Starting phenix.real_space_refine on Mon May 12 10:31:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzf_38794/05_2025/8xzf_38794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzf_38794/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xzf_38794/05_2025/8xzf_38794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzf_38794/05_2025/8xzf_38794.map" model { file = "/net/cci-nas-00/data/ceres_data/8xzf_38794/05_2025/8xzf_38794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzf_38794/05_2025/8xzf_38794.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ARG:plan': 1, 'ASP:plan': 2} 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: 5.05, per 1000 atoms: 0.56 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: 2.11 Conformation dependent library (CDL) restraints added in 987.5 milliseconds 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: 0.93 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: 2.43 Time building geometry restraints manager: 2.46 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.210 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.017 0.002 TRP B 63 HIS 0.003 0.001 HIS B 91 PHE 0.022 0.002 PHE B 151 TYR 0.017 0.002 TYR S 103 ARG 0.006 0.001 ARG B 150 Details of bonding type rmsd link_TRANS : bond 0.00308 ( 1) link_TRANS : angle 0.70348 ( 3) hydrogen bonds : bond 0.15970 ( 453) hydrogen bonds : angle 7.43186 ( 1281) SS BOND : bond 0.00582 ( 5) SS BOND : angle 2.00858 ( 10) covalent geometry : bond 0.00702 ( 9260) covalent geometry : angle 0.71713 (12550) *********************** 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 : 0.960 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: 1.4319 time to fit residues: 255.8301 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 : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 91 HIS B 259 GLN S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.088692 restraints weight = 14393.234| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.77 r_work: 0.3153 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1626 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= 0.139 Angle : 0.584 7.709 12563 Z= 0.309 Chirality : 0.042 0.159 1420 Planarity : 0.004 0.045 1581 Dihedral : 4.701 22.756 1262 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 1.74 % Allowed : 11.85 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.24), residues: 1139 helix: 0.51 (0.25), residues: 407 sheet: -0.81 (0.29), residues: 285 loop : -1.45 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.004 0.001 HIS R 278 PHE 0.012 0.001 PHE L 14 TYR 0.017 0.001 TYR S 178 ARG 0.007 0.001 ARG A 313 Details of bonding type rmsd link_TRANS : bond 0.00262 ( 1) link_TRANS : angle 0.23574 ( 3) hydrogen bonds : bond 0.03806 ( 453) hydrogen bonds : angle 5.36268 ( 1281) SS BOND : bond 0.00253 ( 5) SS BOND : angle 1.41665 ( 10) covalent geometry : bond 0.00309 ( 9260) covalent geometry : angle 0.58340 (12550) *********************** 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 153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 162 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7685 (mmt) REVERT: R 198 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6708 (pm20) REVERT: A 29 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7881 (tppt) REVERT: A 247 MET cc_start: 0.8362 (mtp) cc_final: 0.8057 (mtt) REVERT: A 289 GLU cc_start: 0.7513 (mp0) cc_final: 0.6936 (pm20) REVERT: A 313 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7553 (mtt90) REVERT: B 96 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8126 (mpt-90) REVERT: B 124 TYR cc_start: 0.8800 (m-80) cc_final: 0.8515 (m-80) REVERT: B 130 GLU cc_start: 0.8245 (mp0) cc_final: 0.7900 (mp0) REVERT: B 135 VAL cc_start: 0.8893 (t) cc_final: 0.8606 (p) REVERT: G 52 THR cc_start: 0.8322 (m) cc_final: 0.7995 (p) outliers start: 17 outliers final: 5 residues processed: 142 average time/residue: 1.6183 time to fit residues: 242.6905 Evaluate side-chains 128 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087989 restraints weight = 