Starting phenix.real_space_refine on Thu Mar 5 11:42:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lmu_0920/03_2026/6lmu_0920.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmu_0920/03_2026/6lmu_0920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lmu_0920/03_2026/6lmu_0920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmu_0920/03_2026/6lmu_0920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lmu_0920/03_2026/6lmu_0920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmu_0920/03_2026/6lmu_0920.map" } resolution = 3.4 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= 0.009 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 88 5.16 5 C 14553 2.51 5 N 4026 2.21 5 O 3762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22429 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2039 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 14, 'TRANS': 248} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 2.44, per 1000 atoms: 0.11 Number of scatterers: 22429 At special positions: 0 Unit cell: (152.513, 153.874, 100.767, 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 88 16.00 O 3762 8.00 N 4026 7.00 C 14553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.04 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.04 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.04 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.04 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.04 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.04 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.04 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.04 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.04 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.04 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.04 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " 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: 1.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5522 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 11 sheets defined 69.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 58 " --> pdb=" O TYR A 54 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 79 through 88 removed outlier: 4.094A pdb=" N HIS A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE A 156 " --> pdb=" O HIS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 207 Processing helix chain 'A' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 58 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS B 92 " --> pdb=" O ARG B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 207 removed outlier: 3.500A pdb=" N ARG B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 58 " --> pdb=" O TYR C 54 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS C 92 " --> pdb=" O ARG C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE C 156 " --> pdb=" O HIS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 207 Processing helix chain 'C' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 58 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS D 92 " --> pdb=" O ARG D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.908A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE D 156 " --> pdb=" O HIS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 207 removed outlier: 3.500A pdb=" N ARG D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS E 92 " --> pdb=" O ARG E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.906A pdb=" N ALA E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE E 156 " --> pdb=" O HIS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 207 Processing helix chain 'E' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU F 58 " --> pdb=" O TYR F 54 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS F 92 " --> pdb=" O ARG F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 135 Processing helix chain 'F' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE F 156 " --> pdb=" O HIS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 207 Processing helix chain 'F' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU G 58 " --> pdb=" O TYR G 54 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 79 through 88 removed outlier: 4.094A pdb=" N HIS G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS G 92 " --> pdb=" O ARG G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE G 156 " --> pdb=" O HIS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 207 Processing helix chain 'G' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP G 302 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY H 57 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU H 58 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS H 92 " --> pdb=" O ARG H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 92' Processing helix chain 'H' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'H' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE H 156 " --> pdb=" O HIS H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 207 Processing helix chain 'H' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP H 302 " --> pdb=" O ARG H 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU I 58 " --> pdb=" O TYR I 54 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 92 removed outlier: 3.639A pdb=" N LYS I 92 " --> pdb=" O ARG I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 99 through 113 removed outlier: 3.908A pdb=" N ALA I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 135 Processing helix chain 'I' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 207 Processing helix chain 'I' and resid 214 through 251 removed outlier: 3.541A pdb=" N ALA I 225 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN I 232 " --> pdb=" O ASP I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP I 302 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY J 57 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU J 58 " --> pdb=" O TYR J 54 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS J 92 " --> pdb=" O ARG J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 124 removed outlier: 3.579A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 152 through 158 removed outlier: 4.057A pdb=" N ILE J 156 " --> pdb=" O HIS J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 169 through 207 Processing helix chain 'J' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J 232 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP J 302 " --> pdb=" O ARG J 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 75 removed outlier: 3.895A pdb=" N TYR K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU K 58 " --> pdb=" O TYR K 54 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 79 through 88 removed outlier: 4.095A pdb=" N HIS K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 removed outlier: 3.640A pdb=" N LYS K 92 " --> pdb=" O ARG K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 99 through 113 removed outlier: 3.907A pdb=" N ALA K 113 " --> pdb=" O ARG K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 124 removed outlier: 3.580A pdb=" N ARG K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 152 through 158 removed outlier: 4.058A pdb=" N ILE K 156 " --> pdb=" O HIS K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 169 through 207 Processing helix chain 'K' and resid 214 through 251 removed outlier: 3.542A pdb=" N ALA K 225 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN K 232 " --> pdb=" O ASP K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 297 through 303 removed outlier: 3.586A pdb=" N TRP K 302 " --> pdb=" O ARG K 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG A 288 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 295 " --> pdb=" O ARG A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG B 288 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 295 " --> pdb=" O ARG B 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG C 288 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 295 " --> pdb=" O ARG C 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG D 288 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 295 " --> pdb=" O ARG D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG E 288 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 295 " --> pdb=" O ARG E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG F 288 " --> pdb=" O LEU F 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 295 " --> pdb=" O ARG F 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG G 288 " --> pdb=" O LEU G 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 295 " --> pdb=" O ARG G 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 288 through 289 removed outlier: 3.845A pdb=" N ARG H 288 " --> pdb=" O LEU H 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 295 " --> pdb=" O ARG H 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG I 288 " --> pdb=" O LEU I 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU I 295 " --> pdb=" O ARG I 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG J 288 " --> pdb=" O LEU J 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU J 295 " --> pdb=" O ARG J 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 288 through 289 removed outlier: 3.844A pdb=" N ARG K 288 " --> pdb=" O LEU K 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU K 295 " --> pdb=" O ARG K 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 1307 hydrogen bonds defined for protein. 