Starting phenix.real_space_refine on Wed Aug 5 09:35:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25su_63713/08_2026/25su_63713.cif Found real_map, /net/cci-nas-00/data/ceres_data/25su_63713/08_2026/25su_63713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25su_63713/08_2026/25su_63713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25su_63713/08_2026/25su_63713.map" model { file = "/net/cci-nas-00/data/ceres_data/25su_63713/08_2026/25su_63713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25su_63713/08_2026/25su_63713.cif" } resolution = 3.3 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= 0.089 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 68 5.16 5 C 5743 2.51 5 N 1504 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8989 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2265 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2591 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 4, 'TRANS': 334} Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1885 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 2, 'TRANS': 235} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8989 At special positions: 0 Unit cell: (92.4, 123.2, 137.5, 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 68 16.00 O 1674 8.00 N 1504 7.00 C 5743 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 451.9 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 1 through 31 Processing helix chain 'R' and resid 42 through 71 removed outlier: 3.510A pdb=" N ARG R 46 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 111 Processing helix chain 'R' and resid 115 through 126 removed outlier: 4.398A pdb=" N SER R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 154 removed outlier: 3.502A pdb=" N SER R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 211 removed outlier: 4.042A pdb=" N SER R 184 " --> pdb=" O SER R 180 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN R 188 " --> pdb=" O SER R 184 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 239 Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.507A pdb=" N SER R 243 " --> pdb=" O TYR R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 256 removed outlier: 4.061A pdb=" N GLY R 256 " --> pdb=" O PRO R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 271 removed outlier: 3.706A pdb=" N LYS R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 284 removed outlier: 3.770A pdb=" N GLY R 275 " --> pdb=" O LEU R 271 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS R 276 " --> pdb=" O TYR R 272 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER R 277 " --> pdb=" O SER R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.555A pdb=" N SER N 31 " --> pdb=" O ALA N 28 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.764A pdb=" N LYS N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.536A pdb=" N THR G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 49 through 53 removed outlier: 3.869A pdb=" N LEU G 52 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.660A pdb=" N LEU B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.130A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 3.802A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.803A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.134A pdb=" N ILE A 285 " --> pdb=" O HIS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.519A pdb=" N PHE A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.863A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 146 through 148 removed outlier: 3.990A pdb=" N GLU N 246 " --> pdb=" O VAL N 147 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY N 225 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU N 174 " --> pdb=" O TYR N 190 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR N 190 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP N 176 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR N 190 " --> pdb=" O ASN N 194 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 155 through 160 removed outlier: 4.162A pdb=" N ALA N 211 " --> pdb=" O SER N 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.841A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.017A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS B 91 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.122A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR B 105 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.720A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.573A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 