14780.606| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.76 r_work: 0.3146 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9266 Z= 0.140 Angle : 0.559 8.132 12563 Z= 0.294 Chirality : 0.042 0.144 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.430 20.593 1262 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.15 % Allowed : 14.10 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.33 (0.25), residues: 1139 helix: 1.13 (0.26), residues: 404 sheet: -0.50 (0.29), residues: 285 loop : -1.22 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 PHE 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR S 178 ARG 0.004 0.000 ARG A 313 Details of bonding type rmsd link_TRANS : bond 0.00281 ( 1) link_TRANS : angle 0.32273 ( 3) hydrogen bonds : bond 0.03566 ( 453) hydrogen bonds : angle 5.01427 ( 1281) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.40089 ( 10) covalent geometry : bond 0.00324 ( 9260) covalent geometry : angle 0.55764 (12550) *********************** 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 155 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7103 (tpt) REVERT: R 198 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: R 262 MET cc_start: 0.8028 (tpt) cc_final: 0.7769 (tpt) REVERT: R 271 TYR cc_start: 0.8031 (t80) cc_final: 0.7236 (t80) REVERT: A 29 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7906 (tppt) REVERT: A 243 MET cc_start: 0.7756 (tpp) cc_final: 0.7545 (tpp) REVERT: A 247 MET cc_start: 0.8379 (mtp) cc_final: 0.8089 (mtt) REVERT: A 276 GLU cc_start: 0.7080 (pp20) cc_final: 0.6832 (pp20) REVERT: A 289 GLU cc_start: 0.7436 (mp0) cc_final: 0.6802 (pm20) REVERT: A 313 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7554 (mtt90) REVERT: B 96 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8141 (mpt-90) REVERT: B 124 TYR cc_start: 0.8834 (m-80) cc_final: 0.8541 (m-80) REVERT: B 130 GLU cc_start: 0.8299 (mp0) cc_final: 0.7976 (mp0) REVERT: B 135 VAL cc_start: 0.8885 (t) cc_final: 0.8626 (p) REVERT: G 52 THR cc_start: 0.8347 (m) cc_final: 0.8089 (p) REVERT: S 182 ASN cc_start: 0.8874 (m110) cc_final: 0.8547 (m110) REVERT: S 208 GLU cc_start: 0.7186 (mp0) cc_final: 0.6928 (mp0) REVERT: S 233 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7760 (mp) outliers start: 21 outliers final: 5 residues processed: 147 average time/residue: 1.3201 time to fit residues: 206.1474 Evaluate side-chains 133 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 198 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 83 MET 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 85 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085725 restraints weight = 14546.062| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.76 r_work: 0.3095 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9266 Z= 0.236 Angle : 0.620 8.850 12563 Z= 0.326 Chirality : 0.045 0.171 1420 Planarity : 0.005 0.054 1581 Dihedral : 4.757 20.912 1262 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.96 % Allowed : 15.12 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.32 (0.24), residues: 1139 helix: 1.10 (0.26), residues: 402 sheet: -0.43 (0.29), residues: 282 loop : -1.20 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS R 278 PHE 0.015 0.002 PHE B 151 TYR 0.021 0.002 TYR R 271 ARG 0.004 0.001 ARG B 219 Details of bonding type rmsd link_TRANS : bond 0.00344 ( 1) link_TRANS : angle 0.28731 ( 3) hydrogen bonds : bond 0.03986 ( 453) hydrogen bonds : angle 5.16658 ( 1281) SS BOND : bond 0.00543 ( 5) SS BOND : angle 1.89738 ( 10) covalent geometry : bond 0.00569 ( 9260) covalent geometry : angle 0.61813 (12550) *********************** 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 160 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: R 162 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7811 (mmt) REVERT: R 165 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7203 (tpt) REVERT: R 198 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: R 235 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: R 262 MET cc_start: 0.8110 (tpt) cc_final: 0.7866 (tpt) REVERT: R 271 TYR cc_start: 0.7856 (t80) cc_final: 0.7238 (t80) REVERT: A 29 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7857 (tppt) REVERT: A 275 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7178 (pt0) REVERT: A 289 GLU cc_start: 0.7436 (mp0) cc_final: 0.6781 (pm20) REVERT: B 96 ARG cc_start: 0.8431 (mtt180) cc_final: 0.8214 (mpt-90) REVERT: B 124 TYR cc_start: 0.8865 (m-80) cc_final: 0.8579 (m-80) REVERT: B 130 GLU cc_start: 0.8346 (mp0) cc_final: 0.8046 (mp0) REVERT: B 135 VAL cc_start: 0.8936 (t) cc_final: 0.8662 (p) REVERT: G 52 THR cc_start: 0.8415 (m) cc_final: 0.8065 (p) REVERT: S 180 MET cc_start: 0.8645 (ttp) cc_final: 0.8438 (tmm) REVERT: S 233 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7700 (mp) outliers start: 29 outliers final: 9 residues processed: 148 average time/residue: 1.3488 time to fit residues: 211.6494 Evaluate side-chains 147 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 246 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 145 ILE 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 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.088082 restraints weight = 14634.446| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.73 r_work: 0.3153 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9266 Z= 0.128 Angle : 0.544 8.253 12563 Z= 0.285 Chirality : 0.041 0.158 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.376 20.559 1262 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.86 % Allowed : 16.14 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.02 (0.25), residues: 1139 helix: 1.48 (0.26), residues: 403 sheet: -0.26 (0.30), residues: 278 loop : -1.12 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS R 278 PHE 0.012 0.001 PHE A 189 TYR 0.018 0.001 TYR R 271 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd link_TRANS : bond 0.00260 ( 1) link_TRANS : angle 0.26218 ( 3) hydrogen bonds : bond 0.03334 ( 453) hydrogen bonds : angle 4.80844 ( 1281) SS BOND : bond 0.00280 ( 5) SS BOND : angle 1.34383 ( 10) covalent geometry : bond 0.00289 ( 9260) covalent geometry : angle 0.54325 (12550) *********************** 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 159 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: R 101 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5796 (m-10) REVERT: R 162 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7853 (mmt) REVERT: R 165 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7200 (tpt) REVERT: R 198 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: R 262 MET cc_start: 0.8050 (tpt) cc_final: 0.7798 (tpt) REVERT: R 271 TYR cc_start: 0.7791 (t80) cc_final: 0.7191 (t80) REVERT: A 29 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7905 (tppt) REVERT: A 247 MET cc_start: 0.8327 (mtp) cc_final: 0.7905 (mtt) REVERT: A 275 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: A 289 GLU cc_start: 0.7417 (mp0) cc_final: 0.6685 (pm20) REVERT: A 313 ARG cc_start: 0.7879 (mpt90) cc_final: 0.7527 (mmt-90) REVERT: B 96 ARG cc_start: 0.8420 (mtt180) cc_final: 0.8213 (mtt90) REVERT: B 124 TYR cc_start: 0.8772 (m-80) cc_final: 0.8457 (m-80) REVERT: B 130 GLU cc_start: 0.8348 (mp0) cc_final: 0.8034 (mp0) REVERT: B 135 VAL cc_start: 0.8862 (t) cc_final: 0.8557 (p) REVERT: B 138 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: B 217 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7940 (ppp) REVERT: B 219 ARG cc_start: 0.8390 (mtp85) cc_final: 0.8133 (mtp85) REVERT: G 52 THR cc_start: 0.8348 (m) cc_final: 0.8126 (p) REVERT: S 208 GLU cc_start: 0.7290 (mp0) cc_final: 0.7037 (mp0) outliers start: 28 outliers final: 7 residues processed: 145 average time/residue: 1.3365 time to fit residues: 205.8503 Evaluate side-chains 139 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 186 SER 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 275 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 217 MET 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 17 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN 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 = 0.3579 r_free = 0.3579 target = 0.109080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088588 restraints weight = 14689.761| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.74 r_work: 0.3161 rms_B_bonded: 2.17 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: 0.7979 moved from start: 0.2398 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= 0.121 Angle : 0.529 8.510 12563 Z= 0.276 Chirality : 0.041 0.157 1420 Planarity : 0.004 0.050 1581 Dihedral : 4.210 20.491 1262 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.06 % Allowed : 16.55 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1139 helix: 1.76 (0.26), residues: 403 sheet: -0.23 (0.30), residues: 270 loop : -1.04 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 278 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR R 271 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd link_TRANS : bond 0.00259 ( 1) link_TRANS : angle 0.20278 ( 3) hydrogen bonds : bond 0.03241 ( 453) hydrogen bonds : angle 4.66905 ( 1281) SS BOND : bond 0.00209 ( 5) SS BOND : angle 1.29564 ( 10) covalent geometry : bond 0.00274 ( 9260) covalent geometry : angle 0.52778 (12550) *********************** 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 164 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.946 Fit side-chains REVERT: R 101 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.5811 (m-10) REVERT: R 162 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7833 (mmt) REVERT: R 165 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7147 (tpt) REVERT: R 198 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6645 (pm20) REVERT: R 235 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7196 (mm-30) REVERT: R 262 MET cc_start: 0.8015 (tpt) cc_final: 0.7763 (tpt) REVERT: R 271 TYR cc_start: 0.7650 (t80) cc_final: 0.7054 (t80) REVERT: A 246 SER cc_start: 0.8362 (m) cc_final: 0.7821 (p) REVERT: A 247 MET cc_start: 0.8308 (mtp) cc_final: 0.7843 (mtt) REVERT: A 275 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7110 (pt0) REVERT: A 289 GLU cc_start: 0.7410 (mp0) cc_final: 0.6655 (pm20) REVERT: A 313 ARG cc_start: 0.7858 (mpt90) cc_final: 0.7072 (ptp-110) REVERT: B 124 TYR cc_start: 0.8759 (m-80) cc_final: 0.8430 (m-80) REVERT: B 130 GLU cc_start: 0.8352 (mp0) cc_final: 0.7983 (mp0) REVERT: B 135 VAL cc_start: 0.8826 (t) cc_final: 0.8529 (p) REVERT: B 138 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 237 ASN cc_start: 0.8441 (p0) cc_final: 0.8236 (p0) REVERT: G 21 MET cc_start: 0.7137 (ttt) cc_final: 0.6310 (mpm) REVERT: G 52 THR cc_start: 0.8343 (m) cc_final: 0.8130 (p) REVERT: S 171 GLN cc_start: 0.8128 (mt0) cc_final: 0.7777 (mt0) REVERT: S 182 ASN cc_start: 0.8838 (m110) cc_final: 0.8518 (m110) REVERT: S 208 GLU cc_start: 0.7392 (mp0) cc_final: 0.7157 (mp0) outliers start: 30 outliers final: 11 residues processed: 152 average time/residue: 1.3161 time to fit residues: 214.1245 Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU 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 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 A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 275 GLU 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 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 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.088453 restraints weight = 14857.464| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.75 r_work: 0.3156 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9266 Z= 0.128 Angle : 0.538 8.763 12563 Z= 0.278 Chirality : 0.041 0.161 1420 Planarity : 0.004 0.050 1581 Dihedral : 4.200 19.413 1262 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.68 % Allowed : 16.55 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.27 (0.25), residues: 1139 helix: 1.78 (0.26), residues: 403 sheet: -0.19 (0.30), residues: 270 loop : -1.00 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS R 278 PHE 0.011 0.001 PHE A 189 TYR 0.016 0.001 TYR R 93 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd link_TRANS : bond 0.00292 ( 1) link_TRANS : angle 