3855 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: 4.02 Time building geometry restraints manager: 2.21 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: 7205 1.34 - 1.46: 5886 1.46 - 1.58: 9888 1.58 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 23067 Sorted by residual: bond pdb=" CB THR C 234 " pdb=" CG2 THR C 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR F 234 " pdb=" CG2 THR F 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR G 234 " pdb=" CG2 THR G 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.07e+00 bond pdb=" CB THR H 234 " pdb=" CG2 THR H 234 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB THR E 234 " pdb=" CG2 THR E 234 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 ... (remaining 23062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 28716 1.74 - 3.47: 2077 3.47 - 5.21: 514 5.21 - 6.95: 164 6.95 - 8.68: 55 Bond angle restraints: 31526 Sorted by residual: angle pdb=" C ASN H 290 " pdb=" N GLN H 291 " pdb=" CA GLN H 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN I 290 " pdb=" N GLN I 291 " pdb=" CA GLN I 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASN B 290 " pdb=" N GLN B 291 " pdb=" CA GLN B 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN C 290 " pdb=" N GLN C 291 " pdb=" CA GLN C 291 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN J 290 " pdb=" N GLN J 291 " pdb=" CA GLN J 291 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 ... (remaining 31521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 11409 15.13 - 30.26: 1428 30.26 - 45.39: 539 45.39 - 60.52: 132 60.52 - 75.65: 44 Dihedral angle restraints: 13552 sinusoidal: 5027 harmonic: 8525 Sorted by residual: dihedral pdb=" CB CYS J 46 " pdb=" SG CYS J 46 " pdb=" SG CYS J 130 " pdb=" CB CYS J 130 " ideal model delta sinusoidal sigma weight residual 93.00 168.65 -75.65 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS I 46 " pdb=" SG CYS I 46 " pdb=" SG CYS I 130 " pdb=" CB CYS I 130 " ideal model delta sinusoidal sigma weight residual 93.00 168.63 -75.63 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS D 46 " pdb=" SG CYS D 46 " pdb=" SG CYS D 130 " pdb=" CB CYS D 130 " ideal model delta sinusoidal sigma weight residual 93.00 168.63 -75.63 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 13549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1661 0.036 - 0.071: 1265 0.071 - 0.107: 325 0.107 - 0.143: 203 0.143 - 0.178: 66 Chirality restraints: 3520 Sorted by residual: chirality pdb=" CB VAL B 284 " pdb=" CA VAL B 284 " pdb=" CG1 VAL B 284 " pdb=" CG2 VAL B 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CB VAL C 284 " pdb=" CA VAL C 284 " pdb=" CG1 VAL C 284 " pdb=" CG2 VAL C 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL I 284 " pdb=" CA VAL I 284 " pdb=" CG1 VAL I 284 " pdb=" CG2 VAL I 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3517 not shown) Planarity restraints: 4048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 275 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO I 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO I 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 276 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 275 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO B 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 275 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO E 276 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.038 5.00e-02 4.00e+02 ... (remaining 4045 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 7587 2.84 - 3.35: 20366 3.35 - 3.87: 35871 3.87 - 4.38: 39664 4.38 - 4.90: 67774 Nonbonded interactions: 171262 Sorted by model distance: nonbonded pdb=" O SER I 121 " pdb=" OG SER I 121 " model vdw 2.320 3.040 nonbonded pdb=" O SER A 121 " pdb=" OG SER A 121 " model vdw 2.320 3.040 nonbonded pdb=" O SER F 121 " pdb=" OG SER F 121 " model vdw 2.320 3.040 nonbonded pdb=" O SER H 121 " pdb=" OG SER H 121 " model vdw 2.320 3.040 nonbonded pdb=" O SER B 121 " pdb=" OG SER B 121 " model vdw 2.320 3.040 ... (remaining 171257 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.010 0.067 23089 Z= 0.446 Angle : 1.160 8.683 31570 Z= 0.649 Chirality : 0.057 0.178 3520 Planarity : 0.007 0.068 4048 Dihedral : 16.070 69.241 7964 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 1.50 % Allowed : 14.50 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.98 (0.11), residues: 2871 helix: -4.07 (0.06), residues: 1749 sheet: None (None), residues: 0 loop : -3.54 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 178 TYR 0.033 0.004 TYR E 182 PHE 0.016 0.003 PHE F 253 TRP 0.015 0.002 TRP F 220 HIS 0.008 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.01032 (23067) covalent geometry : angle 1.15707 (31526) SS BOND : bond 0.00512 ( 22) SS BOND : angle 2.56729 ( 44) hydrogen bonds : bond 0.29159 ( 1307) hydrogen bonds : angle 10.19706 ( 3855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 320 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7632 (pp20) cc_final: 0.6948 (pp20) REVERT: A 277 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7544 (tt0) REVERT: B 262 GLU cc_start: 0.7462 (pp20) cc_final: 0.6827 (pp20) REVERT: B 277 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7344 (tt0) REVERT: D 277 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7378 (tt0) REVERT: D 293 LEU cc_start: 0.7867 (mt) cc_final: 0.7643 (mt) REVERT: E 76 ASN cc_start: 0.6340 (p0) cc_final: 0.6003 (p0) REVERT: E 212 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8371 (pp) REVERT: E 301 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8469 (ttpp) REVERT: F 76 ASN cc_start: 0.6366 (p0) cc_final: 0.6111 (p0) REVERT: F 277 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7566 (mm110) REVERT: G 76 ASN cc_start: 0.6387 (p0) cc_final: 0.6162 (p0) REVERT: G 277 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7286 (tt0) REVERT: H 76 ASN cc_start: 0.6463 (p0) cc_final: 0.6169 (p0) REVERT: H 277 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7334 (tt0) REVERT: I 71 ILE cc_start: 0.8816 (mt) cc_final: 0.8614 (mt) REVERT: I 76 ASN cc_start: 0.6460 (p0) cc_final: 0.5971 (p0) REVERT: I 301 LYS cc_start: 0.8953 (ttpp) cc_final: 0.8708 (ttpt) REVERT: J 76 ASN cc_start: 0.6577 (p0) cc_final: 0.6264 (p0) REVERT: J 277 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7336 (tt0) REVERT: K 277 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7471 (tt0) outliers start: 33 outliers final: 25 residues processed: 349 average time/residue: 0.1317 time to fit residues: 75.6326 Evaluate side-chains 280 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 195 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 246 ASN A 300 HIS B 246 ASN B 300 HIS C 246 ASN C 277 GLN C 300 HIS D 246 ASN D 300 HIS E 246 ASN E 300 HIS F 246 ASN F 300 HIS G 246 ASN G 300 HIS H 246 ASN H 300 HIS I 246 ASN I 300 HIS J 246 ASN J 300 HIS K 246 ASN K 300 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.247420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163035 restraints weight = 24930.097| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.55 r_work: 0.3381 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23089 Z= 0.206 Angle : 0.768 8.342 31570 Z= 0.407 