190 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU B 198 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.784A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 232 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 250 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.824A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 56 through 57 removed outlier: 4.489A pdb=" N ILE A 56 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 188 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N CYS A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS A 35 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 233 through 234 452 hydrogen bonds defined for protein. 1296 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: 1.23 Time building geometry restraints manager: 0.75 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: 2858 1.34 - 1.46: 2104 1.46 - 1.58: 4113 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 9175 Sorted by residual: bond pdb=" N VAL N 64 " pdb=" CA VAL N 64 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.69e+00 bond pdb=" N ARG N 67 " pdb=" CA ARG N 67 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.14e-02 7.69e+03 6.14e+00 bond pdb=" N GLY N 66 " pdb=" CA GLY N 66 " ideal model delta sigma weight residual 1.443 1.476 -0.033 1.38e-02 5.25e+03 5.58e+00 bond pdb=" N LYS N 65 " pdb=" CA LYS N 65 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.34e+00 bond pdb=" CA LEU R 271 " pdb=" C LEU R 271 " ideal model delta sigma weight residual 1.522 1.550 -0.027 1.37e-02 5.33e+03 4.01e+00 ... (remaining 9170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12206 2.27 - 4.54: 167 4.54 - 6.82: 20 6.82 - 9.09: 10 9.09 - 11.36: 1 Bond angle restraints: 12404 Sorted by residual: angle pdb=" N ARG N 67 " pdb=" CA ARG N 67 " pdb=" C ARG N 67 " ideal model delta sigma weight residual 114.62 109.25 5.37 1.14e+00 7.69e-01 2.22e+01 angle pdb=" C THR G 30 " pdb=" N ILE G 31 " pdb=" CA ILE G 31 " ideal model delta sigma weight residual 120.33 123.61 -3.28 8.00e-01 1.56e+00 1.68e+01 angle pdb=" CA LEU R 120 " pdb=" CB LEU R 120 " pdb=" CG LEU R 120 " ideal model delta sigma weight residual 116.30 127.66 -11.36 3.50e+00 8.16e-02 1.05e+01 angle pdb=" CA LYS A 304 " pdb=" CB LYS A 304 " pdb=" CG LYS A 304 " ideal model delta sigma weight residual 114.10 120.58 -6.48 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C ILE R 22 " pdb=" N MET R 23 " pdb=" CA MET R 23 " ideal model delta sigma weight residual 120.31 115.51 4.80 1.52e+00 4.33e-01 9.95e+00 ... (remaining 12399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 4749 16.82 - 33.65: 500 33.65 - 50.47: 160 50.47 - 67.30: 27 67.30 - 84.12: 6 Dihedral angle restraints: 5442 sinusoidal: 2120 harmonic: 3322 Sorted by residual: dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ILE R 237 " pdb=" C ILE R 237 " pdb=" N LEU R 238 " pdb=" CA LEU R 238 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 960 0.036 - 0.073: 315 0.073 - 0.109: 117 0.109 - 0.146: 19 0.146 - 0.182: 5 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CB THR R 246 " pdb=" CA THR R 246 " pdb=" OG1 THR R 246 " pdb=" CG2 THR R 246 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA MET R 23 " pdb=" N MET R 23 " pdb=" C MET R 23 " pdb=" CB MET R 23 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA VAL N 64 " pdb=" N VAL N 64 " pdb=" C VAL N 64 " pdb=" CB VAL N 64 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1413 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 49 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO G 50 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 50 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 50 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 97 " -0.019 2.00e-02 2.50e+03 1.30e-02 4.22e+00 pdb=" CG TRP R 97 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP R 97 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP R 97 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 97 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 97 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 97 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 97 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 97 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 97 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 135 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C VAL B 135 