0.25476 ( 3) hydrogen bonds : bond 0.03269 ( 453) hydrogen bonds : angle 4.64116 ( 1281) SS BOND : bond 0.00311 ( 5) SS BOND : angle 1.35047 ( 10) covalent geometry : bond 0.00292 ( 9260) covalent geometry : angle 0.53652 (12550) *********************** 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 171 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.947 Fit side-chains REVERT: R 101 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5719 (m-10) REVERT: R 162 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7808 (mmt) REVERT: R 165 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7188 (tpt) REVERT: R 198 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6311 (pm20) REVERT: R 235 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: R 262 MET cc_start: 0.8008 (tpt) cc_final: 0.7760 (tpt) REVERT: R 271 TYR cc_start: 0.7662 (t80) cc_final: 0.7047 (t80) REVERT: A 246 SER cc_start: 0.8385 (OUTLIER) cc_final: 0.7834 (p) REVERT: A 247 MET cc_start: 0.8317 (mtp) cc_final: 0.7850 (mtt) REVERT: A 275 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: A 289 GLU cc_start: 0.7355 (mp0) cc_final: 0.6630 (pm20) REVERT: A 313 ARG cc_start: 0.7863 (mpt90) cc_final: 0.7075 (ptp-110) REVERT: B 124 TYR cc_start: 0.8754 (m-80) cc_final: 0.8455 (m-80) REVERT: B 130 GLU cc_start: 0.8352 (mp0) cc_final: 0.8034 (mp0) REVERT: B 135 VAL cc_start: 0.8820 (t) cc_final: 0.8551 (p) REVERT: G 21 MET cc_start: 0.6736 (ttt) cc_final: 0.6161 (mpm) REVERT: S 171 GLN cc_start: 0.8088 (mt0) cc_final: 0.7765 (mt0) REVERT: S 182 ASN cc_start: 0.8823 (m110) cc_final: 0.8540 (m110) REVERT: S 208 GLU cc_start: 0.7435 (mp0) cc_final: 0.7164 (mp0) outliers start: 36 outliers final: 18 residues processed: 155 average time/residue: 1.2401 time to fit residues: 204.7290 Evaluate side-chains 156 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 165 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 A residue 18 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 113 GLN 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 47 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 0.0770 chunk 78 optimal weight: 0.0270 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.109932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089495 restraints weight = 14970.730| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.75 r_work: 0.3179 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9266 Z= 0.111 Angle : 0.523 8.876 12563 Z= 0.270 Chirality : 0.041 0.166 1420 Planarity : 0.004 0.050 1581 Dihedral : 4.076 19.092 1262 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.66 % Allowed : 17.98 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1139 helix: 1.94 (0.26), residues: 403 sheet: -0.14 (0.31), residues: 272 loop : -0.94 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 278 PHE 0.011 0.001 PHE A 189 TYR 0.015 0.001 TYR R 185 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd link_TRANS : bond 0.00292 ( 1) link_TRANS : angle 0.23311 ( 3) hydrogen bonds : bond 0.03109 ( 453) hydrogen bonds : angle 4.52585 ( 1281) SS BOND : bond 0.00232 ( 5) SS BOND : angle 1.23066 ( 10) covalent geometry : bond 0.00247 ( 9260) covalent geometry : angle 0.52224 (12550) *********************** 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 170 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.938 Fit side-chains REVERT: R 101 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.5771 (m-10) REVERT: R 162 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7754 (mmt) REVERT: R 198 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6229 (pm20) REVERT: R 262 MET cc_start: 0.7970 (tpt) cc_final: 0.7730 (tpt) REVERT: R 271 TYR cc_start: 0.7539 (t80) cc_final: 0.6985 (t80) REVERT: A 29 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8023 (tppt) REVERT: A 246 SER cc_start: 0.8337 (m) cc_final: 0.7810 (p) REVERT: A 247 MET cc_start: 0.8306 (mtp) cc_final: 0.7839 (mtt) REVERT: A 275 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7099 (pt0) REVERT: A 313 ARG cc_start: 0.7838 (mpt90) cc_final: 