Chirality : 0.042 0.129 3520 Planarity : 0.006 0.045 4048 Dihedral : 6.837 52.140 3231 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.68 % Allowed : 16.68 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.12 (0.14), residues: 2871 helix: -1.50 (0.10), residues: 1804 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 181 TYR 0.017 0.002 TYR J 182 PHE 0.015 0.002 PHE B 172 TRP 0.012 0.002 TRP B 220 HIS 0.007 0.001 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00480 (23067) covalent geometry : angle 0.76740 (31526) SS BOND : bond 0.00143 ( 22) SS BOND : angle 0.92425 ( 44) hydrogen bonds : bond 0.06922 ( 1307) hydrogen bonds : angle 5.21923 ( 3855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 302 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.8506 (t-90) cc_final: 0.7541 (t-90) REVERT: A 81 ASN cc_start: 0.8517 (m-40) cc_final: 0.7713 (t0) REVERT: A 200 PHE cc_start: 0.7608 (t80) cc_final: 0.7275 (t80) REVERT: A 262 GLU cc_start: 0.7921 (pp20) cc_final: 0.7080 (pp20) REVERT: A 266 ASN cc_start: 0.7335 (m-40) cc_final: 0.6727 (m110) REVERT: A 277 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6312 (tt0) REVERT: A 288 ARG cc_start: 0.7858 (mtp-110) cc_final: 0.7592 (mtp85) REVERT: B 81 ASN cc_start: 0.8468 (m-40) cc_final: 0.7860 (t0) REVERT: B 200 PHE cc_start: 0.7395 (t80) cc_final: 0.6975 (t80) REVERT: B 262 GLU cc_start: 0.7864 (pp20) cc_final: 0.7236 (pp20) REVERT: B 266 ASN cc_start: 0.7538 (m-40) cc_final: 0.7185 (m-40) REVERT: B 269 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8573 (m) REVERT: B 277 GLN cc_start: 0.7401 (mm-40) cc_final: 0.6241 (tt0) REVERT: C 81 ASN cc_start: 0.8635 (m-40) cc_final: 0.7861 (t0) REVERT: C 128 TYR cc_start: 0.6320 (p90) cc_final: 0.5809 (p90) REVERT: C 200 PHE cc_start: 0.7326 (t80) cc_final: 0.7009 (t80) REVERT: C 262 GLU cc_start: 0.8001 (pp20) cc_final: 0.7372 (pp20) REVERT: C 266 ASN cc_start: 0.7315 (m-40) cc_final: 0.6885 (m110) REVERT: D 81 ASN cc_start: 0.8551 (m-40) cc_final: 0.7766 (t0) REVERT: D 200 PHE cc_start: 0.7375 (t80) cc_final: 0.7070 (t80) REVERT: D 277 GLN cc_start: 0.7648 (mm-40) cc_final: 0.6507 (tt0) REVERT: D 284 VAL cc_start: 0.7280 (OUTLIER) cc_final: 0.6982 (m) REVERT: E 78 HIS cc_start: 0.8470 (t-90) cc_final: 0.7472 (t-90) REVERT: E 81 ASN cc_start: 0.8891 (m-40) cc_final: 0.8300 (t0) REVERT: E 212 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8126 (pp) REVERT: E 262 GLU cc_start: 0.7905 (pp20) cc_final: 0.7629 (pp20) REVERT: E 277 GLN cc_start: 0.7595 (mm110) cc_final: 0.6397 (tt0) REVERT: E 301 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8436 (ttpt) REVERT: F 78 HIS cc_start: 0.8222 (t-90) cc_final: 0.7379 (t-90) REVERT: F 81 ASN cc_start: 0.8521 (m-40) cc_final: 0.7606 (t0) REVERT: F 128 TYR cc_start: 0.6466 (p90) cc_final: 0.5908 (p90) REVERT: F 185 GLN cc_start: 0.6936 (tp40) cc_final: 0.6662 (tp40) REVERT: F 200 PHE cc_start: 0.7354 (t80) cc_final: 0.6938 (t80) REVERT: F 277 GLN cc_start: 0.7675 (mm-40) cc_final: 0.6282 (tt0) REVERT: G 78 HIS cc_start: 0.8297 (t-90) cc_final: 0.7395 (t-90) REVERT: G 81 ASN cc_start: 0.8657 (m-40) cc_final: 0.7555 (t0) REVERT: G 277 GLN cc_start: 0.7474 (mm-40) cc_final: 0.6207 (tt0) REVERT: H 78 HIS cc_start: 0.8399 (t-90) cc_final: 0.7574 (t-90) REVERT: H 81 ASN cc_start: 0.8555 (m-40) cc_final: 0.7736 (t0) REVERT: H 128 TYR cc_start: 0.6258 (p90) cc_final: 0.5851 (p90) REVERT: H 200 PHE cc_start: 0.7054 (t80) cc_final: 0.6830 (t80) REVERT: H 233 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7972 (ttm170) REVERT: H 262 GLU cc_start: 0.8018 (pp20) cc_final: 0.7730 (pp20) REVERT: H 277 GLN cc_start: 0.7508 (mm-40) cc_final: 0.6548 (tt0) REVERT: H 288 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7875 (mtp-110) REVERT: I 71 ILE cc_start: 0.7152 (mt) cc_final: 0.6946 (mt) REVERT: I 78 HIS cc_start: 0.8383 (t-90) cc_final: 0.7396 (t-90) REVERT: I 81 ASN cc_start: 0.8625 (m-40) cc_final: 0.7805 (t0) REVERT: I 262 GLU cc_start: 0.8239 (pp20) cc_final: 0.7415 (pp20) REVERT: I 266 ASN cc_start: 0.7656 (m-40) cc_final: 0.7264 (m-40) REVERT: I 277 GLN cc_start: 0.7767 (mm110) cc_final: 0.6353 (tt0) REVERT: I 301 LYS cc_start: 0.8944 (ttpp) cc_final: 0.8526 (ttpt) REVERT: J 81 ASN cc_start: 0.8712 (m-40) cc_final: 0.7827 (t0) REVERT: J 200 PHE cc_start: 0.7036 (t80) cc_final: 0.6742 (t80) REVERT: J 262 GLU cc_start: 0.7963 (pp20) cc_final: 0.7690 (pp20) REVERT: J 266 ASN cc_start: 0.7215 (m-40) cc_final: 0.6949 (m-40) REVERT: J 277 GLN cc_start: 0.7494 (mm-40) cc_final: 0.6446 (tt0) REVERT: J 284 VAL cc_start: 0.7081 (OUTLIER) cc_final: 0.6455 (m) REVERT: K 81 ASN cc_start: 0.8565 (m-40) cc_final: 0.8124 (t0) REVERT: K 200 PHE cc_start: 0.7388 (t80) cc_final: 0.7146 (t80) REVERT: K 277 GLN cc_start: 0.7716 (mm-40) cc_final: 0.6759 (tt0) outliers start: 81 outliers final: 45 residues processed: 366 average time/residue: 0.1286 time to fit residues: 77.5707 Evaluate side-chains 320 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 285 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 76 optimal weight: 0.0980 chunk 242 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS B 87 GLN B 152 HIS C 152 HIS E 87 GLN F 87 GLN G 87 GLN I 152 HIS K 87 GLN K 152 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.250396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166641 restraints weight = 24699.447| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.53 r_work: 0.3381 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23089 Z= 0.187 Angle : 0.707 8.000 31570 Z= 0.364 Chirality : 0.042 0.193 3520 Planarity : 0.005 0.044 4048 Dihedral : 5.990 48.118 3220 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.05 % Allowed : 15.77 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.16), residues: 2871 helix: -0.02 (0.12), residues: 1826 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 179 TYR 0.016 0.002 TYR H 285 PHE 0.012 0.001 PHE B 172 TRP 0.011 0.002 TRP F 189 HIS 0.005 0.001 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00438 (23067) covalent geometry : angle 0.70656 (31526) SS BOND : bond 0.00176 ( 22) SS BOND : angle 1.01331 ( 44) hydrogen bonds : bond 0.05843 ( 1307) hydrogen bonds : angle 4.64214 ( 3855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 286 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.8520 (t-90) cc_final: 0.7587 (t-90) REVERT: A 200 PHE cc_start: 0.7572 (t80) cc_final: 0.7243 (t80) REVERT: A 262 GLU cc_start: 0.8010 (pp20) cc_final: 0.7175 (pp20) REVERT: A 266 ASN cc_start: 0.7281 (m-40) cc_final: 0.6689 (m110) REVERT: A 277 GLN cc_start: 0.7383 (mm-40) cc_final: 0.6382 (tt0) REVERT: A 288 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.7419 (mtp85) REVERT: B 78 HIS cc_start: 0.8681 (t-90) cc_final: 0.7627 (t-90) REVERT: B 81 ASN cc_start: 0.8467 (m-40) cc_final: 0.7393 (t0) REVERT: B 200 PHE cc_start: 0.7207 (t80) cc_final: 0.6879 (t80) REVERT: B 262 GLU cc_start: 0.7860 (pp20) cc_final: 0.7218 (pp20) REVERT: B 266 ASN cc_start: 0.7456 (m-40) cc_final: 0.7128 (m-40) REVERT: B 269 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 277 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6363 (tt0) REVERT: C 78 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.7879 (t-90) REVERT: C 81 ASN cc_start: 0.8711 (m-40) cc_final: 0.7892 (t0) REVERT: C 157 LEU cc_start: 0.4351 (OUTLIER) cc_final: 0.4140 (pp) REVERT: C 200 PHE cc_start: 0.7328 (t80) cc_final: 0.7000 (t80) REVERT: C 262 GLU cc_start: 0.7978 (pp20) cc_final: 0.7270 (pp20) REVERT: C 266 ASN cc_start: 0.7282 (m-40) cc_final: 0.6774 (m-40) REVERT: D 78 HIS cc_start: 0.8418 (t-90) cc_final: 0.7920 (t-90) REVERT: D 81 ASN cc_start: 0.8543 (m-40) cc_final: 0.7894 (t0) REVERT: D 200 PHE cc_start: 0.7299 (t80) cc_final: 0.6978 (t80) REVERT: D 262 GLU cc_start: 0.8333 (pp20) cc_final: 0.8081 (pp20) REVERT: D 277 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6378 (tt0) REVERT: D 284 VAL cc_start: 0.6935 (OUTLIER) cc_final: 0.6577 (m) REVERT: E 76 ASN cc_start: 0.7344 (p0) cc_final: 0.7024 (p0) REVERT: E 78 HIS cc_start: 0.8554 (t-90) cc_final: 0.7183 (t-90) REVERT: E 102 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7912 (tp) REVERT: E 212 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8164 (pp) REVERT: E 262 GLU cc_start: 0.7892 (pp20) cc_final: 0.7483 (pp20) REVERT: E 277 GLN