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 135 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 136 " 0.009 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 160 2.69 - 3.24: 8271 3.24 - 3.79: 13174 3.79 - 4.35: 16396 4.35 - 4.90: 28661 Nonbonded interactions: 66662 Sorted by model distance: nonbonded pdb=" OD1 ASP A 341 " pdb=" NZ LYS A 345 " model vdw 2.135 3.120 nonbonded pdb=" O THR B 143 " pdb=" OG1 THR A 181 " model vdw 2.181 3.040 nonbonded pdb=" ND2 ASN B 119 " pdb=" OG1 THR A 181 " model vdw 2.212 3.120 nonbonded pdb=" O SER B 299 " pdb=" OG SER B 299 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.217 3.040 ... (remaining 66657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9176 Z= 0.171 Angle : 0.714 11.360 12406 Z= 0.409 Chirality : 0.042 0.182 1416 Planarity : 0.004 0.053 1554 Dihedral : 15.553 84.124 3297 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 2.99 % Allowed : 24.45 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.25 (0.25), residues: 1136 helix: 2.53 (0.26), residues: 395 sheet: -0.27 (0.30), residues: 278 loop : -1.74 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.021 0.002 TYR R 239 PHE 0.021 0.002 PHE R 88 TRP 0.034 0.002 TRP R 97 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 ( 9175) covalent geometry : angle 0.71363 / 0.41 (12404) SS BOND : bond 0.00888 / 0.47 ( 1) SS BOND : angle 1.65476 / 0.90 ( 2) hydrogen bonds : bond 0.12087 / 8.53 ( 452) hydrogen bonds : angle 4.85386 / 3.61 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 189 PHE cc_start: 0.6341 (t80) cc_final: 0.6115 (t80) REVERT: R 225 HIS cc_start: 0.4813 (OUTLIER) cc_final: 0.4200 (t70) REVERT: N 82 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7502 (tp40) REVERT: N 183 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7688 (mm-40) REVERT: G 26 MET cc_start: 0.8288 (mmm) cc_final: 0.8037 (mmm) REVERT: B 123 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7960 (mt) REVERT: B 155 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7453 (t0) REVERT: B 228 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8151 (p0) REVERT: B 289 TYR cc_start: 0.8396 (m-80) cc_final: 0.8010 (m-80) REVERT: B 307 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8047 (mt) REVERT: A 25 GLU cc_start: 0.7615 (tt0) cc_final: 0.7316 (tm-30) REVERT: A 26 ASP cc_start: 0.7488 (m-30) cc_final: 0.6889 (m-30) REVERT: A 29 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7725 (mmmt) REVERT: A 217 ASP cc_start: 0.7891 (t0) cc_final: 0.7491 (p0) REVERT: A 347 ASN cc_start: 0.5039 (t0) cc_final: 0.4269 (t0) outliers start: 30 outliers final: 13 residues processed: 221 average time/residue: 0.0861 time to fit residues: 27.1668 Evaluate side-chains 162 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.0970 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 201 HIS N 167 HIS B 88 ASN B 155 ASN B 259 GLN B 295 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.216285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.171466 restraints weight = 10461.782| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.51 r_work: 0.3613 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9176 Z= 0.117 Angle : 0.569 9.500 12406 Z= 0.295 Chirality : 0.041 0.139 1416 Planarity : 0.004 0.056 1554 Dihedral : 5.319 50.250 1254 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.30 % Rotamer: Outliers : 4.79 % Allowed : 21.96 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.41 (0.25), residues: 1136 helix: 2.63 (0.25), residues: 408 sheet: -0.30 (0.29), residues: 292 loop : -1.68 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.018 0.001 TYR N 190 PHE 0.018 0.001 PHE R 98 TRP 0.020 0.002 TRP B 211 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 9175) covalent geometry : angle 0.56856 / 0.29 (12404) SS BOND : bond 0.00792 / 0.42 ( 1) SS BOND : angle 1.71774 / 0.93 ( 2) hydrogen bonds : bond 0.04001 / 2.78 ( 452) hydrogen bonds : angle 4.02994 / 3.02 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.254 Fit side-chains REVERT: R 23 MET cc_start: 0.5718 (mpp) cc_final: 0.5448 (mpp) REVERT: R 47 ILE cc_start: 0.4545 (mt) cc_final: 0.4166 (mt) REVERT: R 49 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7109 (t80) REVERT: R 69 PHE cc_start: 0.7001 (t80) cc_final: 0.6716 (t80) REVERT: R 210 MET cc_start: 0.0099 (ttt) cc_final: -0.0305 (tpp) REVERT: R 217 PHE cc_start: 0.4989 (OUTLIER) cc_final: 0.4269 (m-80) REVERT: R 225 HIS cc_start: 0.4449 (OUTLIER) cc_final: 0.3805 (t70) REVERT: B 289 TYR cc_start: 0.8477 (m-80) cc_final: 0.8214 (m-80) REVERT: A 22 ASN cc_start: 0.8091 (m110) cc_final: 0.7669 (m-40) REVERT: A 25 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6870 (mt-10) REVERT: A 26 ASP cc_start: 0.7676 (m-30) cc_final: 0.7437 (m-30) REVERT: A 217 ASP cc_start: 0.7728 (t0) cc_final: 0.7424 (p0) outliers start: 48 outliers final: 28 residues processed: 184 average time/residue: 0.0782 time to fit residues: 20.7940 Evaluate side-chains 162 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 PHE Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 217 PHE Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 296 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 55 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 108 optimal weight: 0.0570 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 124 ASN N 169 ASN B 259 GLN ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.213417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177387 restraints weight = 10299.773| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.14 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9176 Z= 0.112 Angle : 0.534 6.002 12406 Z= 0.280 Chirality : 0.040 0.138 1416 Planarity : 0.004 0.048 1554 Dihedral : 5.028 52.087 1240 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.27 % Rotamer: Outliers : 5.09 % Allowed : 21.26 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.63 (0.25), residues: 1136 helix: 2.86 (0.25), residues: 407 sheet: -0.09 (0.29), residues: 282 loop : -1.66 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.017 0.001 TYR N 190 PHE 0.013 0.001 PHE R 189 TRP 0.019 0.001 TRP B 211 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9175) covalent geometry : angle 0.53325 / 0.28 (12404) SS BOND : bond 0.00731 / 0.38 ( 1) SS BOND : angle 1.47764 / 0.80 ( 2) hydrogen bonds : bond 0.03566 / 2.43 ( 452) hydrogen bonds : angle 3.83890 / 2.89 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 141 time to evaluate : 0.306 Fit side-chains REVERT: R 47 ILE cc_start: 0.5429 (mt) cc_final: 0.5053 (mt) REVERT: R 210 MET cc_start: 0.2042 (ttt) cc_final: 0.1527 (tpp) REVERT: R 217 PHE cc_start: 0.4242 (OUTLIER) cc_final: 0.3563 (m-80) REVERT: R 225 HIS cc_start: 0.5172 (OUTLIER) cc_final: 0.4511 (t70) REVERT: B 294 CYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7060 (m) REVERT: B 307 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7427 (mt) REVERT: A 17 LYS cc_start: 0.8229 (mptt) cc_final: 0.7910 (mtmt) REVERT: A 22 ASN cc_start: 0.7818 (m110) cc_final: 0.7339 (m-40) outliers start: 51 outliers final: 34 residues processed: 177 average time/residue: 0.0696 time to fit residues: 17.7338 Evaluate side-chains 167 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 18 PHE Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 217 PHE Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 89 optimal weight: 0.0270 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 98 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 124 ASN N 169 ASN A 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.213311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.168855 restraints weight = 10441.437| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.41 r_work: 0.3552 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9176 Z= 0.139 Angle : 0.561 6.807 12406 Z= 0.294 Chirality : 0.041 0.137 1416 Planarity : 0.004 0.045 1554 Dihedral : 5.008 53.880 1238 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.27 % Rotamer: Outliers : 5.29 % Allowed : 21.56 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.74 (0.25), residues: 1136 helix: 3.03 (0.25), residues: 401 sheet: -0.04 (0.30), residues: 280 loop : -1.58 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.017 0.002 TYR N 190 PHE 0.011 0.001 PHE A 189 TRP 0.020 0.002 TRP B 211 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9175) covalent geometry : angle 0.56048 / 0.29 (12404) SS BOND : bond 0.00872 / 0.46 ( 1) SS BOND : angle 1.66291 / 0.91 ( 2) hydrogen bonds : bond 0.03634 / 2.48 ( 452) hydrogen bonds : angle 3.87757 / 2.91 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 0.226 Fit side-chains REVERT: R 43 SER cc_start: 0.5124 (OUTLIER) cc_final: 0.4880 (p) REVERT: R 47 ILE cc_start: 0.4577 (mt) cc_final: 0.4292 (mt) REVERT: R 189 PHE cc_start: 0.5429 (t80) cc_final: 0.4884 (t80) REVERT: R 210 MET cc_start: -0.0342 (ttt) cc_final: -0.0591 (tpp) REVERT: R 217 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: R 225 HIS cc_start: 0.4375 (OUTLIER) cc_final: 0.3676 (t70) REVERT: B 294 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7445 (m) REVERT: A 17 LYS cc_start: 0.8218 (mptt) cc_final: 0.7565 (mtmt) REVERT: A 26 ASP cc_start: 0.7807 (m-30) cc_final: 0.7499 (m-30) outliers start: 53 outliers final: 38 residues processed: 169 average time/residue: 0.0655 time to fit residues: 16.3805 Evaluate side-chains 165 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 217 PHE Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 31 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 169 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.215642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.172585 restraints weight = 10499.867| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.41 r_work: 0.3536 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9176 Z= 0.125 Angle : 0.551 8.895 12406 Z= 0.284 Chirality : 0.041 0.145 1416 Planarity : 0.004 0.044 1554 Dihedral : 4.950 55.284 1238 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 5.49 % Allowed : 22.16 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.84 (0.25), residues: 1136 helix: 3.07 (0.25), residues: 401 sheet: 0.03 (0.31), residues: 273 loop : -1.48 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 24 TYR 0.017 0.002 TYR N 95 PHE 0.012 0.001 PHE A 189 TRP 0.020 0.002 TRP B 211 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9175) covalent geometry : angle 0.55042 / 0.28 (12404) SS BOND : bond 0.00823 / 0.43 ( 1) SS BOND : angle 1.50684 / 0.82 ( 2) hydrogen bonds : bond 0.03432 / 2.30 ( 452) hydrogen bonds : angle 3.90206 / 2.93 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.266 Fit side-chains REVERT: R 23 MET cc_start: 0.5999 (mpp) cc_final: 0.5763 (mpp) REVERT: R 43 SER cc_start: 0.5400 (OUTLIER) cc_final: 0.5029 (p) REVERT: R 47 ILE cc_start: 0.4661 (mt) cc_final: 0.4388 (mt) REVERT: R 69 PHE cc_start: 0.7077 (t80) cc_final: 0.6663 (t80) REVERT: R 189 PHE cc_start: 0.5413 (t80) cc_final: 0.4967 (t80) REVERT: R 210 MET cc_start: -0.0365 (ttt) cc_final: -0.0625 (tpp) REVERT: R 225 HIS cc_start: 0.4482 (OUTLIER) cc_final: 0.3743 (t70) REVERT: B 294 CYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7450 (m) REVERT: A 17 LYS cc_start: 0.8209 (mptt) cc_final: 0.7561 (mtmt) REVERT: A 26 ASP cc_start: 0.7770 (m-30) cc_final: 0.7546 (m-30) outliers start: 55 outliers final: 44 residues processed: 168 average time/residue: 0.0669 time to fit residues: 16.4793 Evaluate side-chains 165 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 18 PHE Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.208746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.169716 restraints weight = 10454.665| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.52 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9176 Z= 0.152 Angle : 0.578 8.007 12406 Z= 0.302 Chirality : 0.042 0.141 1416 Planarity : 0.004 0.042 1554 Dihedral : 5.152 56.694 1238 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 5.99 % Allowed : 21.76 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.83 (0.25), residues: 1136 helix: 3.05 (0.25), residues: 402 sheet: -0.05 (0.31), residues: 282 loop : -1.45 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.017 0.002 TYR N 190 PHE 0.016 0.001 PHE A 189 TRP 0.020 0.002 TRP B 211 HIS 0.004 0.001 HIS N 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 9175) covalent geometry : angle 0.57745 / 0.30 (12404) SS BOND : bond 0.00928 / 0.49 ( 1) SS BOND : angle 1.70381 / 0.93 ( 2) hydrogen bonds : bond 0.03606 / 2.44 ( 452) hydrogen bonds : angle 3.98696 / 3.00 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 123 time to evaluate : 0.229 Fit side-chains REVERT: R 47 ILE cc_start: 0.5610 (mt) cc_final: 0.5260 (mt) REVERT: R 68 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.6040 (t80) REVERT: R 105 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.4875 (mt) REVERT: R 189 PHE cc_start: 0.5007 (t80) cc_final: 0.4792 (t80) REVERT: R 210 MET cc_start: 0.1540 (ttt) cc_final: 0.1151 (tpp) REVERT: R 225 HIS cc_start: 0.5169 (OUTLIER) cc_final: 0.4414 (t70) REVERT: B 150 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7733 (mmt180) REVERT: B 290 ASP cc_start: 0.6258 (p0) cc_final: 0.5950 (p0) REVERT: A 17 LYS cc_start: 0.8285 (mptt) cc_final: 0.7907 (mtmt) outliers start: 60 outliers final: 41 residues processed: 173 