Starting phenix.real_space_refine on Sun Apr 5 13:15:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x58_66577/04_2026/9x58_66577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x58_66577/04_2026/9x58_66577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x58_66577/04_2026/9x58_66577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x58_66577/04_2026/9x58_66577.map" model { file = "/net/cci-nas-00/data/ceres_data/9x58_66577/04_2026/9x58_66577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x58_66577/04_2026/9x58_66577.cif" } resolution = 3.2 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= 0.037 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 26 5.16 5 C 6460 2.51 5 N 1922 2.21 5 O 1978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10386 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3028 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3028 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1080 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'CIS': 2, 'TRANS': 213} Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 648 Unresolved non-hydrogen dihedrals: 216 Planarities with less than four sites: {'UNK:plan-1': 216} Unresolved non-hydrogen planarities: 216 Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1080 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'CIS': 2, 'TRANS': 213} Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 648 Unresolved non-hydrogen dihedrals: 216 Planarities with less than four sites: {'UNK:plan-1': 216} Unresolved non-hydrogen planarities: 216 Chain: "C" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1085 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'CIS': 1, 'TRANS': 215} Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 651 Unresolved non-hydrogen dihedrals: 217 Planarities with less than four sites: {'UNK:plan-1': 217} Unresolved non-hydrogen planarities: 217 Chain: "H" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1085 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'CIS': 1, 'TRANS': 215} Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 651 Unresolved non-hydrogen dihedrals: 217 Planarities with less than four sites: {'UNK:plan-1': 217} Unresolved non-hydrogen planarities: 217 Time building chain proxies: 2.65, per 1000 atoms: 0.26 Number of scatterers: 10386 At special positions: 0 Unit cell: (102.3, 185.9, 90.2, 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 26 16.00 O 1978 8.00 N 1922 7.00 C 6460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 345.0 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 30 sheets defined 46.6% alpha, 57.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 18 through 33 removed outlier: 3.572A pdb=" N THR A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.773A pdb=" N ARG A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.548A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.958A pdb=" N ASP A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.687A pdb=" N TYR A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.824A pdb=" N ASN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.719A pdb=" N HIS A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.878A pdb=" N LEU A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.868A pdb=" N TYR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.504A pdb=" N GLU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 33 removed outlier: 3.576A pdb=" N THR B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.778A pdb=" N ARG B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.542A pdb=" N CYS B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.960A pdb=" N ASP B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 removed outlier: 3.633A pdb=" N GLN B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 184 removed outlier: 3.878A pdb=" N TYR B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.172A pdb=" N ASN B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 3.710A pdb=" N HIS B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.882A pdb=" N LEU B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 260 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 298 removed outlier: 3.866A pdb=" N TYR B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.698A pdb=" N GLU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 184 through 191 Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'H' and resid 131 through 136 Processing helix chain 'H' and resid 191 through 196 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.614A pdb=" N GLN A 8 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N PHE A 75 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY A 10 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165 removed outlier: 6.393A pdb=" N LEU A 137 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 4.826A pdb=" N VAL A 239 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET A 354 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR A 369 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 356 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 336 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 7.618A pdb=" N GLN B 8 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N PHE B 75 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY B 10 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 164 through 165 removed outlier: 6.459A pdb=" N LEU B 137 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.839A pdb=" N VAL B 239 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET B 354 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR B 369 " --> pdb=" O MET B 354 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 