Starting phenix.real_space_refine on Wed Sep 17 13:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzf_38794/09_2025/8xzf_38794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzf_38794/09_2025/8xzf_38794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xzf_38794/09_2025/8xzf_38794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzf_38794/09_2025/8xzf_38794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xzf_38794/09_2025/8xzf_38794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzf_38794/09_2025/8xzf_38794.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 5774 2.51 5 N 1534 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9062 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2404 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1736 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2595 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1774 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 79 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 2, 'TRANS': 7} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 2} Time building chain proxies: 2.38, per 1000 atoms: 0.26 Number of scatterers: 9062 At special positions: 0 Unit cell: (98.58, 132.06, 116.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1681 8.00 N 1534 7.00 C 5774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.03 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.02 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " MED L 11 " - " PRO L 10 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 364.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB MED L 11 " Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 37.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 26 through 55 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.063A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 Processing helix chain 'R' and resid 135 through 139 removed outlier: 3.536A pdb=" N ALA R 138 " --> pdb=" O VAL R 135 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG R 139 " --> pdb=" O ALA R 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 135 through 139' Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 167 Processing helix chain 'R' and resid 193 through 211 removed outlier: 3.839A pdb=" N TRP R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 232 Processing helix chain 'R' and resid 236 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 305 Proline residue: R 292 - end of helix removed outlier: 3.561A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS R 303 " --> pdb=" O TYR R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.593A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.835A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 4.181A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.810A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.807A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.519A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.769A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.587A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.440A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.742A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.836A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.679A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.566A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.476A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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: 6.926A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.405A 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: 3.939A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.492A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1281 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: 1.68 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2896 1.34 - 1.46: 2283 1.46 - 1.58: 3976 1.58 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 9260 Sorted by residual: bond pdb=" N MET B 325 " pdb=" CA MET B 325 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.99e+00 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" N TRP R 279 " pdb=" CA TRP R 279 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.17e-02 7.31e+03 8.00e+00 bond pdb=" N ILE A 253 " pdb=" CA ILE A 253 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.79e+00 bond pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.77e+00 ... (remaining 9255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 12107 1.66 - 3.33: 379 3.33 - 4.99: 47 4.99 - 6.66: 10 6.66 - 8.32: 7 Bond angle restraints: 12550 Sorted by residual: angle pdb=" O ILE B 37 " pdb=" C ILE B 37 " pdb=" N ASP B 38 " ideal model delta sigma weight residual 121.83 127.09 -5.26 1.03e+00 9.43e-01 2.61e+01 angle pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" O GLY B 41 " ideal model delta sigma weight residual 122.13 117.72 4.41 8.90e-01 1.26e+00 2.45e+01 angle pdb=" C ASN R 175 " pdb=" N THR R 176 " pdb=" CA THR R 176 " ideal model delta sigma weight residual 121.98 114.54 7.44 1.53e+00 4.27e-01 2.36e+01 angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 119.76 124.60 -4.84 1.03e+00 9.43e-01 2.21e+01 angle pdb=" N MET B 325 " pdb=" CA MET B 325 " pdb=" C MET B 325 " ideal model delta sigma weight residual 111.14 115.52 -4.38 1.08e+00 8.57e-01 1.65e+01 ... (remaining 12545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5014 17.86 - 35.71: 392 35.71 - 53.57: 48 53.57 - 71.43: 10 71.43 - 89.29: 9 Dihedral angle restraints: 5473 sinusoidal: 2106 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 281 " pdb=" CB CYS R 281 " ideal model delta sinusoidal sigma weight residual -86.00 -5.21 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 149.27 -56.27 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" C ASP B 38 " pdb=" N ASP B 38 " pdb=" CA ASP B 38 " pdb=" CB ASP B 38 " ideal model delta harmonic sigma weight residual -122.60 -134.89 12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 5470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1265 0.078 - 0.157: 150 0.157 - 0.235: 4 0.235 - 0.314: 0 0.314 - 0.392: 1 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ASP B 38 " pdb=" N ASP B 38 " pdb=" C ASP B 38 " pdb=" CB ASP B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LEU R 276 " pdb=" N LEU R 276 " pdb=" C LEU R 276 " pdb=" CB LEU R 276 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA LEU R 277 " pdb=" N LEU R 277 " pdb=" C LEU R 277 " pdb=" CB LEU R 277 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1417 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 175 " -0.014 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C ASN R 175 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN R 175 " -0.016 2.00e-02 2.50e+03 pdb=" N THR R 176 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 36 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C ASN B 36 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN B 36 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE B 37 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER S 71 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.04e+00 pdb=" C SER S 71 " 0.039 2.00e-02 2.50e+03 pdb=" O SER S 71 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG S 72 " -0.013 2.00e-02 2.50e+03 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 137 2.65 - 3.21: 8439 3.21 - 3.78: 14543 3.78 - 4.34: 20945 4.34 - 4.90: 34663 Nonbonded interactions: 78727 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.091 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.093 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.231 3.040 nonbonded pdb=" O GLN R 318 " pdb=" OG SER R 322 " model vdw 2.257 3.040 ... (remaining 78722 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.007 0.065 9266 Z= 0.323 Angle : 0.719 8.320 12563 Z= 0.427 Chirality : 0.049 0.392 1420 Planarity : 0.004 0.052 1581 Dihedral : 12.983 89.287 3285 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 0.51 % Allowed : 4.60 % Favored : 94.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.86 % 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: -2.36 (0.22), residues: 1139 helix: -1.03 (0.22), residues: 407 sheet: -1.41 (0.28), residues: 297 loop : -2.01 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.017 0.002 TYR S 103 PHE 0.022 0.002 PHE B 151 TRP 0.017 0.002 TRP B 63 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00702 ( 9260) covalent geometry : angle 0.71713 (12550) SS BOND : bond 0.00582 ( 5) SS BOND : angle 2.00858 ( 10) hydrogen bonds : bond 0.15970 ( 453) hydrogen bonds : angle 7.43186 ( 1281) link_TRANS : bond 0.00308 ( 1) link_TRANS : angle 0.70348 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7409 (mp0) cc_final: 0.7040 (pm20) REVERT: B 124 TYR cc_start: 0.8682 (m-80) cc_final: 0.8464 (m-80) REVERT: B 130 GLU cc_start: 0.7823 (mp0) cc_final: 0.7470 (mp0) REVERT: B 256 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7426 (mtm-85) REVERT: S 83 MET cc_start: 0.8734 (mtm) cc_final: 0.8488 (mtp) outliers start: 5 outliers final: 0 residues processed: 169 average time/residue: 0.7639 time to fit residues: 135.8295 Evaluate side-chains 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 ASN R 112 ASN A 213 HIS B 259 GLN S 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.086623 restraints weight = 14702.504| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.75 r_work: 0.3122 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9266 Z= 0.177 Angle : 0.614 7.714 12563 Z= 0.325 Chirality : 0.043 0.173 1420 Planarity : 