average time/residue: 0.0661 time to fit residues: 17.0489 Evaluate side-chains 160 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 18 PHE Chi-restraints excluded: chain R residue 68 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.210357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.162993 restraints weight = 10554.220| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.71 r_work: 0.3440 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9176 Z= 0.175 Angle : 0.610 10.141 12406 Z= 0.316 Chirality : 0.043 0.183 1416 Planarity : 0.004 0.046 1554 Dihedral : 5.292 55.824 1238 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 5.29 % Allowed : 23.05 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.78 (0.25), residues: 1136 helix: 3.05 (0.25), residues: 402 sheet: -0.13 (0.31), residues: 279 loop : -1.47 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.018 0.002 TYR R 106 PHE 0.020 0.002 PHE A 189 TRP 0.021 0.002 TRP A 211 HIS 0.005 0.001 HIS N 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 ( 9175) covalent geometry : angle 0.60918 / 0.32 (12404) SS BOND : bond 0.00992 / 0.52 ( 1) SS BOND : angle 1.77076 / 0.96 ( 2) hydrogen bonds : bond 0.03766 / 2.55 ( 452) hydrogen bonds : angle 4.07043 / 3.05 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.331 Fit side-chains REVERT: R 68 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5788 (t80) REVERT: R 210 MET cc_start: -0.0554 (ttt) cc_final: -0.0889 (tpp) REVERT: R 225 HIS cc_start: 0.4314 (OUTLIER) cc_final: 0.3709 (t70) REVERT: B 150 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7908 (mmt180) REVERT: A 17 LYS cc_start: 0.8279 (mptt) cc_final: 0.7600 (mtmt) REVERT: A 304 LYS cc_start: 0.7154 (tmtt) cc_final: 0.6860 (ttmt) outliers start: 53 outliers final: 42 residues processed: 163 average time/residue: 0.0682 time to fit residues: 16.0380 Evaluate side-chains 161 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 18 PHE Chi-restraints excluded: chain R residue 68 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.204839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159158 restraints weight = 10437.007| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.99 r_work: 0.3462 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9176 Z= 0.167 Angle : 0.610 8.010 12406 Z= 0.317 Chirality : 0.043 0.215 1416 Planarity : 0.004 0.047 1554 Dihedral : 5.350 57.004 1238 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.39 % Rotamer: Outliers : 4.99 % Allowed : 23.55 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.72 (0.25), residues: 1136 helix: 3.03 (0.25), residues: 402 sheet: -0.34 (0.30), residues: 285 loop : -1.42 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 24 TYR 0.018 0.002 TYR N 190 PHE 0.019 0.002 PHE A 189 TRP 0.020 0.002 TRP B 211 HIS 0.005 0.001 HIS R 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 9175) covalent geometry : angle 0.60963 / 0.32 (12404) SS BOND : bond 0.00968 / 0.51 ( 1) SS BOND : angle 1.70090 / 0.93 ( 2) hydrogen bonds : bond 0.03749 / 2.54 ( 452) hydrogen bonds : angle 4.06429 / 3.03 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 0.325 Fit side-chains REVERT: R 68 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.5716 (t80) REVERT: R 105 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.4468 (mt) REVERT: R 210 MET cc_start: -0.0601 (ttt) cc_final: -0.0853 (tpp) REVERT: R 225 HIS cc_start: 0.4296 (OUTLIER) cc_final: 0.3616 (t70) REVERT: G 26 MET cc_start: 0.8197 (mmm) cc_final: 0.7872 (mmm) REVERT: B 150 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7960 (mmt180) REVERT: A 17 LYS cc_start: 0.8276 (mptt) cc_final: 0.7592 (mtmt) outliers start: 50 outliers final: 43 residues processed: 159 average time/residue: 0.0682 time to fit residues: 16.1140 Evaluate side-chains 159 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 18 PHE Chi-restraints excluded: chain R residue 68 TYR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 348 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.207432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.161519 restraints weight = 10473.964| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.94 r_work: 0.3481 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9176 Z= 0.113 Angle : 0.559 7.932 12406 Z= 0.291 Chirality : 0.041 0.199 1416 Planarity : 0.004 0.059 1554 Dihedral : 5.126 57.233 1238 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.59 % Allowed : 25.15 