Starting phenix.real_space_refine on Sat Jun 7 20:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnm_34916/06_2025/8hnm_34916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnm_34916/06_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_34916/06_2025/8hnm_34916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnm_34916/06_2025/8hnm_34916.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnm_34916/06_2025/8hnm_34916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnm_34916/06_2025/8hnm_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-5710/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: 5.69, per 1000 atoms: 0.65 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 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: 1.19 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: 2.53 Time building geometry restraints manager: 2.93 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: 1.340 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.890 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- 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 : 8.44 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 Details of bonding type rmsd hydrogen bonds : bond 0.11363 ( 454) hydrogen bonds : angle 5.21862 ( 1293) SS BOND : bond 0.00464 ( 3) SS BOND : angle 1.29303 ( 6) covalent geometry : bond 0.00316 ( 8967) covalent geometry : angle 0.59961 (12161) *********************** 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 : 0.992 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: 1.3748 time to fit residues: 175.3268 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 : 0.985 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098635 restraints weight = 12035.505| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.04 r_work: 0.3070 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 8970 Z= 0.132 Angle : 0.576 9.691 12167 Z= 0.287 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 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 454) hydrogen bonds : angle 4.44093 ( 1293) SS BOND : bond 0.00510 ( 3) SS BOND : angle 1.17920 ( 6) covalent geometry : bond 0.00303 ( 8967) covalent geometry : angle 0.57538 (12161) *********************** 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 : 1.018 Fit side-chains REVERT: G 21 MET cc_start: 0.8916 (mmm) cc_final: 0.8067 (tmt) REVERT: R 158 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7994 (tp40) REVERT: R 309 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7910 (ptm) REVERT: S 235 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.7076 (t80) outliers start: 31 outliers final: 14 residues processed: 136 average time/residue: 1.2215 time to fit residues: 177.0881 Evaluate side-chains 124 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 104 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.129108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097944 restraints weight = 12196.375| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.00 r_work: 0.3064 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1048 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= 0.137 Angle : 0.575 8.985 12167 Z= 0.287 Chirality : 0.042 0.216 1391 Planarity : 0.004 0.045 1523 Dihedral : 5.314 38.275 1380 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.18 % Allowed : 19.09 % Favored : 77.73 % 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: 0.46 (0.25), residues: 1101 helix: 2.12 (0.27), residues: 379 sheet: 0.35 (0.32), residues: 258 loop : -1.32 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 PHE 0.011 0.001 PHE B 253 TYR 0.025 0.001 TYR S 235 ARG 0.006 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 454) hydrogen bonds : angle 4.36631 ( 1293) SS BOND : bond 0.00548 ( 3) SS BOND : angle 1.18669 ( 6) covalent geometry : bond 0.00323 ( 8967) covalent geometry : angle 0.57425 (12161) *********************** 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 144 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.987 Fit side-chains REVERT: A 186 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: A 276 GLU cc_start: 0.7364 (mp0) cc_final: 0.7081 (mp0) REVERT: A 305 CYS cc_start: 0.7749 (p) cc_final: 0.7262 (p) REVERT: B 234 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8996 (m-80) REVERT: G 21 MET cc_start: 0.8890 (mmm) cc_final: 0.8013 (tmt) REVERT: R 158 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7880 (tp40) REVERT: R 309 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7942 (ptm) REVERT: S 191 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7927 (mpt-90) REVERT: S 235 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6991 (t80) outliers start: 30 outliers final: 13 residues processed: 133 average time/residue: 1.2645 time to fit residues: 179.1353 Evaluate side-chains 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain B residue 275 SER 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 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 42 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 102 optimal weight: 0.0000 chunk 76 