0.005 0.047 1581 Dihedral : 4.884 22.563 1262 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.04 % Allowed : 11.64 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.07 (0.24), residues: 1139 helix: 0.34 (0.25), residues: 407 sheet: -0.80 (0.28), residues: 296 loop : -1.54 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.016 0.002 TYR S 178 PHE 0.013 0.001 PHE B 151 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9260) covalent geometry : angle 0.61299 (12550) SS BOND : bond 0.00403 ( 5) SS BOND : angle 1.54427 ( 10) hydrogen bonds : bond 0.04069 ( 453) hydrogen bonds : angle 5.50562 ( 1281) link_TRANS : bond 0.00331 ( 1) link_TRANS : angle 0.32164 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 162 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7760 (mmt) REVERT: R 198 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: R 233 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7875 (mtt90) REVERT: R 235 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: R 262 MET cc_start: 0.7954 (tpt) cc_final: 0.7737 (tpt) REVERT: A 29 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7875 (tppt) REVERT: A 289 GLU cc_start: 0.7535 (mp0) cc_final: 0.6952 (pm20) REVERT: B 96 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8159 (mpt-90) REVERT: B 124 TYR cc_start: 0.8836 (m-80) cc_final: 0.8557 (m-80) REVERT: B 130 GLU cc_start: 0.8228 (mp0) cc_final: 0.7940 (mp0) REVERT: G 52 THR cc_start: 0.8354 (m) cc_final: 0.7978 (p) REVERT: S 208 GLU cc_start: 0.7186 (mp0) cc_final: 0.6946 (mp0) outliers start: 20 outliers final: 6 residues processed: 148 average time/residue: 0.8685 time to fit residues: 134.7696 Evaluate side-chains 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 232 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 294 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087795 restraints weight = 14693.026| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.75 r_work: 0.3144 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9266 Z= 0.141 Angle : 0.564 8.358 12563 Z= 0.297 Chirality : 0.042 0.144 1420 Planarity : 0.004 0.052 1581 Dihedral : 4.539 22.307 1262 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.04 % Allowed : 14.50 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.36 (0.25), residues: 1139 helix: 1.08 (0.26), residues: 404 sheet: -0.54 (0.29), residues: 285 loop : -1.19 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 168 TYR 0.014 0.001 TYR S 178 PHE 0.012 0.001 PHE B 151 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9260) covalent geometry : angle 0.56293 (12550) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.41726 ( 10) hydrogen bonds : bond 0.03589 ( 453) hydrogen bonds : angle 5.08236 ( 1281) link_TRANS : bond 0.00285 ( 1) link_TRANS : angle 0.34908 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.371 Fit side-chains REVERT: R 198 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6698 (pm20) REVERT: R 235 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: R 262 MET cc_start: 0.7855 (tpt) cc_final: 0.7600 (tpt) REVERT: R 271 TYR cc_start: 0.8026 (t80) cc_final: 0.7253 (t80) REVERT: A 29 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7907 (tppt) REVERT: A 243 MET cc_start: 0.7802 (tpp) cc_final: 0.7563 (tpp) REVERT: A 289 GLU cc_start: 0.7448 (mp0) cc_final: 0.6812 (pm20) REVERT: A 313 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7616 (mtt90) REVERT: B 96 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8173 (mpt-90) REVERT: B 124 TYR cc_start: 0.8811 (m-80) cc_final: 0.8543 (m-80) REVERT: B 130 GLU cc_start: 0.8270 (mp0) cc_final: 0.7946 (mp0) REVERT: B 135 VAL cc_start: 0.8884 (t) cc_final: 0.8604 (p) REVERT: G 21 MET cc_start: 0.7124 (ttt) cc_final: 0.6225 (mpm) REVERT: G 36 ASP cc_start: 0.8199 (m-30) cc_final: 0.7995 (m-30) REVERT: G 52 THR cc_start: 0.8323 (m) cc_final: 0.8036 (p) REVERT: S 208 GLU cc_start: 0.7217 (mp0) cc_final: 0.6936 (mp0) REVERT: S 233 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7743 (mp) outliers start: 20 outliers final: 4 residues processed: 144 average time/residue: 0.7579 time to fit residues: 115.2219 Evaluate side-chains 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 0.0040 chunk 102 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 259 GLN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.087614 restraints weight = 14826.817| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.75 r_work: 0.3141 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9266 Z= 0.144 Angle : 0.557 7.659 12563 Z= 0.293 Chirality : 0.042 0.175 1420 Planarity : 0.004 0.054 1581 Dihedral : 4.429 20.738 1262 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.45 % Allowed : 16.14 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.09 (0.25), residues: 1139 helix: 1.37 (0.26), residues: 404 sheet: -0.43 (0.29), residues: 287 loop : -1.08 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 168 TYR 0.019 0.001 TYR R 271 PHE 0.012 0.001 PHE B 151 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9260) covalent geometry : angle 0.55614 (12550) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.48243 ( 10) hydrogen bonds : bond 0.03501 ( 453) hydrogen bonds : angle 4.91436 ( 1281) link_TRANS : bond 0.00225 ( 1) link_TRANS : angle 0.30107 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.341 Fit side-chains REVERT: R 162 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7818 (mmt) REVERT: R 198 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: R 235 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: R 262 MET cc_start: 0.7900 (tpt) cc_final: 0.7622 (tpt) REVERT: R 271 TYR cc_start: 0.7843 (t80) cc_final: 0.7197 (t80) REVERT: A 29 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7880 (tppt) REVERT: A 243 MET cc_start: 0.7814 (tpp) cc_final: 0.7519 (tpp) REVERT: A 289 GLU cc_start: 0.7420 (mp0) cc_final: 0.6744 (pm20) REVERT: A 313 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7582 (mmt-90) REVERT: B 96 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8093 (mpt-90) REVERT: B 124 TYR cc_start: 0.8798 (m-80) cc_final: 0.8522 (m-80) REVERT: B 130 GLU cc_start: 0.8348 (mp0) cc_final: 0.8015 (mp0) REVERT: B 135 VAL cc_start: 0.8876 (t) cc_final: 0.8590 (p) REVERT: B 237 ASN cc_start: 0.8462 (p0) cc_final: 0.8220 (p0) REVERT: G 21 MET cc_start: 0.6635 (ttt) cc_final: 0.6305 (mpm) REVERT: G 36 ASP cc_start: 0.8239 (m-30) cc_final: 0.8008 (m-30) REVERT: G 52 THR cc_start: 0.8359 (m) cc_final: 0.8090 (p) REVERT: S 233 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7699 (mp) outliers start: 24 outliers final: 5 residues processed: 143 average time/residue: 0.7448 time to fit residues: 112.4583 Evaluate side-chains 135 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087369 restraints weight = 14722.634| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.75 r_work: 0.3133 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9266 Z= 0.150 Angle : 0.551 8.726 12563 Z= 0.290 Chirality : 0.042 0.162 1420 Planarity : 0.004 0.052 1581 Dihedral : 4.386 20.320 1262 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.96 % Allowed : 16.45 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.05 (0.25), residues: 1139 helix: 1.52 (0.26), residues: 403 sheet: -0.33 (0.29), residues: 280 loop : -1.05 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 168 TYR 0.020 0.001 TYR R 271 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9260) covalent geometry : angle 0.54981 (12550) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.45728 ( 10) hydrogen bonds : bond 0.03478 ( 453) hydrogen bonds : angle 4.85311 ( 1281) link_TRANS : bond 0.00285 ( 1) link_TRANS : angle 0.22235 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.381 Fit side-chains REVERT: R 101 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5797 (m-10) REVERT: R 162 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7770 (mmt) REVERT: R 165 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7435 (tpt) REVERT: R 198 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: R 235 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: R 262 MET cc_start: 0.7912 (tpt) cc_final: 0.7620 (tpt) REVERT: R 271 TYR cc_start: 0.7796 (t80) cc_final: 0.7194 (t80) REVERT: A 243 MET cc_start: 0.7823 (tpp) cc_final: 0.7489 (tpp) REVERT: A 289 GLU cc_start: 0.7406 (mp0) cc_final: 0.6693 (pm20) REVERT: A 313 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7571 (mmt-90) REVERT: B 96 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8222 (mtt90) REVERT: B 124 TYR cc_start: 0.8789 (m-80) cc_final: 0.8472 (m-80) REVERT: B 130 GLU cc_start: 0.8361 (mp0) cc_final: 0.8052 (mp0) REVERT: B 135 VAL cc_start: 0.8862 (t) cc_final: 0.8549 (p) REVERT: B 138 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: B 214 ARG cc_start: 0.7543 (mmp80) cc_final: 0.7265 (mmp80) REVERT: B 217 MET cc_start: 0.8306 (ppp) cc_final: 0.8082 (pp-130) REVERT: B 237 ASN cc_start: 0.8479 (p0) cc_final: 0.8235 (p0) REVERT: G 52 THR cc_start: 0.8375 (m) cc_final: 0.8098 (p) outliers start: 29 outliers final: 9 residues processed: 150 average time/residue: 0.6848 time to fit residues: 108.9285 Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN G 59 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.087607 restraints weight = 14848.384| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.76 r_work: 0.3144 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9266 Z= 0.140 Angle : 0.549 8.195 12563 Z= 0.287 Chirality : 0.042 0.164 1420 Planarity : 0.004 0.050 1581 Dihedral : 