Starting phenix.real_space_refine on Tue Mar 3 17:56:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wha_21669/03_2026/6wha_21669.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wha_21669/03_2026/6wha_21669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2026/6wha_21669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2026/6wha_21669.map" model { file = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2026/6wha_21669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wha_21669/03_2026/6wha_21669.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5016 2.51 5 N 1355 2.21 5 O 1473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1679 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain breaks: 5 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 4, 'PHE:plan': 10, 'TYR:plan': 2, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1650 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'U0G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.21 Number of scatterers: 7888 At special positions: 0 Unit cell: (97.1394, 113.329, 121.85, 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 44 16.00 O 1473 8.00 N 1355 7.00 C 5016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 0.66 Conformation dependent library (CDL) restraints added in 211.2 milliseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 84 through 99 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.919A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 146 through 179 removed outlier: 4.377A pdb=" N VAL A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 removed outlier: 3.691A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 208 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.366A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.297A pdb=" N VAL A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 245 through 261 Processing helix chain 'A' and resid 316 through 347 removed outlier: 3.802A pdb=" N LYS A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.595A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 Proline residue: A 377 - end of helix removed outlier: 3.726A pdb=" N TYR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.684A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.787A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.884A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.356A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.547A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 184 through 203 removed outlier: 3.813A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.963A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.983A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.947A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.867A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.048A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.713A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 72 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 83 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 84 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.481A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.842A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.146A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.984A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.736A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.862A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.633A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.880A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.911A pdb=" N GLN E 219 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 403 hydrogen bonds defined for protein. 1134 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: 1.29 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1289 1.26 - 1.41: 2048 1.41 - 1.55: 4643 1.55 - 1.70: 1 1.70 - 1.84: 61 Bond restraints: 8042 Sorted by residual: bond pdb=" C05 U0G A 501 " pdb=" C06 U0G A 501 " ideal model delta sigma weight residual 1.422 1.536 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C22 U0G A 501 " pdb=" O23 U0G A 501 " ideal model delta sigma weight residual 1.354 1.464 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL E 135 " pdb=" CA VAL E 135 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL D 54 " pdb=" CA VAL D 54 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.70e-03 1.32e+04 1.46e+01 ... (remaining 8037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9769 1.99 - 3.97: 1098 3.97 - 5.96: 75 5.96 - 7.94: 