cc_start: 0.7488 (mm110) cc_final: 0.6442 (tt0) REVERT: E 301 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8414 (ttpt) REVERT: F 78 HIS cc_start: 0.8349 (t-90) cc_final: 0.7445 (t-90) REVERT: F 81 ASN cc_start: 0.8549 (m-40) cc_final: 0.7708 (t0) REVERT: F 200 PHE cc_start: 0.7298 (t80) cc_final: 0.6981 (t80) REVERT: F 277 GLN cc_start: 0.7657 (mm-40) cc_final: 0.6325 (tt0) REVERT: G 78 HIS cc_start: 0.8297 (t-90) cc_final: 0.7219 (t-90) REVERT: G 81 ASN cc_start: 0.8702 (m-40) cc_final: 0.7936 (t0) REVERT: G 277 GLN cc_start: 0.7527 (mm-40) cc_final: 0.6148 (tt0) REVERT: H 76 ASN cc_start: 0.7168 (p0) cc_final: 0.6662 (p0) REVERT: H 78 HIS cc_start: 0.8686 (t-90) cc_final: 0.7365 (t-90) REVERT: H 81 ASN cc_start: 0.8596 (m-40) cc_final: 0.7664 (t0) REVERT: H 128 TYR cc_start: 0.6560 (p90) cc_final: 0.6208 (p90) REVERT: H 200 PHE cc_start: 0.6974 (t80) cc_final: 0.6755 (t80) REVERT: H 262 GLU cc_start: 0.8051 (pp20) cc_final: 0.7743 (pp20) REVERT: H 277 GLN cc_start: 0.7476 (mm-40) cc_final: 0.6520 (tt0) REVERT: I 71 ILE cc_start: 0.7174 (mt) cc_final: 0.6965 (mt) REVERT: I 78 HIS cc_start: 0.8547 (t-90) cc_final: 0.7412 (t-90) REVERT: I 81 ASN cc_start: 0.8616 (m-40) cc_final: 0.7778 (t0) REVERT: I 277 GLN cc_start: 0.7720 (mm110) cc_final: 0.6263 (tt0) REVERT: I 301 LYS cc_start: 0.8860 (ttpp) cc_final: 0.8525 (ttpp) REVERT: J 78 HIS cc_start: 0.8747 (t-90) cc_final: 0.7818 (t-90) REVERT: J 81 ASN cc_start: 0.8720 (m-40) cc_final: 0.8066 (t0) REVERT: J 200 PHE cc_start: 0.7129 (t80) cc_final: 0.6711 (t80) REVERT: J 262 GLU cc_start: 0.8060 (pp20) cc_final: 0.7708 (pp20) REVERT: J 277 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6440 (tt0) REVERT: J 284 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6469 (m) REVERT: K 78 HIS cc_start: 0.8622 (t-90) cc_final: 0.7836 (t-90) REVERT: K 81 ASN cc_start: 0.8582 (m-40) cc_final: 0.8066 (t0) REVERT: K 200 PHE cc_start: 0.7071 (t80) cc_final: 0.6842 (t80) REVERT: K 277 GLN cc_start: 0.7805 (mm-40) cc_final: 0.6857 (tt0) outliers start: 111 outliers final: 70 residues processed: 377 average time/residue: 0.1280 time to fit residues: 80.9727 Evaluate side-chains 335 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 179 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 160 optimal weight: 0.3980 chunk 229 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 130 optimal weight: 0.0980 chunk 271 optimal weight: 30.0000 chunk 211 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 218 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 GLN H 266 ASN J 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.254599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185696 restraints weight = 24738.559| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.41 r_work: 0.3481 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23089 Z= 0.134 Angle : 0.653 9.303 31570 Z= 0.328 Chirality : 0.040 0.149 3520 Planarity : 0.005 0.047 4048 Dihedral : 5.486 45.160 3220 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.05 % Allowed : 17.91 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2871 helix: 0.73 (0.12), residues: 1848 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 181 TYR 0.019 0.001 TYR H 285 PHE 0.010 0.001 PHE D 250 TRP 0.010 0.001 TRP H 189 HIS 0.003 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00306 (23067) covalent geometry : angle 0.65258 (31526) SS BOND : bond 0.00196 ( 22) SS BOND : angle 0.93768 ( 44) hydrogen bonds : bond 0.04694 ( 1307) hydrogen bonds : angle 4.16075 ( 3855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 280 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.7971 (t-90) REVERT: A 200 PHE cc_start: 0.7802 (t80) cc_final: 0.7477 (t80) REVERT: A 262 GLU cc_start: 0.7900 (pp20) cc_final: 0.7176 (pp20) REVERT: A 266 ASN cc_start: 0.7688 (m-40) cc_final: 0.7236 (m-40) REVERT: A 269 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8127 (m) REVERT: A 277 GLN cc_start: 0.7595 (mm-40) cc_final: 0.6617 (tt0) REVERT: A 288 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7471 (mtp85) REVERT: B 78 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.7763 (t-90) REVERT: B 200 PHE cc_start: 0.7607 (t80) cc_final: 0.7316 (t80) REVERT: B 262 GLU cc_start: 0.7666 (pp20) cc_final: 0.6840 (pp20) REVERT: B 266 ASN cc_start: 0.7728 (m-40) cc_final: 0.7311 (m-40) REVERT: B 277 GLN cc_start: 0.7625 (mm-40) cc_final: 0.6706 (tt0) REVERT: C 78 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7287 (t-90) REVERT: C 200 PHE cc_start: 0.7709 (t80) cc_final: 0.7249 (t80) REVERT: C 262 GLU cc_start: 0.7796 (pp20) cc_final: 0.7167 (pp20) REVERT: C 266 ASN cc_start: 0.7626 (m-40) cc_final: 0.7052 (m-40) REVERT: D 81 ASN cc_start: 0.8549 (m-40) cc_final: 0.7983 (t0) REVERT: D 200 PHE cc_start: 0.7597 (t80) cc_final: 0.7292 (t80) REVERT: D 262 GLU cc_start: 0.8007 (pp20) cc_final: 0.7752 (pp20) REVERT: D 277 GLN cc_start: 0.7549 (mm-40) cc_final: 0.6647 (tt0) REVERT: D 284 VAL cc_start: 0.6866 (OUTLIER) cc_final: 0.6649 (m) REVERT: D 301 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8600 (ttmm) REVERT: E 76 ASN cc_start: 0.7517 (p0) cc_final: 0.7179 (p0) REVERT: E 78 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7463 (t-90) REVERT: E 204 CYS cc_start: 0.8137 (m) cc_final: 0.7237 (t) REVERT: E 212 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8160 (pp) REVERT: E 262 GLU cc_start: 0.7756 (pp20) cc_final: 0.7370 (pp20) REVERT: E 277 GLN cc_start: 0.7588 (mm110) cc_final: 0.6682 (tt0) REVERT: E 301 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8523 (ttpt) REVERT: F 78 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7501 (t-90) REVERT: F 200 PHE cc_start: 0.7448 (t80) cc_final: 0.7176 (t80) REVERT: F 277 GLN cc_start: 0.7719 (mm-40) cc_final: 0.6672 (tt0) REVERT: F 288 ARG cc_start: 0.7855 (mtp-110) cc_final: 0.7616 (mtm110) REVERT: G 78 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7340 (t-90) REVERT: G 81 ASN cc_start: 0.8605 (m-40) cc_final: 0.7839 (t0) REVERT: G 277 GLN cc_start: 0.7641 (mm-40) cc_final: 0.6572 (tt0) REVERT: H 78 HIS cc_start: 0.8400 (OUTLIER) cc_final: 0.7638 (t-90) REVERT: H 262 GLU cc_start: 0.8028 (pp20) cc_final: 0.7616 (pp20) REVERT: H 269 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8262 (m) REVERT: H 277 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6777 (tt0) REVERT: I 78 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.7674 (t-90) REVERT: I 81 ASN cc_start: 0.8505 (m-40) cc_final: 0.7723 (t0) REVERT: I 204 CYS cc_start: 0.8047 (m) cc_final: 0.7153 (t) REVERT: I 262 GLU cc_start: 0.8142 (pp20) cc_final: 0.7578 (pp20) REVERT: I 277 GLN cc_start: 0.7860 (mm110) cc_final: 0.6654 (tt0) REVERT: I 301 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8787 (tttm) REVERT: J 78 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7733 (t-90) REVERT: J 81 ASN cc_start: 0.8649 (m-40) cc_final: 0.8098 (t0) REVERT: J 200 PHE cc_start: 0.7367 (t80) cc_final: 0.6941 (t80) REVERT: J 262 GLU cc_start: 0.8047 (pp20) cc_final: 0.7786 (pp20) REVERT: J 269 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8110 (m) REVERT: J 270 GLU cc_start: 0.7021 (tt0) cc_final: 0.6662 (tt0) REVERT: J 277 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6602 (tt0) REVERT: J 284 VAL cc_start: 0.6383 (OUTLIER) cc_final: 0.6001 (m) REVERT: K 78 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.8058 (t-90) REVERT: K 81 ASN cc_start: 0.8748 (m-40) cc_final: 0.8208 (t0) REVERT: K 200 PHE cc_start: 0.7376 (t80) cc_final: 0.7015 (t80) REVERT: K 277 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7144 (tt0) outliers start: 89 outliers final: 53 residues processed: 342 average time/residue: 0.1285 time to fit residues: 72.3504 Evaluate side-chains 328 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 164 optimal weight: 0.0770 chunk 150 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 268 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 290 ASN J 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.254651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171650 restraints weight = 24438.628| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.86 r_work: 0.3536 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23089 Z= 0.128 Angle : 0.645 7.707 31570 Z= 0.319 Chirality : 0.040 0.137 3520 Planarity : 0.005 