4.317 20.330 1262 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 15.73 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.17 (0.25), residues: 1139 helix: 1.65 (0.26), residues: 403 sheet: -0.25 (0.30), residues: 278 loop : -1.01 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 168 TYR 0.016 0.001 TYR R 271 PHE 0.012 0.001 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9260) covalent geometry : angle 0.54783 (12550) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.40522 ( 10) hydrogen bonds : bond 0.03396 ( 453) hydrogen bonds : angle 4.79726 ( 1281) link_TRANS : bond 0.00299 ( 1) link_TRANS : angle 0.23349 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.380 Fit side-chains REVERT: R 101 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5817 (m-10) REVERT: R 162 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7834 (mmt) REVERT: R 198 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: R 235 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: R 262 MET cc_start: 0.7902 (tpt) cc_final: 0.7616 (tpt) REVERT: R 271 TYR cc_start: 0.7687 (t80) cc_final: 0.7095 (t80) REVERT: A 29 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7939 (tppt) REVERT: A 289 GLU cc_start: 0.7414 (mp0) cc_final: 0.6695 (pm20) REVERT: A 313 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7550 (mmt-90) REVERT: B 96 ARG cc_start: 0.8355 (mtt180) cc_final: 0.8146 (mtt90) REVERT: B 124 TYR cc_start: 0.8780 (m-80) cc_final: 0.8479 (m-80) REVERT: B 130 GLU cc_start: 0.8333 (mp0) cc_final: 0.8027 (mp0) REVERT: B 135 VAL cc_start: 0.8853 (t) cc_final: 0.8546 (p) REVERT: B 138 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: B 201 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8554 (p) REVERT: B 237 ASN cc_start: 0.8484 (p0) cc_final: 0.8265 (p0) REVERT: G 22 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: G 52 THR cc_start: 0.8361 (m) cc_final: 0.8101 (p) REVERT: S 171 GLN cc_start: 0.8124 (mt0) cc_final: 0.7916 (mt0) REVERT: S 190 ARG cc_start: 0.7012 (mtp180) cc_final: 0.6609 (ptt180) outliers start: 35 outliers final: 18 residues processed: 156 average time/residue: 0.6674 time to fit residues: 110.6116 Evaluate side-chains 154 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 137 ASN Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 0.0970 chunk 88 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088516 restraints weight = 14753.934| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.73 r_work: 0.3161 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9266 Z= 0.120 Angle : 0.533 8.111 12563 Z= 0.278 Chirality : 0.041 0.164 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.181 20.119 1262 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.96 % Allowed : 16.75 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.33 (0.25), residues: 1139 helix: 1.85 (0.26), residues: 403 sheet: -0.16 (0.30), residues: 268 loop : -0.97 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 168 TYR 0.015 0.001 TYR R 185 PHE 0.015 0.001 PHE A 189 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9260) covalent geometry : angle 0.53226 (12550) SS BOND : bond 0.00136 ( 5) SS BOND : angle 1.31737 ( 10) hydrogen bonds : bond 0.03258 ( 453) hydrogen bonds : angle 4.69004 ( 1281) link_TRANS : bond 0.00273 ( 1) link_TRANS : angle 0.24802 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.376 Fit side-chains REVERT: R 101 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5785 (m-10) REVERT: R 162 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7766 (mmt) REVERT: R 198 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6323 (pm20) REVERT: R 262 MET cc_start: 0.7903 (tpt) cc_final: 0.7615 (tpt) REVERT: R 271 TYR cc_start: 0.7652 (t80) cc_final: 0.7024 (t80) REVERT: A 29 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7974 (tppt) REVERT: A 243 MET cc_start: 0.7858 (tpp) cc_final: 0.7253 (tpp) REVERT: A 246 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.7850 (p) REVERT: A 289 GLU cc_start: 0.7406 (mp0) cc_final: 0.6678 (pm20) REVERT: B 96 ARG cc_start: 0.8365 (mtt180) cc_final: 0.8085 (mpt-90) REVERT: B 124 TYR cc_start: 0.8755 (m-80) cc_final: 0.8444 (m-80) REVERT: B 130 GLU cc_start: 0.8351 (mp0) cc_final: 0.8028 (mp0) REVERT: B 135 VAL cc_start: 0.8816 (t) cc_final: 0.8526 (p) REVERT: B 138 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: B 197 ARG cc_start: 0.8129 (tpt170) cc_final: 0.7873 (tpp-160) REVERT: B 201 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8444 (p) REVERT: B 237 ASN cc_start: 0.8482 (p0) cc_final: 0.8281 (p0) REVERT: G 22 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6581 (tt0) REVERT: G 52 THR cc_start: 0.8355 (m) cc_final: 0.8121 (p) REVERT: S 171 GLN cc_start: 0.8132 (mt0) cc_final: 0.7905 (mt0) outliers