9 7.94 - 9.93: 2 Bond angle restraints: 10953 Sorted by residual: angle pdb=" CA GLY E 10 " pdb=" C GLY E 10 " pdb=" O GLY E 10 " ideal model delta sigma weight residual 122.37 117.88 4.49 7.30e-01 1.88e+00 3.78e+01 angle pdb=" N PRO A 209 " pdb=" CA PRO A 209 " pdb=" C PRO A 209 " ideal model delta sigma weight residual 113.53 120.38 -6.85 1.39e+00 5.18e-01 2.43e+01 angle pdb=" CA GLY E 230 " pdb=" C GLY E 230 " pdb=" O GLY E 230 " ideal model delta sigma weight residual 121.88 118.38 3.50 7.80e-01 1.64e+00 2.02e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 109.81 119.50 -9.69 2.21e+00 2.05e-01 1.92e+01 angle pdb=" CA VAL B 86 " pdb=" C VAL B 86 " pdb=" O VAL B 86 " ideal model delta sigma weight residual 121.68 118.42 3.26 7.90e-01 1.60e+00 1.70e+01 ... (remaining 10948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 4381 21.04 - 42.09: 272 42.09 - 63.13: 38 63.13 - 84.18: 5 84.18 - 105.22: 3 Dihedral angle restraints: 4699 sinusoidal: 1595 harmonic: 3104 Sorted by residual: dihedral pdb=" C THR E 198 " pdb=" N THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual -122.00 -132.23 10.23 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" C ARG E 179 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " pdb=" CB ARG E 179 " ideal model delta harmonic sigma weight residual -122.60 -132.45 9.85 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR E 102 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" CB TYR E 102 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 748 0.063 - 0.126: 357 0.126 - 0.189: 144 0.189 - 0.251: 32 0.251 - 0.314: 4 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ARG E 179 " pdb=" N ARG E 179 " pdb=" C ARG E 179 " pdb=" CB ARG E 179 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1282 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 240 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PHE A 240 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE A 240 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 163 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C ILE A 163 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 163 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 164 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARG E 179 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG E 179 " -0.015 2.00e-02 2.50e+03 pdb=" N MET E 180 " -0.013 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1873 2.81 - 3.33: 6931 3.33 - 3.85: 11304 3.85 - 4.38: 13025 4.38 - 4.90: 23519 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 204 " pdb=" OG SER B 204 " model vdw 2.291 3.040 nonbonded pdb=" O ASP C 195 " pdb=" OG1 THR C 196 " model vdw 2.381 3.040 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.384 3.040 nonbonded pdb=" OG SER C 161 " pdb=" N GLY C 162 " model vdw 2.391 3.120 ... (remaining 56647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.010 Find NCS groups from input model: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.012 0.114 8044 Z= 0.756 Angle : 1.196 9.929 10957 Z= 0.828 Chirality : 0.084 0.314 1285 Planarity : 0.005 0.049 1392 Dihedral : 13.683 105.222 2683 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.99 % Allowed : 15.99 % Favored : 81.01 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.33 % 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: -0.19 (0.26), residues: 1042 helix: 1.17 (0.28), residues: 352 sheet: 0.33 (0.35), residues: 263 loop : -1.54 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 137 TYR 0.023 0.002 TYR C 289 PHE 0.031 0.002 PHE B 197 TRP 0.024 0.002 TRP C 169 HIS 0.009 0.002 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.01197 ( 8042) covalent geometry : angle 1.19579 (10953) SS BOND : bond 0.00807 ( 2) SS BOND : angle 1.99247 ( 4) hydrogen bonds : bond 0.21028 ( 393) hydrogen bonds : angle 6.64832 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.271 Fit side-chains REVERT: A 343 ASN cc_start: 0.6964 (t0) cc_final: 0.6685 (t0) REVERT: B 73 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8072 (tmtt) REVERT: B 126 LYS cc_start: 0.8836 (tttt) cc_final: 0.8467 (ttpt) REVERT: B 164 PHE cc_start: 0.7415 (m-80) cc_final: 0.7177 (m-80) REVERT: B 166 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6257 (tm-30) REVERT: B 195 LYS cc_start: 0.8872 (tmmt) cc_final: 0.8599 (tppt) REVERT: C 76 ASP cc_start: 0.7410 (p0) cc_final: 0.7003 (p0) REVERT: C 153 ASP cc_start: 0.7201 (m-30) cc_final: 0.6999 (m-30) REVERT: C 268 ASN cc_start: 0.6963 (m-40) cc_final: 0.6618 (t0) REVERT: D 42 GLU cc_start: 0.7674 (tt0) cc_final: 0.7414 (tt0) REVERT: E 116 THR cc_start: 0.8275 (t) cc_final: 0.8058 (m) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 0.0931 time to fit residues: 18.0609 Evaluate side-chains 115 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.105567 restraints weight = 11160.523| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.03 r_work: 0.2964 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8044 Z= 0.173 Angle : 0.615 8.094 10957 Z= 0.333 Chirality : 0.045 0.154 1285 Planarity : 0.004 0.042 1392 Dihedral : 6.957 106.423 1166 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.03 % Allowed : 16.64 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.47 (0.26), residues: 1042 helix: 2.08 (0.27), residues: 355 sheet: 0.43 (0.33), residues: 269 loop : -1.38 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.013 0.001 TYR E 178 PHE 0.015 0.002 PHE C 199 TRP 0.013 0.001 TRP C 169 HIS 0.005 0.002 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8042) covalent geometry : angle 0.61376 (10953) SS BOND : bond 0.01125 ( 2) SS BOND : angle 1.78036 ( 4) hydrogen bonds : bond 0.07322 ( 393) hydrogen bonds : angle 4.77718 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.210 Fit side-chains REVERT: A 259 LYS cc_start: 0.8054 (tttt) cc_final: 0.7822 (ttmm) REVERT: A 318 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6577 (mt-10) REVERT: A 343 ASN cc_start: 0.6766 (t0) cc_final: 0.6489 (t0) REVERT: B 73 LYS cc_start: 0.8685 (ttpt) cc_final: 0.7956 (tmtt) REVERT: B 77 ASP cc_start: 0.7740 (t0) cc_final: 0.7534 (t0) REVERT: B 126 LYS cc_start: 0.8797 (tttt) cc_final: 0.8328 (ttpt) REVERT: B 164 PHE cc_start: 0.7065 (m-80) cc_final: 0.6666 (m-80) REVERT: B 166 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6555 (tm-30) REVERT: B 195 LYS cc_start: 0.8827 (tmmt) cc_final: 0.8244 (tppt) REVERT: C 138 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8474 (mt-10) REVERT: C 268 ASN cc_start: 0.6842 (m-40) cc_final: 0.5997 (t0) REVERT: D 42 GLU cc_start: 0.7866 (tt0) cc_final: 0.7560 (tt0) outliers start: 31 outliers final: 21 residues processed: 138 average time/residue: 0.0829 time to fit residues: 15.6086 Evaluate side-chains 128 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 0.0050 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109533 restraints weight = 11100.733| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.59 r_work: 0.3084 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8044 Z= 0.154 Angle : 0.571 7.962 10957 Z= 0.306 Chirality : 0.044 0.147 1285 Planarity : 0.004 0.038 1392 Dihedral : 6.749 105.185 1159 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.03 % Allowed : 17.69 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.80 (0.26), residues: 1042 helix: 2.48 (0.27), residues: 361 sheet: 0.53 (0.32), residues: 276 loop : -1.33 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 67 TYR 0.016 0.001 TYR E 178 PHE 0.014 0.002 PHE C 199 TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8042) covalent geometry : angle 0.57006 (10953) SS BOND : bond 0.00992 ( 2) SS BOND : angle 1.59067 ( 4) hydrogen bonds : bond 0.06270 ( 393) hydrogen bonds : angle 4.29160 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.235 Fit side-chains REVERT: A 179 ASN cc_start: 0.8409 (p0) cc_final: 0.8072 (p0) REVERT: A 343 ASN cc_start: 0.6971 (t0) cc_final: 0.6696 (t0) REVERT: B 73 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8143 (tmtt) REVERT: B 77 ASP cc_start: 0.7709 (t0) cc_final: 0.7492 (t0) REVERT: B 126 LYS cc_start: 0.9021 (tttt) cc_final: 0.8649 (ttpt) REVERT: B 164 PHE cc_start: 0.7445 (m-80) cc_final: 0.7068 (m-80) REVERT: B 166 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: B 195 LYS cc_start: 0.8871 (tmmt) cc_final: 0.8401 (tppt) REVERT: C 268 ASN cc_start: 0.6940 (m-40) cc_final: 0.6260 (t0) REVERT: D 42 GLU cc_start: 0.8066 (tt0) cc_final: 0.7782 (tt0) outliers start: 31 outliers final: 24 residues processed: 136 average time/residue: 0.0714 time to fit residues: 13.5932 Evaluate side-chains 130 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111663 restraints weight = 11215.880| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.69 r_work: 0.3111 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8044 Z= 0.108 Angle : 0.505 8.059 10957 Z= 0.270 Chirality : 0.042 0.157 1285 Planarity : 0.003 0.037 1392 Dihedral : 6.359 96.049 1157 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.51 % Allowed : 19.51 