0.7059 (ptp-110) REVERT: B 124 TYR cc_start: 0.8743 (m-80) cc_final: 0.8428 (m-80) REVERT: B 130 GLU cc_start: 0.8376 (mp0) cc_final: 0.8011 (mp0) REVERT: B 135 VAL cc_start: 0.8752 (t) cc_final: 0.8499 (p) REVERT: B 175 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7812 (mm110) REVERT: B 237 ASN cc_start: 0.8455 (p0) cc_final: 0.8246 (p0) REVERT: G 21 MET cc_start: 0.6820 (ttt) cc_final: 0.6066 (mpm) REVERT: S 171 GLN cc_start: 0.8047 (mt0) cc_final: 0.7720 (mt0) REVERT: S 182 ASN cc_start: 0.8812 (m110) cc_final: 0.8532 (m110) REVERT: S 190 ARG cc_start: 0.6778 (mtp180) cc_final: 0.6498 (ptt180) REVERT: S 222 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7958 (mt-10) outliers start: 26 outliers final: 12 residues processed: 158 average time/residue: 1.2194 time to fit residues: 205.5680 Evaluate side-chains 152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 189 PHE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 44 optimal weight: 0.0070 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.0030 chunk 30 optimal weight: 0.8980 overall best weight: 0.5812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3594 r_free = 0.3594 target = 0.109938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089517 restraints weight = 14718.882| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.75 r_work: 0.3180 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2712 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= 0.115 Angle : 0.532 8.850 12563 Z= 0.275 Chirality : 0.041 0.166 1420 Planarity : 0.004 0.051 1581 Dihedral : 4.049 19.167 1262 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.45 % Allowed : 18.69 % 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 (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 (0.26), residues: 1139 helix: 1.96 (0.26), residues: 403 sheet: -0.10 (0.30), residues: 272 loop : -0.89 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS R 278 PHE 0.011 0.001 PHE A 189 TYR 0.017 0.001 TYR R 185 ARG 0.012 0.000 ARG A 24 Details of bonding type rmsd link_TRANS : bond 0.00282 ( 1) link_TRANS : angle 0.23593 ( 3) hydrogen bonds : bond 0.03105 ( 453) hydrogen bonds : angle 4.49622 ( 1281) SS BOND : bond 0.00266 ( 5) SS BOND : angle 1.20523 ( 10) covalent geometry : bond 0.00258 ( 9260) covalent geometry : angle 0.53125 (12550) *********************** 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 163 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.071 Fit side-chains REVERT: R 101 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5799 (m-10) REVERT: R 162 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7751 (mmt) REVERT: R 198 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6132 (pm20) REVERT: R 262 MET cc_start: 0.8018 (tpt) cc_final: 0.7775 (tpt) REVERT: R 271 TYR cc_start: 0.7532 (t80) cc_final: 0.6941 (t80) REVERT: A 24 ARG cc_start: 0.7723 (mtm110) cc_final: 0.6696 (mtm-85) REVERT: A 29 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7948 (tppt) REVERT: A 246 SER cc_start: 0.8349 (m) cc_final: 0.7825 (p) REVERT: A 247 MET cc_start: 0.8285 (mtp) cc_final: 0.7873 (mtt) REVERT: A 275 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7079 (pt0) REVERT: A 313 ARG cc_start: 0.7834 (mpt90) cc_final: 0.7072 (ptp-110) REVERT: B 44 GLN cc_start: 0.8696 (mt0) cc_final: 0.8410 (mt0) REVERT: B 124 TYR cc_start: 0.8739 (m-80) cc_final: 0.8438 (m-80) REVERT: B 130 GLU cc_start: 0.8351 (mp0) cc_final: 0.8048 (mp0) REVERT: B 135 VAL cc_start: 0.8745 (t) cc_final: 0.8482 (p) REVERT: B 197 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7797 (tpp-160) REVERT: G 21 MET cc_start: 0.6794 (ttt) cc_final: 0.6022 (mpm) REVERT: S 171 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7700 (mt0) REVERT: S 182 ASN cc_start: 0.8757 (m110) cc_final: 0.8509 (m110) REVERT: S 208 GLU cc_start: 0.7274 (mp0) cc_final: 0.6976 (mp0) REVERT: S 222 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7890 (mt-10) outliers start: 24 outliers final: 12 residues processed: 153 average time/residue: 1.3182 time to fit residues: 214.8193 Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 171 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.089480 restraints weight = 14809.532| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.77 r_work: 0.3180 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2766 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 : 0.543 10.146 12563 Z= 0.278 Chirality : 0.041 0.165 1420 Planarity : 0.004 0.053 1581 Dihedral : 4.068 19.142 1262 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 2.25 % Allowed : 19.31 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1139 helix: 1.96 (0.26), residues: 403 sheet: -0.05 (0.30), residues: 272 loop : -0.88 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS R 278 PHE 0.011 0.001 PHE A 189 TYR 0.019 0.001 TYR R 93 ARG 0.012 0.000 ARG A 24 Details of bonding type rmsd link_TRANS : bond 0.00306 ( 1) link_TRANS : angle 0.22960 ( 3) hydrogen bonds : bond 0.03117 ( 453) hydrogen bonds : angle 4.48349 ( 1281) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.19563 ( 10) covalent geometry : bond 0.00266 ( 9260) covalent geometry : angle 0.54215 (12550) ********************** 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 157 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.003 Fit side-chains REVERT: R 101 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5800 (m-10) REVERT: R 162 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7744 (mmt) REVERT: R 198 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5785 (pm20) REVERT: R 262 MET cc_start: 0.7995 (tpt) cc_final: 0.7753 (tpt) REVERT: R 271 TYR cc_start: 0.7518 (t80) cc_final: 0.6912 (t80) REVERT: A 24 ARG cc_start: 0.7704 (mtm110) cc_final: 0.6610 (mtm-85) REVERT: A 29 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7977 (tppt) REVERT: A 246 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.7836 (p) REVERT: A 247 MET cc_start: 0.8289 (mtp) cc_final: 0.7876 (mtt) REVERT: A 275 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7115 (pt0) REVERT: A 313 ARG cc_start: 0.7752 (mpt90) cc_final: 0.7011 (ptp-110) REVERT: B 124 TYR cc_start: 0.8735 (m-80) cc_final: 0.8444 (m-80) REVERT: B 130 GLU cc_start: 0.8327 (mp0) cc_final: 0.8036 (mp0) REVERT: B 135 VAL cc_start: 0.8751 (t) cc_final: 0.8493 (p) REVERT: B 197 ARG cc_start: 0.8021 (tpt170) cc_final: 0.7742 (tpp-160) REVERT: G 21 MET cc_start: 0.6944 (ttt) cc_final: 0.6047 (mpm) REVERT: S 171 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: S 182 ASN cc_start: 0.8796 (m110) cc_final: 0.8534 (m110) REVERT: S 222 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7850 (mt-10) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 1.2670 time to fit residues: 198.2463 Evaluate side-chains 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 PHE 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 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 171 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 3 GLN S 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.088727 restraints weight = 14780.962| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.76 r_work: 0.3171 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9266 Z= 0.133 Angle : 0.554 9.745 12563 Z= 0.284 Chirality : 0.042 0.163 1420 Planarity : 0.004 0.052 1581 Dihedral : 4.136 19.009 1262 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 2.86 % Allowed : 19.20 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1139 helix: 1.92 (0.26), residues: 403 sheet: -0.07 (0.30), residues: 272 loop : -0.90 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE B 151 TYR 0.021 0.001 TYR R 185 ARG 0.011 0.000 ARG A 24 Details of bonding type rmsd link_TRANS : bond 0.00352 ( 1) link_TRANS : angle 0.27662 ( 3) hydrogen bonds : bond 0.03217 ( 453) hydrogen bonds : angle 4.53507 ( 1281) SS BOND : bond 0.00281 ( 5) SS BOND : angle 1.24994 ( 10) covalent geometry : bond 0.00306 ( 9260) covalent geometry : angle 0.55271 (12550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7018.24 seconds wall clock time: 121 minutes 34.29 seconds (7294.29 seconds total)