0.049 4048 Dihedral : 5.207 42.882 3220 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.68 % Allowed : 18.14 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2871 helix: 1.14 (0.12), residues: 1848 sheet: None (None), residues: 0 loop : -2.64 (0.21), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 181 TYR 0.016 0.001 TYR B 285 PHE 0.009 0.001 PHE D 250 TRP 0.010 0.001 TRP F 189 HIS 0.004 0.001 HIS G 45 Details of bonding type rmsd covalent geometry : bond 0.00292 (23067) covalent geometry : angle 0.64435 (31526) SS BOND : bond 0.00213 ( 22) SS BOND : angle 0.97245 ( 44) hydrogen bonds : bond 0.04422 ( 1307) hydrogen bonds : angle 3.94697 ( 3855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 274 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7725 (t-90) REVERT: A 200 PHE cc_start: 0.7244 (t80) cc_final: 0.6957 (t80) REVERT: A 262 GLU cc_start: 0.7772 (pp20) cc_final: 0.7094 (pp20) REVERT: A 266 ASN cc_start: 0.7215 (m-40) cc_final: 0.6784 (m-40) REVERT: A 269 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8064 (m) REVERT: A 277 GLN cc_start: 0.7168 (mm-40) cc_final: 0.5998 (tt0) REVERT: A 288 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7199 (mtp85) REVERT: B 78 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.7562 (t-90) REVERT: B 262 GLU cc_start: 0.7789 (pp20) cc_final: 0.7008 (pp20) REVERT: B 266 ASN cc_start: 0.7132 (m-40) cc_final: 0.6686 (m-40) REVERT: B 277 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6203 (tt0) REVERT: C 78 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7325 (t-90) REVERT: C 200 PHE cc_start: 0.7304 (t80) cc_final: 0.6886 (t80) REVERT: C 262 GLU cc_start: 0.8069 (pp20) cc_final: 0.7620 (pp20) REVERT: C 266 ASN cc_start: 0.7156 (m-40) cc_final: 0.6815 (m-40) REVERT: D 78 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.7643 (t-90) REVERT: D 200 PHE cc_start: 0.7118 (t80) cc_final: 0.6838 (t80) REVERT: D 262 GLU cc_start: 0.8162 (pp20) cc_final: 0.7906 (pp20) REVERT: D 270 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: D 277 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6124 (tt0) REVERT: E 76 ASN cc_start: 0.7364 (p0) cc_final: 0.7018 (p0) REVERT: E 78 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7285 (t-90) REVERT: E 82 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8945 (mt) REVERT: E 204 CYS cc_start: 0.7838 (m) cc_final: 0.7033 (t) REVERT: E 212 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7981 (pp) REVERT: E 262 GLU cc_start: 0.7769 (pp20) cc_final: 0.7337 (pp20) REVERT: E 277 GLN cc_start: 0.7274 (mm110) cc_final: 0.5939 (tt0) REVERT: E 301 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8251 (ttpt) REVERT: F 78 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7409 (t-90) REVERT: F 277 GLN cc_start: 0.7326 (mm-40) cc_final: 0.6033 (tt0) REVERT: F 288 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.7187 (mtm110) REVERT: G 78 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.7727 (t-90) REVERT: G 277 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6134 (tt0) REVERT: H 78 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: H 233 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7323 (mtp180) REVERT: H 269 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8185 (m) REVERT: H 277 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6217 (tt0) REVERT: I 78 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.7624 (t-90) REVERT: I 81 ASN cc_start: 0.8548 (m-40) cc_final: 0.7816 (t0) REVERT: I 204 CYS cc_start: 0.7671 (m) cc_final: 0.6912 (t) REVERT: I 277 GLN cc_start: 0.7555 (mm110) cc_final: 0.6125 (tt0) REVERT: I 301 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8484 (tttm) REVERT: J 78 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.7702 (t-90) REVERT: J 81 ASN cc_start: 0.8647 (m-40) cc_final: 0.8065 (t0) REVERT: J 200 PHE cc_start: 0.6866 (t80) cc_final: 0.6488 (t80) REVERT: J 236 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: J 262 GLU cc_start: 0.8027 (pp20) cc_final: 0.7798 (pp20) REVERT: J 269 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8139 (m) REVERT: J 270 GLU cc_start: 0.7242 (tt0) cc_final: 0.6843 (tt0) REVERT: J 277 GLN cc_start: 0.7105 (mm-40) cc_final: 0.6124 (tt0) REVERT: J 284 VAL cc_start: 0.6320 (OUTLIER) cc_final: 0.6006 (m) REVERT: K 78 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7885 (t-90) REVERT: K 200 PHE cc_start: 0.6967 (t80) cc_final: 0.6730 (t80) REVERT: K 277 GLN cc_start: 0.7575 (mm-40) cc_final: 0.6712 (tt0) REVERT: K 288 ARG cc_start: 0.7435 (mtp-110) cc_final: 0.7205 (mtp85) outliers start: 103 outliers final: 51 residues processed: 343 average time/residue: 0.1223 time to fit residues: 71.5480 Evaluate side-chains 328 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 228 ASP Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 234 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 228 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 290 ASN K 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.254682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.185020 restraints weight = 24718.004| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.47 r_work: 0.3695 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23089 Z= 0.147 Angle : 0.652 9.199 31570 Z= 0.324 Chirality : 0.041 0.133 3520 Planarity : 0.005 0.049 4048 Dihedral : 5.086 41.659 3219 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.05 % Allowed : 19.91 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2871 helix: 1.26 (0.12), residues: 1859 sheet: None (None), residues: 0 loop : -2.51 (0.22), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 181 TYR 0.012 0.001 TYR K 287 PHE 0.009 0.001 PHE G 69 TRP 0.010 0.001 TRP B 189 HIS 0.004 0.001 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00345 (23067) covalent geometry : angle 0.65125 (31526) SS BOND : bond 0.00233 ( 22) SS BOND : angle 1.26048 ( 44) hydrogen bonds : bond 0.04584 ( 1307) hydrogen bonds : angle 3.92466 ( 3855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 273 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7571 (p0) cc_final: 0.7247 (p0) REVERT: A 78 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.7908 (t-90) REVERT: A 181 ARG cc_start: 0.6136 (mmm-85) cc_final: 0.5503 (mmt180) REVERT: A 200 PHE cc_start: 0.7631 (t80) cc_final: 0.7283 (t80) REVERT: A 262 GLU cc_start: 0.7802 (pp20) cc_final: 0.7101 (pp20) REVERT: A 266 ASN cc_start: 0.7622 (m-40) cc_final: 0.7141 (m-40) REVERT: A 269 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8270 (m) REVERT: A 277 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6345 (tt0) REVERT: A 288 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7636 (mtp85) REVERT: B 78 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.7696 (t-90) REVERT: B 262 GLU cc_start: 0.7823 (pp20) cc_final: 0.7213 (pp20) REVERT: B 266 ASN cc_start: 0.7650 (m-40) cc_final: 0.7356 (m-40) REVERT: B 277 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6784 (tt0) REVERT: C 78 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7238 (t-90) REVERT: C 200 PHE cc_start: 0.7502 (t80) cc_final: 0.7122 (t80) REVERT: C 262 GLU cc_start: 0.8173 (pp20) cc_final: 0.7524 (pp20) REVERT: C 266 ASN cc_start: 0.7537 (m-40) cc_final: 0.7029 (m-40) REVERT: D 78 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7826 (t-90) REVERT: D 81 ASN cc_start: 0.8648 (m-40) cc_final: 0.8037 (t0) REVERT: D 200 PHE cc_start: 0.7549 (t80) cc_final: 0.7293 (t80) REVERT: D 270 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: D 277 GLN cc_start: 0.7490 (mm-40) cc_final: 0.6511 (tt0) REVERT: E 76 ASN cc_start: 0.7448 (p0) cc_final: 0.7017 (p0) REVERT: E 78 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.7708 (t-90) REVERT: E 204 CYS cc_start: 0.8137 (m) cc_final: 0.7221 (t) REVERT: E 212 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8209 (pp) REVERT: E 262 GLU cc_start: 0.7820 (pp20) cc_final: 0.7422 (pp20) REVERT: E 277 GLN cc_start: 0.7609 (mm110) cc_final: 0.6405 (tt0) REVERT: E 301 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8478 (ttpt) REVERT: F 78 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: F 277 GLN cc_start: 0.7598 (mm-40) cc_final: 0.6437 (tt0) REVERT: F 288 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7654 (mtm110) REVERT: G 78 