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.00 (0.26), residues: 1042 helix: 2.78 (0.27), residues: 360 sheet: 0.44 (0.32), residues: 275 loop : -1.18 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 67 TYR 0.014 0.001 TYR E 178 PHE 0.012 0.001 PHE E 80 TRP 0.013 0.001 TRP A 151 HIS 0.002 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8042) covalent geometry : angle 0.50371 (10953) SS BOND : bond 0.01171 ( 2) SS BOND : angle 1.68907 ( 4) hydrogen bonds : bond 0.04808 ( 393) hydrogen bonds : angle 3.99836 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.289 Fit side-chains REVERT: A 179 ASN cc_start: 0.8129 (p0) cc_final: 0.7856 (p0) REVERT: A 343 ASN cc_start: 0.6813 (t0) cc_final: 0.6535 (t0) REVERT: B 8 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5616 (mp0) REVERT: B 73 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8177 (tmtt) REVERT: B 77 ASP cc_start: 0.7693 (t0) cc_final: 0.7486 (t0) REVERT: B 126 LYS cc_start: 0.9025 (tttt) cc_final: 0.8656 (ttpt) REVERT: B 164 PHE cc_start: 0.7429 (m-80) cc_final: 0.7046 (m-80) REVERT: B 166 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: B 195 LYS cc_start: 0.8805 (tmmt) cc_final: 0.8363 (tppt) REVERT: B 242 GLU cc_start: 0.7510 (tt0) cc_final: 0.7060 (tp30) REVERT: C 268 ASN cc_start: 0.6948 (m-40) cc_final: 0.6302 (t0) REVERT: D 42 GLU cc_start: 0.8089 (tt0) cc_final: 0.7839 (tt0) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.0810 time to fit residues: 14.3197 Evaluate side-chains 123 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.133187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110049 restraints weight = 11106.995| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.67 r_work: 0.3077 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8044 Z= 0.138 Angle : 0.537 7.739 10957 Z= 0.288 Chirality : 0.043 0.148 1285 Planarity : 0.003 0.038 1392 Dihedral : 5.744 92.391 1153 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.29 % Allowed : 18.60 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.94 (0.26), residues: 1042 helix: 2.74 (0.27), residues: 361 sheet: 0.40 (0.32), residues: 279 loop : -1.24 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 32 TYR 0.015 0.001 TYR E 178 PHE 0.013 0.001 PHE C 199 TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8042) covalent geometry : angle 0.53537 (10953) SS BOND : bond 0.00977 ( 2) SS BOND : angle 1.97977 ( 4) hydrogen bonds : bond 0.05613 ( 393) hydrogen bonds : angle 4.02683 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.295 Fit side-chains REVERT: A 179 ASN cc_start: 0.8185 (p0) cc_final: 0.7890 (p0) REVERT: A 343 ASN cc_start: 0.6868 (t0) cc_final: 0.6582 (t0) REVERT: B 8 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5760 (mp0) REVERT: B 73 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8189 (tmtt) REVERT: B 77 ASP cc_start: 0.7715 (t0) cc_final: 0.7501 (t0) REVERT: B 126 LYS cc_start: 0.9046 (tttt) cc_final: 0.8701 (ttpt) REVERT: B 151 GLU cc_start: 0.8438 (tp30) cc_final: 0.7871 (tt0) REVERT: B 164 PHE cc_start: 0.7450 (m-80) cc_final: 0.7058 (m-80) REVERT: B 166 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6627 (tm-30) REVERT: C 268 ASN cc_start: 0.7013 (m-40) cc_final: 0.6367 (t0) REVERT: D 42 GLU cc_start: 0.8134 (tt0) cc_final: 0.7886 (tt0) outliers start: 33 outliers final: 24 residues processed: 127 average time/residue: 0.0738 time to fit residues: 13.2220 Evaluate side-chains 125 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112453 restraints weight = 11129.643| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.58 r_work: 0.3131 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8044 Z= 0.107 Angle : 0.486 7.396 10957 Z= 0.261 Chirality : 0.042 0.144 1285 Planarity : 0.003 0.036 1392 Dihedral : 5.441 91.347 1153 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.55 % Allowed : 18.73 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.08 (0.26), residues: 1042 helix: 2.93 (0.27), residues: 360 sheet: 0.37 (0.32), residues: 278 loop : -1.15 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 32 TYR 0.023 0.001 TYR B 115 PHE 0.012 0.001 PHE C 199 TRP 0.012 0.001 TRP A 151 HIS 0.002 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8042) covalent geometry : angle 0.48516 (10953) SS BOND : bond 0.00702 ( 2) SS BOND : angle 1.27436 ( 4) hydrogen bonds : bond 0.04628 ( 393) hydrogen bonds : angle 3.82319 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.305 Fit side-chains REVERT: A 343 ASN cc_start: 0.6782 (t0) cc_final: 0.6500 (t0) REVERT: B 8 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5566 (mp0) REVERT: B 73 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8131 (tmtt) REVERT: B 77 ASP cc_start: 0.7672 (t0) cc_final: 0.7436 (t0) REVERT: B 126 LYS cc_start: 0.9005 (tttt) cc_final: 0.8617 (ttpt) REVERT: B 164 PHE cc_start: 0.7318 (m-80) cc_final: 0.6940 (m-80) REVERT: B 166 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: B 242 GLU cc_start: 0.7437 (tt0) cc_final: 0.6880 (tp30) REVERT: C 268 ASN cc_start: 0.6919 (m-40) cc_final: 0.6272 (t0) REVERT: D 42 GLU cc_start: 0.8067 (tt0) cc_final: 0.7804 (tt0) outliers start: 35 outliers final: 27 residues processed: 125 average time/residue: 0.0750 time to fit residues: 13.4509 Evaluate side-chains 129 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0000 chunk 67 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117259 restraints weight = 11117.690| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.64 r_work: 0.3167 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8044 Z= 0.089 Angle : 0.456 6.925 10957 Z= 0.242 Chirality : 0.041 0.142 1285 Planarity : 0.003 0.032 1392 Dihedral : 5.060 88.215 1153 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.25 % Allowed : 20.68 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.30 (0.26), residues: 1042 helix: 3.11 (0.27), residues: 360 sheet: 0.44 (0.32), residues: 282 loop : -0.98 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.016 0.001 TYR B 115 PHE 0.010 0.001 PHE C 199 TRP 0.011 0.001 TRP C 169 HIS 0.002 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 8042) covalent geometry : angle 0.45629 (10953) SS BOND : bond 0.00466 ( 2) SS BOND : angle 0.81026 ( 4) hydrogen bonds : bond 0.03469 ( 393) hydrogen bonds : angle 3.59483 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.306 Fit side-chains REVERT: A 327 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8092 (tp) REVERT: A 343 ASN cc_start: 0.6587 (t0) cc_final: 0.6292 (t0) REVERT: B 73 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8119 (tmtt) REVERT: B 77 ASP cc_start: 0.7473 (t0) cc_final: 0.7168 (t0) REVERT: B 126 LYS cc_start: 0.8960 (tttt) cc_final: 0.8552 (ttpt) REVERT: B 164 PHE cc_start: 0.7247 (m-80) cc_final: 0.6880 (m-80) REVERT: B 166 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: C 268 ASN cc_start: 0.6870 (m-40) cc_final: 0.6247 (t0) REVERT: D 42 GLU cc_start: 0.8018 (tt0) cc_final: 0.7779 (tt0) outliers start: 25 outliers final: 17 residues processed: 127 average time/residue: 0.0634 time to fit residues: 11.8098 Evaluate side-chains 116 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105712 restraints weight = 11099.827| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.95 r_work: 0.2946 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8044 Z= 0.184 Angle : 0.587 8.227 10957 Z= 0.316 Chirality : 0.045 0.146 1285 Planarity : 0.004 0.041 1392 Dihedral : 5.641 92.922 1151 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.16 % Allowed : 20.68 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.99 (0.26), residues: 1042 helix: 2.72 (0.26), residues: 363 sheet: 0.31 (0.30), residues: 297 loop : -1.14 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 32 TYR 0.020 0.002 TYR B 115 PHE 0.014 0.002 PHE C 199 TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8042) covalent geometry : angle 0.58615 (10953) SS BOND : bond 0.01177 ( 2) SS BOND : angle 2.07576 ( 4) hydrogen bonds : bond 0.06185 ( 393) hydrogen bonds : angle 3.98695 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.311 Fit side-chains REVERT: A 179 ASN cc_start: 0.8016 (p0) cc_final: 0.7717 (p0) REVERT: A 206 ILE cc_start: 0.6373 (tp) cc_final: 0.6166 (tp) REVERT: A 343 ASN cc_start: 0.6623 (t0) cc_final: 0.6344 (t0) REVERT: B 8 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.5816 (mp0) REVERT: B 73 LYS cc_start: 0.8673 (ttpt) cc_final: 0.7941 (tmtt) REVERT: B 77 ASP cc_start: 0.7728 (t0) cc_final: 0.7452 (t0) REVERT: B 126 LYS cc_start: 0.8806 (tttt) cc_final: 0.8345 (ttpt) REVERT: B 164 PHE cc_start: 0.6980 (m-80) cc_final: 0.6601 (m-80) REVERT: B 166 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: C 268 ASN cc_start: 0.6966 (m-40) cc_final: 0.6142 (t0) REVERT: D 42 GLU cc_start: 0.7939 (tt0) cc_final: 0.7670 (tt0) outliers start: 32 outliers final: 27 residues processed: 133 average time/residue: 0.0777 time to fit residues: 14.7957 Evaluate side-chains 131 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107723 