356 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.529A pdb=" N UNK L 105 " --> pdb=" O UNK L 11 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.794A pdb=" N UNK L 135 " --> pdb=" O UNK L 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK L 140 " --> pdb=" O UNK L 175 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N UNK L 175 " --> pdb=" O UNK L 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 156 through 157 removed outlier: 4.265A pdb=" N UNK L 150 " --> pdb=" O UNK L 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.529A pdb=" N UNK D 105 " --> pdb=" O UNK D 11 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N UNK D 37 " --> pdb=" O UNK D 46 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N UNK D 46 " --> pdb=" O UNK D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.792A pdb=" N UNK D 135 " --> pdb=" O UNK D 120 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N UNK D 140 " --> pdb=" O UNK D 175 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N UNK D 175 " --> pdb=" O UNK D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 156 through 157 removed outlier: 4.280A pdb=" N UNK D 150 " --> pdb=" O UNK D 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.509A pdb=" N UNK C 3 " --> pdb=" O UNK C 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N UNK C 80 " --> pdb=" O UNK C 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 37 removed outlier: 6.654A pdb=" N UNK C 99 " --> pdb=" O UNK C 105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 52 removed outlier: 3.517A pdb=" N UNK C 60 " --> pdb=" O UNK C 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 124 through 128 removed outlier: 3.523A pdb=" N UNK C 147 " --> pdb=" O UNK C 124 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK C 145 " --> pdb=" O UNK C 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N UNK C 143 " --> pdb=" O UNK C 128 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N UNK C 148 " --> pdb=" O UNK C 180 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N UNK C 180 " --> pdb=" O UNK C 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 124 through 128 removed outlier: 3.523A pdb=" N UNK C 147 " --> pdb=" O UNK C 124 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N UNK C 145 " --> pdb=" O UNK C 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N UNK C 143 " --> pdb=" O UNK C 128 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N UNK C 148 " --> pdb=" O UNK C 180 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N UNK C 180 " --> pdb=" O UNK C 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.508A pdb=" N UNK H 3 " --> pdb=" O UNK H 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK H 80 " --> pdb=" O UNK H 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 35 through 37 removed outlier: 6.655A pdb=" N UNK H 99 " --> pdb=" O UNK H 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AC9, first strand: chain 'H' and resid 51 through 52 removed outlier: 3.526A pdb=" N UNK H 60 " --> pdb=" O UNK H 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.518A pdb=" N UNK H 147 " --> pdb=" O UNK H 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK H 145 " --> pdb=" O UNK H 126 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N UNK H 143 " --> pdb=" O UNK H 128 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N UNK H 148 " --> pdb=" O UNK H 180 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N UNK H 180 " --> pdb=" O UNK H 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.518A pdb=" N UNK H 147 " --> pdb=" O UNK H 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N UNK H 145 " --> pdb=" O UNK H 126 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N UNK H 143 " --> pdb=" O UNK H 128 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N UNK H 148 " --> pdb=" O UNK H 180 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N UNK H 180 " --> pdb=" O UNK H 148 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 154 through 158 463 hydrogen bonds defined for protein. 1269 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: 1.63 Time building geometry restraints manager: 1.16 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: 3724 1.34 - 1.46: 2168 1.46 - 1.58: 4592 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 10524 Sorted by residual: bond pdb=" C ALA A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C ALA B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.46e+00 bond pdb=" CA UNK D 30 " pdb=" CB UNK D 30 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" CA UNK L 30 " pdb=" CB UNK L 30 " ideal model delta sigma weight residual 1.530 1.508 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CB ASN A 170 " pdb=" CG ASN A 170 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.91e-01 ... (remaining 10519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 13823 1.81 - 3.61: 556 3.61 - 5.42: 51 5.42 - 7.22: 11 7.22 - 9.03: 3 Bond angle restraints: 14444 Sorted by residual: angle pdb=" C UNK L 7 " pdb=" N UNK L 8 " pdb=" CA UNK L 8 " ideal model delta sigma weight residual 121.70 128.81 -7.11 1.80e+00 3.09e-01 1.56e+01 angle pdb=" C UNK D 7 " pdb=" N UNK D 8 " pdb=" CA UNK D 8 " ideal model delta sigma weight residual 121.70 128.79 -7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" C UNK C 9 " pdb=" N UNK C 10 " pdb=" CA UNK C 10 " ideal model delta sigma weight residual 121.70 127.40 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" C UNK H 9 " pdb=" N UNK H 10 " pdb=" CA UNK H 10 " ideal model delta sigma weight residual 121.70 127.29 -5.59 1.80e+00 3.09e-01 9.63e+00 angle pdb=" CG1 ILE B 300 " pdb=" CB ILE B 300 " pdb=" CG2 ILE B 300 " ideal model delta sigma weight residual 110.70 101.67 9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 14439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 5708 17.44 - 34.87: 420 34.87 - 52.31: 118 52.31 - 69.74: 22 69.74 - 87.18: 4 Dihedral angle restraints: 6272 sinusoidal: 1492 harmonic: 4780 Sorted by residual: dihedral pdb=" CA UNK D 94 " pdb=" C UNK D 94 " pdb=" N UNK D 95 " pdb=" CA UNK D 95 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA UNK L 94 " pdb=" C UNK L 94 " pdb=" N UNK L 95 " pdb=" CA UNK L 95 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA UNK H 37 " pdb=" C UNK H 37 " pdb=" N UNK H 38 " pdb=" CA UNK H 38 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 6269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1323 0.044 - 0.087: 385 0.087 - 0.131: 63 0.131 - 0.175: 7 0.175 - 0.219: 2 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A 218 " pdb=" CA ILE A 218 " pdb=" CG1 ILE A 218 " pdb=" CG2 ILE A 218 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1777 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 363 " 0.026 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 364 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 218 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ILE A 218 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE A 218 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 219 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 218 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C ILE B 218 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE B 218 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 219 " -0.009 2.00e-02 2.50e+03 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 987 2.75 - 3.28: 8995 3.28 - 3.82: 14459 3.82 - 4.36: 15101 4.36 - 4.90: 29333 Nonbonded interactions: 68875 Sorted by model distance: nonbonded pdb=" OD2 ASP A 139 " pdb=" NH1 ARG A 197 " model vdw 2.206 3.120 nonbonded pdb=" OD2 ASP B 139 " pdb=" NH1 ARG B 197 " model vdw 2.217 3.120 nonbonded pdb=" O TYR B 267 " pdb=" OG SER B 270 " model vdw 2.253 3.040 nonbonded pdb=" O TYR A 267 " pdb=" OG SER A 270 " model vdw 2.256 3.040 nonbonded pdb=" OE1 GLU B 39 " pdb=" NE ARG B 293 " model vdw 2.406 3.120 ... (remaining 68870 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 3 through 218) selection = chain 'D' selection = (chain 'H' and resid 3 through 218) selection = chain 'L' } 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: 4.090 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.900 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.004 0.038 10526 Z= 0.195 Angle : 0.822 9.026 14448 Z= 0.408 Chirality : 0.041 0.219 1780 Planarity : 0.003 0.040 1952 Dihedral : 14.892 87.178 3130 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 26.29 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.91 (0.29), residues: 750 helix: -1.32 (0.28), residues: 314 sheet: -2.02 (0.47), residues: 116 loop : -2.42 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.014 0.002 TYR A 282 PHE 0.018 0.002 PHE B 134 TRP 0.007 0.001 TRP A 319 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00431 (10524) covalent geometry : angle 0.82210 (14444) SS BOND : bond 0.00292 ( 2) SS BOND : angle 1.26626 ( 4) hydrogen bonds : bond 0.19337 ( 441) hydrogen bonds : angle 6.29078 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.289 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1569 time to fit residues: 6.5354 Evaluate side-chains 26 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 335 GLN A 340 ASN B 66 GLN B 335 GLN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.178642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133494 restraints weight = 13138.429| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.73 r_work: 0.3204 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.062 10526 Z= 0.433 Angle : 1.043 11.131 14448 Z= 0.489 Chirality : 0.051 0.208 1780 Planarity : 0.005 0.046 1952 Dihedral : 5.473 32.324 1692 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Rotamer: Outliers : 4.10 % Allowed : 22.64 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -3.24 (0.28), residues: 750 helix: -1.48 (0.27), residues: 304 sheet: -2.37 (0.45), residues: 116 loop : -2.64 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 293 TYR 0.020 0.004 TYR B 282 PHE 0.022 0.004 PHE A 134 TRP 0.017 0.003 TRP A 259 HIS 0.014 0.003 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.01066 (10524) covalent geometry : angle 1.04251 (14444) SS BOND : bond 0.00453 ( 2) SS BOND : angle 2.40168 ( 4) hydrogen bonds : bond 0.07514 ( 441) hydrogen bonds : angle 4.57420 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 35 time to evaluate : 0.282 Fit side-chains REVERT: A 49 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: A 260 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7416 (mmtt) REVERT: B 49 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: B 194 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: B 260 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7469 (mmtt) outliers start: 27 outliers final: 16 residues processed: 60 average time/residue: 0.1040 time to fit residues: 9.0831 Evaluate side-chains 49 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 28 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.184570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136992 restraints weight = 13056.290| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.34 r_work: 0.3257 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10526 Z= 0.134 Angle : 0.637 7.222 14448 Z= 0.303 Chirality : 0.036 0.208 1780 Planarity : 0.003 0.040 1952 Dihedral : 4.225 20.091 1692 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.56 % Allowed : 22.95 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.49 (0.30), residues: 750 helix: -0.71 (0.29), residues: 304 sheet: -1.91 (0.44), residues: 134 loop : -2.42 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 183 TYR 0.016 0.002 TYR A 369 PHE 0.015 0.002 PHE A 134 TRP 0.008 0.001 TRP B 259 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00308 (10524) covalent geometry : angle 0.63728 (14444) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.97446 ( 4) hydrogen bonds : bond 0.04080 ( 441) hydrogen bonds : angle 3.87596 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 34 time to evaluate : 0.296 Fit side-chains REVERT: A 49 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: A 194 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: A 260 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7343 (mmtt) REVERT: A 296 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5578 (ttm-80) REVERT: B 49 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: B 260 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7383 (mmtt) REVERT: B 296 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5566 (ttm-80) outliers start: 30 outliers final: 12 residues processed: 59 average time/residue: 0.1327 time to fit residues: 10.6417 Evaluate side-chains 44 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 33 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.179528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.133883 restraints weight = 13213.178| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.70 r_work: 0.3215 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 10526 Z= 0.373 Angle : 0.934 10.103 14448 Z= 0.438 Chirality : 0.047 0.185 1780 Planarity : 0.004 0.036 1952 Dihedral : 5.132 29.832 1692 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.13 % Favored : 85.87 % Rotamer: Outliers : 6.53 % Allowed : 20.97 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.90 (0.29), residues: 750 helix: -0.95 (0.29), residues: 300 sheet: -2.34 (0.46), residues: 116 loop : -2.65 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 184 TYR 0.019 0.003 TYR B 276 PHE 0.022 0.003 PHE B 134 TRP 0.015 0.003 TRP B 259 HIS 0.007 0.002 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00920 (10524) covalent geometry : angle 0.93314 (14444) SS BOND : bond 0.00239 ( 2) SS BOND : angle 1.93257 ( 4) hydrogen bonds : bond 0.06792 ( 441) hydrogen bonds : angle 4.25882 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 31 time to evaluate : 0.294 Fit side-chains REVERT: A 49 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: A 177 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8225 (tp) REVERT: A 194 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: A 260 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7419 (mmtt) REVERT: A 296 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.5895 (ttm-80) REVERT: B 49 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: B 194 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: B 260 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7437 (mmtt) REVERT: B 296 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.5892 (ttm-80) outliers start: 43 outliers final: 21 residues processed: 69 average time/residue: 0.1295 time to fit residues: 12.1062 Evaluate side-chains 56 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 26 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 150 optimal weight: 40.0000 chunk 134 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.183000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134924 restraints weight = 13122.781| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.34 r_work: 0.3230 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10526 Z= 0.158 Angle : 0.658 8.128 14448 Z= 0.312 Chirality : 0.037 0.212 1780 Planarity : 0.003 0.039 1952 Dihedral : 4.322 20.816 1692 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 5.17 % Allowed : 23.40 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.41 (0.30), residues: 750 helix: -0.48 (0.30), residues: 296 sheet: -1.89 (0.45), residues: 134 loop : -2.51 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 183 TYR 0.014 0.002 TYR A 369 PHE 0.019 0.002 PHE A 134 TRP 0.009 0.001 TRP A 259 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00372 (10524) covalent geometry : angle 0.65801 (14444) SS BOND : bond 0.00190 ( 2) SS BOND : angle 1.09455 ( 4) hydrogen bonds : bond 0.04304 ( 441) hydrogen bonds : angle 3.79680 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 30 time to evaluate : 0.298 Fit side-chains REVERT: A 49 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: A 194 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: A 260 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7361 (mmtt) REVERT: A 296 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.5702 (ttm-80) REVERT: B 49 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: B 260 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7295 (mmtt) REVERT: B 296 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.5647 (ttm-80) outliers start: 34 outliers final: 22 residues processed: 59 average time/residue: 0.1184 time to fit residues: 9.8246 Evaluate side-chains 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 24 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 139 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 overall best weight: 1.7564 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.179912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132661 restraints weight = 