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.7877 (t-90) REVERT: G 277 GLN cc_start: 0.7624 (mm-40) cc_final: 0.6493 (tt0) REVERT: H 78 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7785 (t-90) REVERT: H 107 LEU cc_start: 0.7278 (mt) cc_final: 0.7058 (mm) REVERT: H 262 GLU cc_start: 0.8104 (pp20) cc_final: 0.7826 (pp20) REVERT: H 269 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8295 (m) REVERT: H 277 GLN cc_start: 0.7579 (mm-40) cc_final: 0.6696 (tt0) REVERT: I 78 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.7779 (t-90) REVERT: I 81 ASN cc_start: 0.8672 (m-40) cc_final: 0.8004 (t0) REVERT: I 204 CYS cc_start: 0.7947 (m) cc_final: 0.7102 (t) REVERT: I 277 GLN cc_start: 0.7852 (mm110) cc_final: 0.6653 (tt0) REVERT: I 301 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8682 (tttm) REVERT: J 78 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7746 (t-90) REVERT: J 81 ASN cc_start: 0.8768 (m-40) cc_final: 0.8221 (t0) REVERT: J 200 PHE cc_start: 0.7399 (t80) cc_final: 0.6946 (t80) REVERT: J 236 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: J 262 GLU cc_start: 0.8092 (pp20) cc_final: 0.7884 (pp20) REVERT: J 269 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8114 (m) REVERT: J 270 GLU cc_start: 0.7262 (tt0) cc_final: 0.6894 (tt0) REVERT: J 277 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6518 (tt0) REVERT: J 284 VAL cc_start: 0.6463 (OUTLIER) cc_final: 0.6160 (m) REVERT: K 78 HIS cc_start: 0.8694 (OUTLIER) cc_final: 0.7928 (t-90) REVERT: K 81 ASN cc_start: 0.8844 (m-40) cc_final: 0.8245 (t0) REVERT: K 200 PHE cc_start: 0.7374 (t80) cc_final: 0.7155 (t80) REVERT: K 277 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7080 (tt0) outliers start: 89 outliers final: 55 residues processed: 330 average time/residue: 0.1279 time to fit residues: 70.0329 Evaluate side-chains 340 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 204 CYS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 256 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 236 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 176 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN E 45 HIS G 76 ASN G 290 ASN I 277 GLN J 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.252984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.174894 restraints weight = 24515.027| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.79 r_work: 0.3373 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23089 Z= 0.166 Angle : 0.669 9.191 31570 Z= 0.332 Chirality : 0.042 0.125 3520 Planarity : 0.005 0.049 4048 Dihedral : 5.070 39.806 3219 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.45 % Allowed : 20.55 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2871 helix: 1.31 (0.12), residues: 1859 sheet: None (None), residues: 0 loop : -2.40 (0.22), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 181 TYR 0.012 0.001 TYR H 287 PHE 0.010 0.001 PHE I 69 TRP 0.010 0.001 TRP K 189 HIS 0.005 0.001 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00391 (23067) covalent geometry : angle 0.66789 (31526) SS BOND : bond 0.00211 ( 22) SS BOND : angle 1.22804 ( 44) hydrogen bonds : bond 0.04788 ( 1307) hydrogen bonds : angle 3.94498 ( 3855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 271 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7819 (t-90) REVERT: A 181 ARG cc_start: 0.5811 (mmm-85) cc_final: 0.5282 (mmt180) REVERT: A 262 GLU cc_start: 0.7779 (pp20) cc_final: 0.7045 (pp20) REVERT: A 266 ASN cc_start: 0.7304 (m-40) cc_final: 0.6789 (m-40) REVERT: A 269 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8018 (m) REVERT: A 277 GLN cc_start: 0.7135 (mm-40) cc_final: 0.5935 (tt0) REVERT: A 288 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7330 (mtp85) REVERT: B 78 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7748 (t-90) REVERT: B 262 GLU cc_start: 0.7785 (pp20) cc_final: 0.7165 (pp20) REVERT: B 266 ASN cc_start: 0.7358 (m-40) cc_final: 0.7009 (m-40) REVERT: B 277 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6636 (tt0) REVERT: C 78 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.6917 (t-90) REVERT: C 81 ASN cc_start: 0.8417 (m-40) cc_final: 0.7579 (t0) REVERT: C 200 PHE cc_start: 0.7391 (t80) cc_final: 0.6796 (t80) REVERT: C 262 GLU cc_start: 0.8155 (pp20) cc_final: 0.7464 (pp20) REVERT: C 266 ASN cc_start: 0.7309 (m-40) cc_final: 0.6761 (m-40) REVERT: D 78 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7761 (t-90) REVERT: D 81 ASN cc_start: 0.8635 (m-40) cc_final: 0.8251 (t0) REVERT: D 200 PHE cc_start: 0.7309 (t80) cc_final: 0.7040 (t80) REVERT: D 270 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: D 277 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6212 (tt0) REVERT: E 78 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.7662 (t-90) REVERT: E 81 ASN cc_start: 0.8185 (m-40) cc_final: 0.7272 (t0) REVERT: E 212 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7834 (pp) REVERT: E 262 GLU cc_start: 0.7788 (pp20) cc_final: 0.7403 (pp20) REVERT: E 277 GLN cc_start: 0.7324 (mm110) cc_final: 0.5997 (tt0) REVERT: E 301 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8317 (ttpt) REVERT: F 78 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7520 (t-90) REVERT: F 81 ASN cc_start: 0.8619 (m-40) cc_final: 0.8064 (t0) REVERT: F 277 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6078 (tt0) REVERT: F 288 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7374 (mtm110) REVERT: G 78 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.7834 (t-90) REVERT: G 81 ASN cc_start: 0.8656 (m-40) cc_final: 0.7851 (t0) REVERT: G 277 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6261 (tt0) REVERT: H 78 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.7665 (t-90) REVERT: H 277 GLN cc_start: 0.7326 (mm-40) cc_final: 0.6320 (tt0) REVERT: I 78 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.7696 (t-90) REVERT: I 81 ASN cc_start: 0.8713 (m-40) cc_final: 0.8222 (t0) REVERT: I 262 GLU cc_start: 0.8260 (pp20) cc_final: 0.7794 (pp20) REVERT: I 277 GLN cc_start: 0.7577 (mm-40) cc_final: 0.6200 (tt0) REVERT: I 301 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8381 (tttm) REVERT: J 78 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7675 (t-90) REVERT: J 81 ASN cc_start: 0.8739 (m-40) cc_final: 0.8182 (t0) REVERT: J 200 PHE cc_start: 0.7143 (t80) cc_final: 0.6750 (t80) REVERT: J 236 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: J 269 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8168 (m) REVERT: J 270 GLU cc_start: 0.7193 (tt0) cc_final: 0.6812 (tt0) REVERT: J 277 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6330 (tt0) REVERT: J 284 VAL cc_start: 0.6744 (OUTLIER) cc_final: 0.6438 (m) REVERT: K 78 HIS cc_start: 0.8556 (OUTLIER) cc_final: 0.7777 (t-90) REVERT: K 81 ASN cc_start: 0.8665 (m-40) cc_final: 0.8160 (t0) REVERT: K 277 GLN cc_start: 0.7485 (mm-40) cc_final: 0.6803 (tt0) outliers start: 98 outliers final: 62 residues processed: 337 average time/residue: 0.1255 time to fit residues: 71.4543 Evaluate side-chains 339 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 204 CYS Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 54 optimal weight: 0.9980 chunk 168 optimal weight: 0.0980 chunk 243 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN C 88 HIS F 87 GLN G 76 ASN H 88 HIS H 290 ASN J 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.255543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.179841 restraints weight = 24540.686| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.05 r_work: 0.3369 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23089 Z= 0.136 Angle : 0.653 9.231 31570 Z= 0.321 Chirality : 0.040 0.112 3520 Planarity : 0.005 0.051 4048 Dihedral : 4.981 38.296 3219 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.18 % Allowed : 21.50 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2871 helix: 1.45 (0.12), residues: 1859 sheet: None (None), residues: 0 loop : -2.37 (0.22), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 179 TYR 0.018 0.001 TYR C 285 PHE 0.007 0.001 PHE I 69 TRP 0.011 0.001 TRP B 189 HIS 0.015 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00317 (23067) covalent geometry : angle 0.65151 (31526) SS BOND : bond 0.00217 ( 22) SS BOND : angle 1.16380 ( 44) hydrogen bonds : bond 0.04422 ( 1307) hydrogen