restraints weight = 10980.092| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.97 r_work: 0.2970 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8044 Z= 0.128 Angle : 0.524 7.560 10957 Z= 0.281 Chirality : 0.043 0.143 1285 Planarity : 0.003 0.040 1392 Dihedral : 5.480 92.220 1151 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.25 % Allowed : 21.85 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.04 (0.26), residues: 1042 helix: 2.80 (0.26), residues: 363 sheet: 0.38 (0.30), residues: 291 loop : -1.17 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.023 0.001 TYR B 115 PHE 0.013 0.001 PHE C 199 TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8042) covalent geometry : angle 0.52298 (10953) SS BOND : bond 0.00881 ( 2) SS BOND : angle 1.49094 ( 4) hydrogen bonds : bond 0.05181 ( 393) hydrogen bonds : angle 3.86770 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.319 Fit side-chains REVERT: A 179 ASN cc_start: 0.7934 (p0) cc_final: 0.7649 (p0) REVERT: A 343 ASN cc_start: 0.6599 (t0) cc_final: 0.6338 (t0) REVERT: B 73 LYS cc_start: 0.8664 (ttpt) cc_final: 0.7927 (tmtt) REVERT: B 77 ASP cc_start: 0.7679 (t0) cc_final: 0.7396 (t0) REVERT: B 126 LYS cc_start: 0.8805 (tttt) cc_final: 0.8351 (ttpt) REVERT: B 164 PHE cc_start: 0.6907 (m-80) cc_final: 0.6526 (m-80) REVERT: B 166 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: C 268 ASN cc_start: 0.6980 (m-40) cc_final: 0.6153 (t0) REVERT: D 42 GLU cc_start: 0.7906 (tt0) cc_final: 0.7618 (tt0) outliers start: 25 outliers final: 23 residues processed: 122 average time/residue: 0.0719 time to fit residues: 12.6661 Evaluate side-chains 124 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106690 restraints weight = 10976.293| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.96 r_work: 0.2960 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8044 Z= 0.147 Angle : 0.551 7.946 10957 Z= 0.295 Chirality : 0.043 0.144 1285 Planarity : 0.003 0.041 1392 Dihedral : 5.558 93.051 1151 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.77 % Allowed : 21.59 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.99 (0.26), residues: 1042 helix: 2.74 (0.26), residues: 363 sheet: 0.30 (0.30), residues: 297 loop : -1.15 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.023 0.001 TYR B 115 PHE 0.014 0.001 PHE C 199 TRP 0.012 0.001 TRP A 151 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8042) covalent geometry : angle 0.55018 (10953) SS BOND : bond 0.01011 ( 2) SS BOND : angle 1.71514 ( 4) hydrogen bonds : bond 0.05628 ( 393) hydrogen bonds : angle 3.91870 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.324 Fit side-chains REVERT: A 179 ASN cc_start: 0.7950 (p0) cc_final: 0.7660 (p0) REVERT: A 206 ILE cc_start: 0.6328 (tp) cc_final: 0.6111 (tp) REVERT: A 343 ASN cc_start: 0.6597 (t0) cc_final: 0.6347 (t0) REVERT: B 73 LYS cc_start: 0.8663 (ttpt) cc_final: 0.7784 (mttp) REVERT: B 77 ASP cc_start: 0.7650 (t0) cc_final: 0.7401 (t0) REVERT: B 126 LYS cc_start: 0.8798 (tttt) cc_final: 0.8348 (ttpt) REVERT: B 164 PHE cc_start: 0.6948 (m-80) cc_final: 0.6570 (m-80) REVERT: B 166 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: C 268 ASN cc_start: 0.7066 (m-40) cc_final: 0.6250 (t0) REVERT: D 42 GLU cc_start: 0.7928 (tt0) cc_final: 0.7639 (tt0) outliers start: 29 outliers final: 27 residues processed: 128 average time/residue: 0.0737 time to fit residues: 13.9931 Evaluate side-chains 131 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105977 restraints weight = 11128.163| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.99 r_work: 0.2941 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8044 Z= 0.179 Angle : 0.594 8.540 10957 Z= 0.319 Chirality : 0.045 0.144 1285 Planarity : 0.004 0.043 1392 Dihedral : 5.793 94.345 1151 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.16 % Allowed : 21.20 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.80 (0.26), residues: 1042 helix: 2.56 (0.26), residues: 363 sheet: 0.31 (0.30), residues: 290 loop : -1.31 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 32 TYR 0.023 0.002 TYR B 115 PHE 0.015 0.002 PHE C 199 TRP 0.012 0.001 TRP A 151 HIS 0.005 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8042) covalent geometry : angle 0.59324 (10953) SS BOND : bond 0.01198 ( 2) SS BOND : angle 2.02421 ( 4) hydrogen bonds : bond 0.06422 ( 393) hydrogen bonds : angle 4.09305 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.77 seconds wall clock time: 34 minutes 6.70 seconds (2046.70 seconds total)