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.88 (0.25), residues: 1136 helix: 3.18 (0.25), residues: 401 sheet: -0.05 (0.32), residues: 273 loop : -1.45 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 24 TYR 0.018 0.001 TYR N 190 PHE 0.015 0.001 PHE A 189 TRP 0.022 0.001 TRP B 211 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9175) covalent geometry : angle 0.55922 / 0.29 (12404) SS BOND : bond 0.00699 / 0.37 ( 1) SS BOND : angle 1.24905 / 0.68 ( 2) hydrogen bonds : bond 0.03290 / 2.20 ( 452) hydrogen bonds : angle 3.95443 / 2.96 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.335 Fit side-chains REVERT: R 68 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.5731 (t80) REVERT: R 189 PHE cc_start: 0.5128 (t80) cc_final: 0.4884 (t80) REVERT: R 210 MET cc_start: -0.0570 (ttt) cc_final: -0.0808 (tpp) REVERT: R 225 HIS cc_start: 0.4372 (OUTLIER) cc_final: 0.3673 (t70) REVERT: N 113 GLN cc_start: 0.7960 (tp40) cc_final: 0.7689 (tp-100) REVERT: A 17 LYS cc_start: 0.8263 (mptt) cc_final: 0.7557 (mtmt) outliers start: 36 outliers final: 31 residues processed: 146 average time/residue: 0.0676 time to fit residues: 14.7842 Evaluate side-chains 147 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 18 PHE Chi-restraints excluded: chain R residue 68 TYR Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 0.0010 chunk 91 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 106 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.208248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.161875 restraints weight = 10433.414| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.66 r_work: 0.3473 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9176 Z= 0.110 Angle : 0.558 9.106 12406 Z= 0.286 Chirality : 0.041 0.182 1416 Planarity : 0.004 0.046 1554 Dihedral : 4.995 57.150 1238 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.29 % Allowed : 25.45 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.97 (0.25), residues: 1136 helix: 3.24 (0.25), residues: 401 sheet: -0.05 (0.31), residues: 281 loop : -1.37 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.018 0.001 TYR N 190 PHE 0.013 0.001 PHE A 189 TRP 0.022 0.001 TRP B 211 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9175) covalent geometry : angle 0.55796 / 0.29 (12404) SS BOND : bond 0.00657 / 0.35 ( 1) SS BOND : angle 1.21191 / 0.66 ( 2) hydrogen bonds : bond 0.03179 / 2.14 ( 452) hydrogen bonds : angle 3.87454 / 2.89 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.353 Fit side-chains REVERT: R 225 HIS cc_start: 0.4295 (OUTLIER) cc_final: 0.3582 (t70) REVERT: N 113 GLN cc_start: 0.7939 (tp40) cc_final: 0.7731 (tp-100) REVERT: G 26 MET cc_start: 0.8105 (mmm) cc_final: 0.7812 (mmm) REVERT: A 17 LYS cc_start: 0.8193 (mptt) cc_final: 0.7575 (mtmt) REVERT: A 24 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.7288 (mtm110) outliers start: 33 outliers final: 30 residues processed: 141 average time/residue: 0.0684 time to fit residues: 14.3773 Evaluate side-chains 143 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 PHE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 225 HIS Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 261 THR Chi-restraints excluded: chain R residue 268 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 204 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.207658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.162048 restraints weight = 10340.614| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.68 r_work: 0.3496 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9176 Z= 0.136 Angle : 0.578 8.389 12406 Z= 0.300 Chirality : 0.041 0.173 1416 Planarity : 0.004 0.048 1554 Dihedral : 5.100 57.459 1238 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.89 % Allowed : 24.95 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.89 (0.25), residues: 1136 helix: 3.21 (0.25), residues: 401 sheet: -0.19 (0.31), residues: 279 loop : -1.38 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.019 0.002 TYR A 302 PHE 0.016 0.001 PHE A 189 TRP 0.021 0.002 TRP A 211 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9175) covalent geometry : angle 0.57759 / 0.30 (12404) SS BOND : bond 0.00825 / 0.43 ( 1) SS BOND : angle 1.53653 / 0.84 ( 2) hydrogen bonds : bond 0.03453 / 2.34 ( 452) hydrogen bonds : angle 3.93116 / 2.93 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.80 seconds wall clock time: 32 minutes 56.28 seconds (1976.28 seconds total)