bonds : angle 3.83356 ( 3855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 273 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7677 (p0) cc_final: 0.7463 (p0) REVERT: A 78 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.7884 (t-90) REVERT: A 181 ARG cc_start: 0.5785 (mmm-85) cc_final: 0.5226 (mmt180) REVERT: A 262 GLU cc_start: 0.7750 (pp20) cc_final: 0.7022 (pp20) REVERT: A 266 ASN cc_start: 0.7226 (m-40) cc_final: 0.6722 (m-40) REVERT: A 269 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8137 (m) REVERT: A 277 GLN cc_start: 0.7060 (mm-40) cc_final: 0.5917 (tt0) REVERT: A 288 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.7090 (mtp85) REVERT: B 78 HIS cc_start: 0.8556 (OUTLIER) cc_final: 0.7711 (t-90) REVERT: B 81 ASN cc_start: 0.8490 (m-40) cc_final: 0.7533 (t0) REVERT: B 201 LEU cc_start: 0.7367 (tp) cc_final: 0.7154 (tp) REVERT: B 262 GLU cc_start: 0.7710 (pp20) cc_final: 0.7103 (pp20) REVERT: B 266 ASN cc_start: 0.7279 (m-40) cc_final: 0.6962 (m-40) REVERT: B 277 GLN cc_start: 0.7461 (mm-40) cc_final: 0.6440 (tt0) REVERT: C 81 ASN cc_start: 0.8431 (m-40) cc_final: 0.7693 (t0) REVERT: C 200 PHE cc_start: 0.7383 (t80) cc_final: 0.6807 (t80) REVERT: C 262 GLU cc_start: 0.8114 (pp20) cc_final: 0.7436 (pp20) REVERT: C 266 ASN cc_start: 0.7217 (m-40) cc_final: 0.6674 (m-40) REVERT: D 78 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7763 (t-90) REVERT: D 81 ASN cc_start: 0.8596 (m-40) cc_final: 0.8188 (t0) REVERT: D 200 PHE cc_start: 0.7236 (t80) cc_final: 0.7003 (t80) REVERT: D 270 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: D 277 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6109 (tt0) REVERT: E 78 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.7831 (t-90) REVERT: E 204 CYS cc_start: 0.7959 (m) cc_final: 0.7096 (t) REVERT: E 212 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7776 (pp) REVERT: E 262 GLU cc_start: 0.7753 (pp20) cc_final: 0.7387 (pp20) REVERT: E 277 GLN cc_start: 0.7245 (mm110) cc_final: 0.5915 (tt0) REVERT: E 301 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8357 (ttpt) REVERT: F 78 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7472 (t-90) REVERT: F 81 ASN cc_start: 0.8622 (m-40) cc_final: 0.8062 (t0) REVERT: F 277 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6018 (tt0) REVERT: F 288 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7279 (mtm110) REVERT: G 78 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7842 (t-90) REVERT: G 277 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6121 (tt0) REVERT: H 78 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.7651 (t-90) REVERT: H 262 GLU cc_start: 0.8058 (pp20) cc_final: 0.7812 (pp20) REVERT: H 277 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6145 (tt0) REVERT: I 78 HIS cc_start: 0.8668 (OUTLIER) cc_final: 0.7827 (t-90) REVERT: I 81 ASN cc_start: 0.8626 (m-40) cc_final: 0.7938 (t0) REVERT: I 204 CYS cc_start: 0.7789 (m) cc_final: 0.7024 (t) REVERT: I 262 GLU cc_start: 0.8227 (pp20) cc_final: 0.7758 (pp20) REVERT: I 277 GLN cc_start: 0.7414 (mm-40) cc_final: 0.6109 (tt0) REVERT: I 301 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8335 (tttm) REVERT: J 78 HIS cc_start: 0.8515 (OUTLIER) cc_final: 0.7631 (t-90) REVERT: J 81 ASN cc_start: 0.8735 (m-40) cc_final: 0.8161 (t0) REVERT: J 200 PHE cc_start: 0.7106 (t80) cc_final: 0.6745 (t80) REVERT: J 236 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: J 269 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7993 (m) REVERT: J 270 GLU cc_start: 0.7150 (tt0) cc_final: 0.6757 (tt0) REVERT: J 277 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6172 (tt0) REVERT: J 284 VAL cc_start: 0.6389 (OUTLIER) cc_final: 0.6081 (m) REVERT: K 78 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.7787 (t-90) REVERT: K 81 ASN cc_start: 0.8639 (m-40) cc_final: 0.8106 (t0) REVERT: K 277 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6734 (tt0) outliers start: 92 outliers final: 60 residues processed: 335 average time/residue: 0.1226 time to fit residues: 69.8437 Evaluate side-chains 332 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 256 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 228 ASP Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 10 optimal weight: 20.0000 chunk 224 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 160 optimal weight: 0.3980 chunk 141 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN B 88 HIS C 88 HIS E 277 GLN G 76 ASN H 88 HIS H 290 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.253683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.168519 restraints weight = 24732.883| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.57 r_work: 0.3547 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23089 Z= 0.172 Angle : 0.670 8.956 31570 Z= 0.334 Chirality : 0.042 0.139 3520 Planarity : 0.005 0.050 4048 Dihedral : 5.021 37.616 3219 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.36 % Allowed : 21.77 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2871 helix: 1.36 (0.12), residues: 1881 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 181 TYR 0.014 0.001 TYR K 287 PHE 0.009 0.001 PHE J 69 TRP 0.009 0.001 TRP K 189 HIS 0.017 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00410 (23067) covalent geometry : angle 0.66917 (31526) SS BOND : bond 0.00216 ( 22) SS BOND : angle 1.17227 ( 44) hydrogen bonds : bond 0.04737 ( 1307) hydrogen bonds : angle 3.90672 ( 3855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 271 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7684 (p0) cc_final: 0.7436 (p0) REVERT: A 78 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.7897 (t-90) REVERT: A 181 ARG cc_start: 0.5817 (mmm-85) cc_final: 0.5278 (mmt180) REVERT: A 262 GLU cc_start: 0.7820 (pp20) cc_final: 0.7067 (pp20) REVERT: A 266 ASN cc_start: 0.7444 (m-40) cc_final: 0.6942 (m-40) REVERT: A 277 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6107 (tt0) REVERT: A 288 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7315 (mtp85) REVERT: B 78 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7709 (t-90) REVERT: B 81 ASN cc_start: 0.8563 (m-40) cc_final: 0.7641 (t0) REVERT: B 201 LEU cc_start: 0.7397 (tp) cc_final: 0.7177 (tp) REVERT: B 262 GLU cc_start: 0.7814 (pp20) cc_final: 0.7187 (pp20) REVERT: B 266 ASN cc_start: 0.7527 (m-40) cc_final: 0.7205 (m-40) REVERT: B 277 GLN cc_start: 0.7436 (mm-40) cc_final: 0.6709 (tt0) REVERT: C 78 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.6997 (t-90) REVERT: C 81 ASN cc_start: 0.8497 (m-40) cc_final: 0.7696 (t0) REVERT: C 200 PHE cc_start: 0.7462 (t80) cc_final: 0.6878 (t80) REVERT: C 262 GLU cc_start: 0.8175 (pp20) cc_final: 0.7489 (pp20) REVERT: C 266 ASN cc_start: 0.7391 (m-40) cc_final: 0.6843 (m-40) REVERT: D 78 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.7754 (t-90) REVERT: D 81 ASN cc_start: 0.8621 (m-40) cc_final: 0.8219 (t0) REVERT: D 200 PHE cc_start: 0.7340 (t80) cc_final: 0.7083 (t80) REVERT: D 270 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: D 277 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6352 (tt0) REVERT: E 78 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.7841 (t-90) REVERT: E 81 ASN cc_start: 0.8658 (m-40) cc_final: 0.7641 (t0) REVERT: E 82 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8989 (mt) REVERT: E 212 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7892 (pp) REVERT: E 262 GLU cc_start: 0.7782 (pp20) cc_final: 0.7414 (pp20) REVERT: E 277 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6155 (tt0) REVERT: E 301 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8435 (tttm) REVERT: F 78 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.7899 (t-90) REVERT: F 81 ASN cc_start: 0.8569 (m-40) cc_final: 0.7974 (t0) REVERT: F 277 GLN cc_start: 0.7443 (mm-40) cc_final: 0.6266 (tt0) REVERT: F 288 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7489 (mtm110) REVERT: G 78 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7842 (t-90) REVERT: G 81 ASN cc_start: 0.8643 (m-40) cc_final: 0.7837 (t0) REVERT: G 277 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6305 (tt0) REVERT: H 78 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.7650 (t-90) REVERT: H 277 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6357 (tt0) REVERT: I 78 HIS cc_start: 