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.128963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097926 restraints weight = 11950.501| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.98 r_work: 0.3066 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1122 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= 0.136 Angle : 0.566 9.433 12167 Z= 0.284 Chirality : 0.042 0.213 1391 Planarity : 0.004 0.044 1523 Dihedral : 5.232 39.806 1380 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.03 % Allowed : 18.98 % Favored : 76.99 % 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: 2.14 (0.27), residues: 379 sheet: 0.37 (0.32), residues: 258 loop : -1.33 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 187 TYR 0.025 0.001 TYR S 235 ARG 0.007 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 454) hydrogen bonds : angle 4.33585 ( 1293) SS BOND : bond 0.00535 ( 3) SS BOND : angle 1.30590 ( 6) covalent geometry : bond 0.00318 ( 8967) covalent geometry : angle 0.56547 (12161) *********************** 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 149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.941 Fit side-chains REVERT: A 186 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: A 276 GLU cc_start: 0.7422 (mp0) cc_final: 0.7059 (mp0) REVERT: A 305 CYS cc_start: 0.7787 (p) cc_final: 0.7268 (p) REVERT: G 21 MET cc_start: 0.8871 (mmm) cc_final: 0.7976 (tmt) REVERT: G 42 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: R 158 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7877 (tp40) REVERT: R 309 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7926 (ptm) REVERT: S 191 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7921 (mpt-90) REVERT: S 235 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6982 (t80) outliers start: 38 outliers final: 13 residues processed: 134 average time/residue: 1.3117 time to fit residues: 186.8668 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 : 0.943 ------------------------------------------------------------------------------- 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 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 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 98 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.129657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098533 restraints weight = 11945.907| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.99 r_work: 0.3080 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1171 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= 0.122 Angle : 0.557 9.707 12167 Z= 0.278 Chirality : 0.042 0.204 1391 Planarity : 0.004 0.044 1523 Dihedral : 5.088 40.141 1380 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.24 % Allowed : 19.30 % 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: 0.52 (0.26), residues: 1101 helix: 2.20 (0.27), residues: 379 sheet: 0.46 (0.32), residues: 256 loop : -1.34 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS A 195 PHE 0.011 0.001 PHE R 187 TYR 0.024 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 454) hydrogen bonds : angle 4.29534 ( 1293) SS BOND : bond 0.00510 ( 3) SS BOND : angle 1.17564 ( 6) covalent geometry : bond 0.00284 ( 8967) covalent geometry : angle 0.55685 (12161) *********************** 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 152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.988 Fit side-chains REVERT: A 186 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: A 276 GLU cc_start: 0.7404 (mp0) cc_final: 0.7081 (mp0) REVERT: A 305 CYS cc_start: 0.7922 (p) cc_final: 0.7384 (p) REVERT: G 21 MET cc_start: 0.8875 (mmm) cc_final: 0.7992 (tmt) REVERT: R 158 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7963 (tp40) REVERT: R 309 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8011 (ptm) REVERT: S 82 GLN cc_start: 0.8809 (tp40) cc_final: 0.8546 (tp40) REVERT: S 235 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.6990 (t80) outliers start: 40 outliers final: 17 residues processed: 139 average time/residue: 1.2121 time to fit residues: 179.6824 Evaluate side-chains 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 70 LEU 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 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 217 VAL Chi-restraints excluded: chain R residue 309 MET 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 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 81 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.130798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099676 restraints weight = 11866.252| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.02 r_work: 0.3095 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1301 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 : 0.560 9.766 12167 Z= 0.278 Chirality : 0.041 0.189 1391 Planarity : 0.004 0.044 1523 Dihedral : 4.877 39.561 1380 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.92 % Allowed : 19.62 % 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: 0.55 (0.25), residues: 1101 helix: 2.24 (0.27), residues: 380 sheet: 0.39 (0.32), residues: 248 loop : -1.27 