (0.27), residues: 381 sheet: 0.44 (0.32), residues: 248 loop : -1.21 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.018 0.001 TYR S 235 PHE 0.015 0.001 PHE R 187 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8967) covalent geometry : angle 0.55212 (12161) SS BOND : bond 0.00394 ( 3) SS BOND : angle 0.93203 ( 6) hydrogen bonds : bond 0.02940 ( 454) hydrogen bonds : angle 4.13045 ( 1293) *********************** 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 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.352 Fit side-chains REVERT: A 276 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 305 CYS cc_start: 0.7931 (p) cc_final: 0.7411 (p) REVERT: G 21 MET cc_start: 0.8837 (mmm) cc_final: 0.7967 (tmt) REVERT: R 108 LEU cc_start: 0.6466 (tp) cc_final: 0.6263 (tt) REVERT: R 124 CYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5710 (t) REVERT: R 158 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7971 (tp40) REVERT: R 309 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8024 (ptm) REVERT: S 235 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6672 (t80) outliers start: 32 outliers final: 15 residues processed: 136 average time/residue: 0.6133 time to fit residues: 88.6407 Evaluate side-chains 126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain A residue 276 GLU 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 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 124 CYS 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 274 VAL Chi-restraints excluded: chain R residue 309 MET Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 155 VAL 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 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 0.0470 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 35 ASN B 237 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101092 restraints weight = 11559.892| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.99 r_work: 0.3126 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8970 Z= 0.113 Angle : 0.576 12.225 12167 Z= 0.283 Chirality : 0.042 0.186 1391 Planarity : 0.003 0.044 1523 Dihedral : 4.548 34.051 1378 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.86 % Allowed : 22.06 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1101 helix: 2.28 (0.27), residues: 381 sheet: 0.46 (0.32), residues: 248 loop : -1.18 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.019 0.001 TYR S 235 PHE 0.013 0.001 PHE R 187 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8967) covalent geometry : angle 0.57566 (12161) SS BOND : bond 0.00445 ( 3) SS BOND : angle 1.07259 ( 6) hydrogen bonds : bond 0.03141 ( 454) hydrogen bonds : angle 4.19017 ( 1293) *********************** 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 139 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.359 Fit side-chains REVERT: A 276 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 305 CYS cc_start: 0.7908 (p) cc_final: 0.7384 (p) REVERT: G 21 MET cc_start: 0.8829 (mmm) cc_final: 0.7945 (tmt) REVERT: R 108 LEU cc_start: 0.6429 (tp) cc_final: 0.6155 (tt) REVERT: R 124 CYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5738 (t) REVERT: R 158 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7960 (tp40) REVERT: R 309 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8047 (ptm) REVERT: S 235 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6750 (t80) outliers start: 27 outliers final: 16 residues processed: 130 average time/residue: 0.6198 time to fit residues: 86.0835 Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 268 LEU 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 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 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 309 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 306 GLN B 35 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099767 restraints weight = 11628.359| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.99 r_work: 0.3107 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8970 Z= 0.124 Angle : 0.594 12.224 12167 Z= 0.291 Chirality : 0.042 0.189 1391 Planarity : 0.003 0.044 1523 Dihedral : 4.637 33.020 1378 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.39 % Allowed : 21.74 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.26), residues: 1101 helix: 2.21 (0.27), residues: 381 sheet: 0.46 (0.32), residues: 258 loop : -1.20 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.021 0.001 TYR S 235 PHE 0.013 0.001 PHE R 187 TRP 0.009 0.001 TRP B 169 HIS 0.005 0.001 HIS R 272 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8967) covalent geometry : angle 0.59362 (12161) SS BOND : bond 0.00480 ( 3) SS BOND : angle 1.12168 ( 6) hydrogen bonds : bond 0.03282 ( 454) hydrogen bonds : angle 4.26076 ( 1293) *********************** 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 139 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.369 Fit side-chains REVERT: A 276 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 305 CYS cc_start: 0.7867 (p) cc_final: 0.7335 (p) REVERT: G 21 MET cc_start: 0.8837 (mmm) cc_final: 0.7916 (tmt) REVERT: R 124 CYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5684 (t) REVERT: R 158 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7888 (tp40) REVERT: R 170 LEU cc_start: 0.7911 (tt) cc_final: 0.7664 (tm) REVERT: R 309 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: S 82 GLN cc_start: 0.8696 (tp40) cc_final: 0.8386 (tp40) REVERT: S 235 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6745 (t80) outliers start: 32 outliers final: 19 residues processed: 127 average time/residue: 0.6577 time to fit residues: 88.8078 Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 70 LEU 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 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 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 274 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 S 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100484 restraints weight = 11814.291| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.01 r_work: 0.3117 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8970 Z= 0.116 Angle : 0.593 13.326 12167 Z= 0.291 Chirality : 0.042 0.197 1391 Planarity : 0.003 0.046 1523 Dihedral : 4.564 31.159 1378 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1101 helix: 2.20 (0.27), residues: 382 sheet: 0.43 (0.32), residues: 247 loop : -1.18 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 191 TYR 0.020 0.001 TYR S 235 PHE 0.014 0.001 PHE R 187 TRP 0.011 0.001 TRP B 169 HIS 0.008 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8967) covalent geometry : angle 0.59247 (12161) SS BOND : bond 0.00443 ( 3) SS BOND : angle 1.04005 ( 6) hydrogen bonds : bond 0.03193 ( 454) hydrogen bonds : angle 4.24009 ( 1293) ********************** 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 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.423 Fit side-chains REVERT: A 276 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 305 CYS cc_start: 0.7951 (p) cc_final: 0.7425 (p) REVERT: G 21 MET cc_start: 0.8784 (mmm) cc_final: 0.7944 (tmt) REVERT: R 124 CYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5627 (t) REVERT: R 158 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7984 (tp40) REVERT: R 309 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: S 235 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6770 (t80) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.5629 time to fit residues: 70.7288 Evaluate side-chains 124 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 268 LEU 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 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 124 CYS Chi-restraints excluded: chain R residue 158 GLN Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 274 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103058 restraints weight = 11833.036| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.02 r_work: 0.3162 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8970 Z= 0.104 Angle : 0.567 11.951 12167 Z= 0.279 Chirality : 0.041 0.187 1391 Planarity : 0.003 0.045 1523 Dihedral : 4.363 26.502 1378 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.86 % Allowed : 22.59 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1101 helix: 2.23 (0.27), residues: 382 sheet: 0.51 (0.32), residues: 247 loop : -1.14 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.017 0.001 TYR S 235 PHE 0.013 0.001 PHE R 187 TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8967) covalent geometry : angle 0.56648 (12161) SS BOND : bond 0.00374 ( 3) SS BOND : angle 0.89112 ( 6) hydrogen bonds : bond 0.02941 ( 454) hydrogen bonds : angle 4.15862 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3344.18 seconds wall clock time: 57 minutes 51.10 seconds (3471.10 seconds total)