start: 29 outliers final: 12 residues processed: 156 average time/residue: 0.6747 time to fit residues: 111.6753 Evaluate side-chains 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 60 optimal weight: 0.0070 chunk 10 optimal weight: 0.2980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089007 restraints weight = 14820.701| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.76 r_work: 0.3167 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9266 Z= 0.118 Angle : 0.536 8.473 12563 Z= 0.277 Chirality : 0.041 0.160 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.101 20.089 1262 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.47 % Allowed : 16.24 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.39 (0.26), residues: 1139 helix: 1.90 (0.26), residues: 403 sheet: -0.14 (0.30), residues: 270 loop : -0.94 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.016 0.001 TYR R 185 PHE 0.012 0.001 PHE A 189 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9260) covalent geometry : angle 0.53516 (12550) SS BOND : bond 0.00278 ( 5) SS BOND : angle 1.24928 ( 10) hydrogen bonds : bond 0.03231 ( 453) hydrogen bonds : angle 4.61313 ( 1281) link_TRANS : bond 0.00296 ( 1) link_TRANS : angle 0.23333 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.443 Fit side-chains REVERT: R 101 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: R 162 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7731 (mmt) REVERT: R 198 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6272 (pm20) REVERT: R 262 MET cc_start: 0.7920 (tpt) cc_final: 0.7624 (tpt) REVERT: R 271 TYR cc_start: 0.7556 (t80) cc_final: 0.6993 (t80) REVERT: A 29 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7981 (tppt) REVERT: A 243 MET cc_start: 0.7833 (tpp) cc_final: 0.7190 (tpp) REVERT: A 246 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.7803 (p) REVERT: A 247 MET cc_start: 0.8261 (mtp) cc_final: 0.7842 (mtt) REVERT: A 289 GLU cc_start: 0.7385 (mp0) cc_final: 0.6626 (pm20) REVERT: B 96 ARG cc_start: 0.8335 (mtt180) cc_final: 0.8069 (mpt-90) REVERT: B 124 TYR cc_start: 0.8752 (m-80) cc_final: 0.8468 (m-80) REVERT: B 130 GLU cc_start: 0.8369 (mp0) cc_final: 0.8065 (mp0) REVERT: B 135 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8505 (p) REVERT: B 138 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: B 197 ARG cc_start: 0.8086 (tpt170) cc_final: 0.7821 (tpp-160) REVERT: B 201 SER cc_start: 0.8530 (m) cc_final: 0.8319 (p) REVERT: B 217 MET cc_start: 0.8166 (pp-130) cc_final: 0.7825 (pp-130) REVERT: G 52 THR cc_start: 0.8322 (m) cc_final: 0.8115 (p) REVERT: S 171 GLN cc_start: 0.8069 (mt0) cc_final: 0.7837 (mt0) REVERT: S 182 ASN cc_start: 0.8819 (m110) cc_final: 0.8525 (m110) outliers start: 34 outliers final: 14 residues processed: 157 average time/residue: 0.6947 time to fit residues: 115.6374 Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089060 restraints weight = 14745.692| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.74 r_work: 0.3168 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9266 Z= 0.119 Angle : 0.559 13.850 12563 Z= 0.286 Chirality : 0.042 0.210 1420 Planarity : 0.004 0.056 1581 Dihedral : 4.163 33.282 1262 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.96 % Allowed : 17.36 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.40 (0.26), residues: 1139 helix: 1.84 (0.26), residues: 404 sheet: -0.08 (0.31), residues: 270 loop : -0.91 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 24 TYR 0.021 0.001 TYR R 185 PHE 0.012 0.001 PHE A 189 TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9260) covalent geometry : angle 0.55782 (12550) SS BOND : bond 0.00257 ( 5) SS BOND : angle 1.30045 ( 10) hydrogen bonds : bond 0.03297 ( 453) hydrogen bonds : angle 4.59600 ( 1281) link_TRANS : bond 0.00299 ( 1) link_TRANS : angle 0.22191 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.393 Fit side-chains REVERT: R 101 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5822 (m-10) REVERT: R 162 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7730 (mmt) REVERT: R 198 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6094 (pm20) REVERT: R 262 MET cc_start: 0.7895 (tpt) cc_final: 0.7609 (tpt) REVERT: R 271 TYR cc_start: 0.7540 (t80) cc_final: 0.6987 (t80) REVERT: A 24 ARG cc_start: 0.7778 (mtm110) cc_final: 0.6770 (mtm-85) REVERT: A 29 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7988 (tppt) REVERT: A 243 MET cc_start: 0.7863 (tpp) cc_final: 0.7230 (tpp) REVERT: A 246 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.7845 (p) REVERT: A 247 MET cc_start: 0.8287 (mtp) cc_final: 0.7866 (mtt) REVERT: B 78 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8381 (mtmt) REVERT: B 96 ARG cc_start: 0.8349 (mtt180) cc_final: 0.8083 (mpt-90) REVERT: B 124 TYR cc_start: 0.8751 (m-80) cc_final: 0.8434 (m-80) REVERT: B 130 GLU cc_start: 0.8346 (mp0) cc_final: 0.7998 (mp0) REVERT: B 135 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 138 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: B 197 ARG cc_start: 0.8059 (tpt170) cc_final: 0.7817 (tpp-160) REVERT: B 201 SER cc_start: 0.8483 (m) cc_final: 0.8235 (p) REVERT: S 182 ASN cc_start: 0.8813 (m110) cc_final: 0.8536 (m110) outliers start: 29 outliers final: 13 residues processed: 153 average time/residue: 0.7107 time to fit residues: 115.1105 Evaluate side-chains 152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 197 TRP Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 103 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 340 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089873 restraints weight = 14738.121| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.74 r_work: 0.3187 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9266 Z= 0.110 Angle : 0.529 9.076 12563 Z= 0.273 Chirality : 0.041 0.158 1420 Planarity : 0.004 0.052 1581 Dihedral : 4.011 21.791 1262 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.55 % Allowed : 18.28 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.49 (0.26), residues: 1139 helix: 1.92 (0.27), residues: 403 sheet: -0.04 (0.31), residues: 272 loop : -0.86 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 24 TYR 0.019 0.001 TYR R 93 PHE 0.011 0.001 PHE A 189 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9260) covalent geometry : angle 0.52794 (12550) SS BOND : bond 0.00211 ( 5) SS BOND : angle 1.16710 ( 10) hydrogen bonds : bond 0.03067 ( 453) hydrogen bonds : angle 4.48490 ( 1281) link_TRANS : bond 0.00293 ( 1) link_TRANS : angle 0.28531 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.348 Fit side-chains REVERT: R 101 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5782 (m-10) REVERT: R 162 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7722 (mmt) REVERT: R 198 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5916 (pm20) REVERT: R 262 MET cc_start: 0.7882 (tpt) cc_final: 0.7598 (tpt) REVERT: R 271 TYR cc_start: 0.7522 (t80) cc_final: 0.6931 (t80) REVERT: A 24 ARG cc_start: 0.7724 (mtm110) cc_final: 0.6696 (mtm-85) REVERT: A 29 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8012 (tppt) REVERT: A 243 MET cc_start: 0.7863 (tpp) cc_final: 0.7236 (tpp) REVERT: A 246 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7865 (p) REVERT: A 247 MET cc_start: 0.8296 (mtp) cc_final: 0.7875 (mtt) REVERT: B 78 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8329 (mtmt) REVERT: B 96 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8153 (mpt-90) REVERT: B 124 TYR cc_start: 0.8709 (m-80) cc_final: 0.8419 (m-80) REVERT: B 130 GLU cc_start: 0.8301 (mp0) cc_final: 0.7924 (mp0) REVERT: B 135 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 138 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: B 197 ARG cc_start: 0.8072 (tpt170) cc_final: 0.7798 (tpp-160) REVERT: B 201 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8221 (p) REVERT: G 21 MET cc_start: 0.6628 (ptm) cc_final: 0.5805 (mpm) REVERT: S 182 ASN cc_start: 0.8777 (m110) cc_final: 0.8531 (m110) outliers start: 25 outliers final: 12 residues processed: 154 average time/residue: 0.6870 time to fit residues: 112.2944 Evaluate side-chains 154 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 0.0570 chunk 97 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 47 optimal weight: 0.0270 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 91 HIS S 3 GLN S 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.110254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.089906 restraints weight = 14638.194| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.74 r_work: 0.3191 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9266 Z= 0.112 Angle : 0.532 9.186 12563 Z= 0.274 Chirality : 0.041 0.159 1420 Planarity : 0.004 0.050 1581 Dihedral : 4.101 38.273 1262 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 2.86 % Allowed : 18.28 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.51 (0.26), residues: 1139 helix: 1.94 (0.26), residues: 403 sheet: -0.02 (0.31), residues: 272 loop : -0.85 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 24 TYR 0.018 0.001 TYR R 185 PHE 0.011 0.001 PHE A 189 TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9260) covalent geometry : angle 0.53072 (12550) SS BOND : bond 0.00217 ( 5) SS BOND : angle 1.21268 ( 10) hydrogen bonds : bond 0.03053 ( 453) hydrogen bonds : angle 4.44734 ( 1281) link_TRANS : bond 0.00271 ( 1) link_TRANS : angle 0.21235 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3810.19 seconds wall clock time: 65 minutes 54.11 seconds (3954.11 seconds total)