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE R 187 TYR 0.022 0.001 TYR S 235 ARG 0.007 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 454) hydrogen bonds : angle 4.23758 ( 1293) SS BOND : bond 0.00467 ( 3) SS BOND : angle 1.25731 ( 6) covalent geometry : bond 0.00255 ( 8967) covalent geometry : angle 0.55947 (12161) *********************** 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 148 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 1.960 Fit side-chains REVERT: A 276 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 305 CYS cc_start: 0.7829 (p) cc_final: 0.7304 (p) REVERT: G 21 MET cc_start: 0.8890 (mmm) cc_final: 0.7936 (tmt) REVERT: R 158 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7868 (tp40) REVERT: R 309 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8042 (ptm) REVERT: S 235 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6815 (t80) outliers start: 37 outliers final: 16 residues processed: 134 average time/residue: 1.4206 time to fit residues: 202.6438 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 : 1.009 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098210 restraints weight = 11780.635| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.00 r_work: 0.3071 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1336 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= 0.139 Angle : 0.592 10.512 12167 Z= 0.291 Chirality : 0.042 0.211 1391 Planarity : 0.004 0.045 1523 Dihedral : 4.984 39.875 1378 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.71 % Allowed : 20.15 % 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: 2.15 (0.27), residues: 380 sheet: 0.38 (0.32), residues: 259 loop : -1.32 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE R 187 TYR 0.024 0.001 TYR S 235 ARG 0.004 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 454) hydrogen bonds : angle 4.32451 ( 1293) SS BOND : bond 0.00533 ( 3) SS BOND : angle 1.43474 ( 6) covalent geometry : bond 0.00329 ( 8967) covalent geometry : angle 0.59101 (12161) *********************** 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 140 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.521 Fit side-chains REVERT: A 276 GLU cc_start: 0.7439 (mp0) cc_final: 0.7090 (mp0) REVERT: A 305 CYS cc_start: 0.7846 (p) cc_final: 0.7317 (p) REVERT: G 21 MET cc_start: 0.8893 (mmm) cc_final: 0.7932 (tmt) REVERT: R 158 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7924 (tp40) REVERT: R 309 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8056 (ptm) REVERT: S 235 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6974 (t80) outliers start: 35 outliers final: 18 residues processed: 129 average time/residue: 1.4104 time to fit residues: 194.6428 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 : 1.048 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 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 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 155 VAL 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 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 0.0000 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 0.0170 chunk 55 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102471 restraints weight = 11756.652| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.00 r_work: 0.3148 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1538 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= 0.102 Angle : 0.564 11.401 12167 Z= 0.277 Chirality : 0.041 0.189 1391 Planarity : 0.003 0.044 1523 Dihedral : 4.557 36.907 1378 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.76 % Allowed : 21.53 % Favored : 75.72 % 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: 0.59 (0.25), residues: 1101 helix: 2.23 (0.27), residues: 382 sheet: 0.50 (0.33), residues: 242 loop : -1.25 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 272 PHE 0.014 0.001 PHE R 187 TYR 0.018 0.001 TYR S 235 ARG 0.003 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 454) hydrogen bonds : angle 4.19334 ( 1293) SS BOND : bond 0.00384 ( 3) SS BOND : angle 1.00868 ( 6) covalent geometry : bond 0.00222 ( 8967) covalent geometry : angle 0.56321 (12161) *********************** 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: 26 poor density : 112 time to evaluate : 0.902 Fit side-chains REVERT: A 276 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: A 305 CYS cc_start: 0.7870 (p) cc_final: 0.7337 (p) REVERT: G 21 MET cc_start: 0.8884 (mmm) cc_final: 0.7961 (tmt) REVERT: R 158 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7953 (tp40) REVERT: R 309 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8027 (ptm) REVERT: S 235 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6648 (t80) outliers start: 26 outliers final: 12 residues processed: 127 average time/residue: 1.2824 time to fit residues: 173.6305 Evaluate side-chains 120 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 G residue 25 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097974 restraints weight = 11653.306| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.94 r_work: 0.3076 