13215.495| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.95 r_work: 0.3225 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 10526 Z= 0.290 Angle : 0.835 9.687 14448 Z= 0.391 Chirality : 0.043 0.202 1780 Planarity : 0.004 0.032 1952 Dihedral : 4.863 27.105 1692 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.20 % Favored : 86.80 % Rotamer: Outliers : 6.69 % Allowed : 23.10 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.70 (0.29), residues: 750 helix: -0.64 (0.30), residues: 294 sheet: -2.22 (0.47), residues: 116 loop : -2.68 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 184 TYR 0.018 0.003 TYR A 276 PHE 0.020 0.003 PHE B 134 TRP 0.013 0.002 TRP B 259 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00709 (10524) covalent geometry : angle 0.83423 (14444) SS BOND : bond 0.00186 ( 2) SS BOND : angle 1.65475 ( 4) hydrogen bonds : bond 0.05992 ( 441) hydrogen bonds : angle 4.06314 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 27 time to evaluate : 0.296 Fit side-chains REVERT: A 49 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: A 177 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 194 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: A 260 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7401 (mmtt) REVERT: A 261 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7060 (ttpt) REVERT: A 296 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.5908 (ttm-80) REVERT: B 49 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: B 194 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: B 260 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7413 (mmtt) REVERT: B 296 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.5892 (ttm-80) outliers start: 44 outliers final: 32 residues processed: 67 average time/residue: 0.1130 time to fit residues: 10.6794 Evaluate side-chains 68 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 27 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 76 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 108 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 135 optimal weight: 40.0000 chunk 64 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.182015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134352 restraints weight = 13084.978| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.19 r_work: 0.3233 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10526 Z= 0.183 Angle : 0.686 8.540 14448 Z= 0.324 Chirality : 0.038 0.211 1780 Planarity : 0.003 0.035 1952 Dihedral : 4.389 21.558 1692 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 6.84 % Allowed : 22.64 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.44 (0.30), residues: 750 helix: -0.47 (0.30), residues: 296 sheet: -1.78 (0.46), residues: 126 loop : -2.61 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 183 TYR 0.015 0.002 TYR A 282 PHE 0.019 0.002 PHE B 134 TRP 0.010 0.001 TRP B 259 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00442 (10524) covalent geometry : angle 0.68533 (14444) SS BOND : bond 0.00176 ( 2) SS BOND : angle 1.15493 ( 4) hydrogen bonds : bond 0.04586 ( 441) hydrogen bonds : angle 3.78359 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 31 time to evaluate : 0.271 Fit side-chains REVERT: A 49 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: A 177 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8052 (tp) REVERT: A 194 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: A 260 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7263 (mmtt) REVERT: A 296 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5769 (ttm-80) REVERT: B 49 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: B 260 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7304 (mmtt) REVERT: B 296 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5776 (ttm-80) outliers start: 45 outliers final: 33 residues processed: 71 average time/residue: 0.1074 time to fit residues: 10.9223 Evaluate side-chains 65 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 24 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 86 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 54 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.178312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130734 restraints weight = 13120.880| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.08 r_work: 0.3196 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 10526 Z= 0.398 Angle : 0.977 10.664 14448 Z= 0.459 Chirality : 0.048 0.186 1780 Planarity : 0.004 0.038 1952 Dihedral : 5.322 31.769 1692 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.53 % Favored : 85.47 % Rotamer: Outliers : 7.45 % Allowed : 23.71 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.95 (0.29), residues: 750 helix: -0.89 (0.29), residues: 306 sheet: -2.39 (0.46), residues: 116 loop : -2.81 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 184 TYR 0.021 0.003 TYR B 276 PHE 0.022 0.004 PHE A 13 TRP 0.015 0.003 TRP A 259 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00976 (10524) covalent geometry : angle 0.97630 (14444) SS BOND : bond 0.00360 ( 2) SS BOND : angle 2.03695 ( 4) hydrogen bonds : bond 0.07075 ( 441) hydrogen bonds : angle 4.30506 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 29 time to evaluate : 0.301 Fit side-chains REVERT: A 49 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: A 177 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 194 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: A 260 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7368 (mmtt) REVERT: A 271 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6458 (pm20) REVERT: A 296 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6027 (ttm-80) REVERT: B 49 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: B 194 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: B 260 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7365 (mmtt) REVERT: B 271 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6516 (pm20) REVERT: B 296 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6036 (ttm-80) outliers start: 49 outliers final: 33 residues processed: 74 average time/residue: 0.0980 time to fit residues: 10.4639 Evaluate side-chains 70 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 26 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 92 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.180659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132993 restraints weight = 13061.968| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.27 r_work: 0.3232 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10526 Z= 0.156 Angle : 0.671 9.039 14448 Z= 0.318 Chirality : 0.037 0.201 1780 Planarity : 0.003 0.041 1952 Dihedral : 4.376 20.691 1692 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 6.38 % Allowed : 23.86 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.51 (0.30), residues: 750 helix: -0.48 (0.30), residues: 296 sheet: -2.16 (0.48), residues: 124 loop : -2.55 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 183 TYR 0.015 0.002 TYR A 276 PHE 0.018 0.002 PHE B 134 TRP 0.009 0.001 TRP B 259 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00373 (10524) covalent geometry : angle 0.67119 (14444) SS BOND : bond 0.00139 ( 2) SS BOND : angle 1.13022 ( 4) hydrogen bonds : bond 0.04297 ( 441) hydrogen bonds : angle 3.79103 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 33 time to evaluate : 0.274 Fit side-chains REVERT: A 49 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: A 177 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 194 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: A 260 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7185 (mmtt) REVERT: A 296 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.5805 (ttm-80) REVERT: B 49 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: B 260 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7218 (mmtt) REVERT: B 296 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.5811 (ttm-80) outliers start: 42 outliers final: 28 residues processed: 68 average time/residue: 0.1183 time to fit residues: 11.1997 Evaluate side-chains 62 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 26 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.177839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130100 restraints weight = 13027.648| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.26 r_work: 0.3182 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 10526 Z= 0.279 Angle : 0.819 9.199 14448 Z= 0.385 Chirality : 0.042 0.190 1780 Planarity : 0.004 0.035 1952 Dihedral : 4.797 26.430 1692 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 6.53 % Allowed : 24.16 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.72 (0.29), residues: 750 helix: -0.66 (0.30), residues: 296 sheet: -2.17 (0.48), residues: 116 loop : -2.71 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 184 TYR 0.017 0.003 TYR A 276 PHE 0.020 0.003 PHE B 134 TRP 0.012 0.002 TRP B 259 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00682 (10524) covalent geometry : angle 0.81831 (14444) SS BOND : bond 0.00122 ( 2) SS BOND : angle 1.78082 ( 4) hydrogen bonds : bond 0.05762 ( 441) hydrogen bonds : angle 3.98637 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 25 time to evaluate : 0.317 Fit side-chains REVERT: A 49 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: A 177 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8083 (tp) REVERT: A 194 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: A 260 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7272 (mmtt) REVERT: A 271 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: A 296 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.5982 (ttm-80) REVERT: B 49 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: B 260 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7381 (mmtt) REVERT: B 296 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.5988 (ttm-80) outliers start: 43 outliers final: 33 residues processed: 64 average time/residue: 0.1141 time to fit residues: 10.1744 Evaluate side-chains 67 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 25 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 151 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.180632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133432 restraints weight = 13082.954| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.15 r_work: 0.3244 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10526 Z= 0.154 Angle : 0.655 8.642 14448 Z= 0.311 Chirality : 0.037 0.201 1780 Planarity : 0.003 0.036 1952 Dihedral : 4.227 18.911 1692 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 6.38 % Allowed : 24.01 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.33 (0.30), residues: 750 helix: -0.39 (0.31), residues: 296 sheet: -1.77 (0.46), residues: 134 loop : -2.53 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 183 TYR 0.015 0.002 TYR A 276 PHE 0.018 0.002 PHE B 134 TRP 0.010 0.001 TRP B 259 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00366 (10524) covalent geometry : angle 0.65523 (14444) SS BOND : bond 0.00105 ( 2) SS BOND : angle 1.13739 ( 4) hydrogen bonds : bond 0.04166 ( 441) hydrogen bonds : angle 3.67256 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2528.57 seconds wall clock time: 43 minutes 42.34 seconds (2622.34 seconds total)