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8970 Z= 0.151 Angle : 0.628 12.711 12167 Z= 0.306 Chirality : 0.043 0.212 1391 Planarity : 0.004 0.048 1523 Dihedral : 4.922 37.162 1378 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.29 % Allowed : 21.42 % Favored : 75.29 % 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: 2.14 (0.27), residues: 380 sheet: 0.38 (0.32), residues: 259 loop : -1.30 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.006 0.001 HIS R 272 PHE 0.016 0.001 PHE R 187 TYR 0.024 0.001 TYR S 235 ARG 0.001 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 454) hydrogen bonds : angle 4.35293 ( 1293) SS BOND : bond 0.00561 ( 3) SS BOND : angle 1.42713 ( 6) covalent geometry : bond 0.00360 ( 8967) covalent geometry : angle 0.62728 (12161) *********************** 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 137 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.920 Fit side-chains REVERT: A 276 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 305 CYS cc_start: 0.8005 (p) cc_final: 0.7473 (p) REVERT: G 21 MET cc_start: 0.8860 (mmm) cc_final: 0.7981 (tmt) REVERT: R 158 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8000 (tp40) REVERT: R 309 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8041 (ptm) REVERT: S 235 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.7031 (t80) outliers start: 31 outliers final: 15 residues processed: 124 average time/residue: 1.1814 time to fit residues: 156.8199 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 : 0.924 ------------------------------------------------------------------------------- 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 276 GLU Chi-restraints excluded: chain A residue 329 THR 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 102 LEU Chi-restraints excluded: chain R residue 106 LEU 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 138 ILE 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 59 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN B 35 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098357 restraints weight = 11587.220| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.94 r_work: 0.3080 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8970 Z= 0.140 Angle : 0.627 13.438 12167 Z= 0.305 Chirality : 0.043 0.207 1391 Planarity : 0.003 0.046 1523 Dihedral : 4.914 37.607 1378 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.55 % Allowed : 22.69 % 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: 0.45 (0.25), residues: 1101 helix: 2.08 (0.27), residues: 382 sheet: 0.35 (0.32), residues: 259 loop : -1.30 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 117 HIS 0.004 0.001 HIS R 272 PHE 0.015 0.001 PHE R 187 TYR 0.024 0.001 TYR S 235 ARG 0.002 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 454) hydrogen bonds : angle 4.35959 ( 1293) SS BOND : bond 0.00519 ( 3) SS BOND : angle 1.31094 ( 6) covalent geometry : bond 0.00331 ( 8967) covalent geometry : angle 0.62598 (12161) ********************** 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 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.911 Fit side-chains REVERT: A 276 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: A 305 CYS cc_start: 0.7991 (p) cc_final: 0.7453 (p) REVERT: G 21 MET cc_start: 0.8881 (mmm) cc_final: 0.7990 (tmt) REVERT: R 158 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7991 (tp40) REVERT: R 309 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8033 (ptm) REVERT: S 235 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6932 (t80) outliers start: 24 outliers final: 12 residues processed: 115 average time/residue: 1.2634 time to fit residues: 154.8854 Evaluate side-chains 114 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 276 GLU Chi-restraints excluded: chain A residue 329 THR 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 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 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 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098348 restraints weight = 11670.575| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.95 r_work: 0.3085 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1473 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= 0.137 Angle : 0.628 12.725 12167 Z= 0.305 Chirality : 0.043 0.204 1391 Planarity : 0.004 0.047 1523 Dihedral : 4.905 37.736 1378 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.44 % Allowed : 23.12 % Favored : 74.44 % 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: 0.42 (0.25), residues: 1101 helix: 2.05 (0.27), residues: 381 sheet: 0.34 (0.32), residues: 259 loop : -1.32 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 117 HIS 0.004 0.001 HIS R 272 PHE 0.015 0.001 PHE R 187 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 454) hydrogen bonds : angle 4.35639 ( 1293) SS BOND : bond 0.00513 ( 3) SS BOND : angle 1.28484 ( 6) covalent geometry : bond 0.00322 ( 8967) covalent geometry : angle 0.62787 (12161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7058.53 seconds wall clock time: 123 minutes 11.61 seconds (7391.61 seconds total)