0.8627 (OUTLIER) cc_final: 0.7832 (t-90) REVERT: I 81 ASN cc_start: 0.8707 (m-40) cc_final: 0.8044 (t0) REVERT: I 262 GLU cc_start: 0.8269 (pp20) cc_final: 0.7798 (pp20) REVERT: I 277 GLN cc_start: 0.7535 (mm-40) cc_final: 0.6305 (tt0) REVERT: I 301 LYS cc_start: 0.8764 (ttpp) cc_final: 0.8458 (tttm) REVERT: J 78 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7633 (t-90) REVERT: J 81 ASN cc_start: 0.8748 (m-40) cc_final: 0.8181 (t0) REVERT: J 200 PHE cc_start: 0.7169 (t80) cc_final: 0.6788 (t80) REVERT: J 236 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: J 269 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8135 (m) REVERT: J 270 GLU cc_start: 0.7223 (tt0) cc_final: 0.6854 (tt0) REVERT: J 277 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6469 (tt0) REVERT: J 284 VAL cc_start: 0.6568 (OUTLIER) cc_final: 0.6261 (m) REVERT: K 78 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.7779 (t-90) REVERT: K 81 ASN cc_start: 0.8642 (m-40) cc_final: 0.8130 (t0) REVERT: K 277 GLN cc_start: 0.7538 (mm-40) cc_final: 0.6908 (tt0) outliers start: 96 outliers final: 68 residues processed: 336 average time/residue: 0.1200 time to fit residues: 68.0848 Evaluate side-chains 349 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 264 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 195 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 281 ILE Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 263 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 156 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 162 optimal weight: 0.3980 chunk 154 optimal weight: 0.0040 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN H 88 HIS H 290 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.258002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.180317 restraints weight = 24830.971| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.19 r_work: 0.3605 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23089 Z= 0.129 Angle : 0.645 8.700 31570 Z= 0.317 Chirality : 0.040 0.118 3520 Planarity : 0.005 0.052 4048 Dihedral : 4.844 37.455 3219 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.68 % Allowed : 22.64 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2871 helix: 1.61 (0.12), residues: 1881 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 178 TYR 0.019 0.001 TYR C 285 PHE 0.007 0.001 PHE D 250 TRP 0.012 0.001 TRP J 189 HIS 0.008 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00298 (23067) covalent geometry : angle 0.64386 (31526) SS BOND : bond 0.00227 ( 22) SS BOND : angle 1.16391 ( 44) hydrogen bonds : bond 0.04160 ( 1307) hydrogen bonds : angle 3.75459 ( 3855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5742 Ramachandran restraints generated. 2871 Oldfield, 0 Emsley, 2871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 279 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASN cc_start: 0.7701 (p0) cc_final: 0.7495 (p0) REVERT: A 78 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.7904 (t-90) REVERT: A 181 ARG cc_start: 0.5735 (mmm-85) cc_final: 0.5195 (mmt180) REVERT: A 236 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: A 262 GLU cc_start: 0.7838 (pp20) cc_final: 0.7130 (pp20) REVERT: A 266 ASN cc_start: 0.7395 (m-40) cc_final: 0.6902 (m-40) REVERT: A 269 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8049 (m) REVERT: A 277 GLN cc_start: 0.7191 (mm-40) cc_final: 0.6085 (tt0) REVERT: A 288 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.7219 (mtp85) REVERT: B 78 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.7664 (t-90) REVERT: B 81 ASN cc_start: 0.8592 (m-40) cc_final: 0.7662 (t0) REVERT: B 201 LEU cc_start: 0.7329 (tp) cc_final: 0.7114 (tp) REVERT: B 262 GLU cc_start: 0.7711 (pp20) cc_final: 0.7112 (pp20) REVERT: B 266 ASN cc_start: 0.7424 (m-40) cc_final: 0.7132 (m-40) REVERT: B 277 GLN cc_start: 0.7551 (mm-40) cc_final: 0.6517 (tt0) REVERT: C 66 LEU cc_start: 0.6622 (tp) cc_final: 0.6336 (mp) REVERT: C 78 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: C 81 ASN cc_start: 0.8397 (m-40) cc_final: 0.7655 (t0) REVERT: C 200 PHE cc_start: 0.7281 (t80) cc_final: 0.6734 (t80) REVERT: C 262 GLU cc_start: 0.8135 (pp20) cc_final: 0.7680 (pp20) REVERT: C 266 ASN cc_start: 0.7141 (m-40) cc_final: 0.6764 (m-40) REVERT: D 78 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.7666 (t-90) REVERT: D 81 ASN cc_start: 0.8588 (m-40) cc_final: 0.8191 (t0) REVERT: D 128 TYR cc_start: 0.6304 (p90) cc_final: 0.5638 (p90) REVERT: D 270 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: D 277 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6271 (tt0) REVERT: E 78 HIS cc_start: 0.8646 (OUTLIER) cc_final: 0.7972 (t-90) REVERT: E 81 ASN cc_start: 0.8084 (m-40) cc_final: 0.7203 (t0) REVERT: E 204 CYS cc_start: 0.8035 (m) cc_final: 0.7253 (t) REVERT: E 212 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7741 (pp) REVERT: E 277 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6104 (tt0) REVERT: E 301 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8417 (ttpt) REVERT: F 78 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.7847 (t-90) REVERT: F 81 ASN cc_start: 0.8522 (m-40) cc_final: 0.7982 (t0) REVERT: F 277 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6211 (tt0) REVERT: F 288 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.7415 (mtm110) REVERT: G 78 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7866 (t-90) REVERT: G 269 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7918 (m) REVERT: G 277 GLN cc_start: 0.7454 (mm-40) cc_final: 0.6353 (tt0) REVERT: H 78 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.7669 (t-90) REVERT: H 233 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7392 (mtp180) REVERT: H 277 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6373 (tt0) REVERT: I 78 HIS cc_start: 0.8662 (OUTLIER) cc_final: 0.7908 (t-90) REVERT: I 81 ASN cc_start: 0.8756 (m-40) cc_final: 0.8234 (t0) REVERT: I 204 CYS cc_start: 0.7720 (m) cc_final: 0.6984 (t) REVERT: I 262 GLU cc_start: 0.8238 (pp20) cc_final: 0.7792 (pp20) REVERT: I 277 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6275 (tt0) REVERT: I 301 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8431 (tttm) REVERT: J 78 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7672 (t-90) REVERT: J 81 ASN cc_start: 0.8752 (m-40) cc_final: 0.8180 (t0) REVERT: J 200 PHE cc_start: 0.7091 (t80) cc_final: 0.6800 (t80) REVERT: J 236 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: J 266 ASN cc_start: 0.7137 (m-40) cc_final: 0.6808 (m110) REVERT: J 269 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8186 (m) REVERT: J 270 GLU cc_start: 0.7042 (tt0) cc_final: 0.6714 (tt0) REVERT: J 277 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6333 (tt0) REVERT: J 284 VAL cc_start: 0.6306 (OUTLIER) cc_final: 0.6037 (m) REVERT: K 78 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.7798 (t-90) REVERT: K 81 ASN cc_start: 0.8662 (m-40) cc_final: 0.8142 (t0) REVERT: K 277 GLN cc_start: 0.7497 (mm-40) cc_final: 0.6867 (tt0) outliers start: 81 outliers final: 56 residues processed: 332 average time/residue: 0.1220 time to fit residues: 68.5678 Evaluate side-chains 344 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 269 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 78 HIS Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 46 CYS Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 46 CYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 78 HIS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 78 HIS Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain J residue 78 HIS Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 284 VAL Chi-restraints excluded: chain K residue 46 CYS Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 78 HIS Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 212 LEU Chi-restraints excluded: chain K residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 152 optimal weight: 0.8980 chunk 273 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 204 optimal weight: 0.0270 chunk 255 optimal weight: 0.3980 chunk 190 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 290 ASN C 87 GLN E 45 HIS E 76 ASN H 88 HIS J 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.259017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.190414 restraints weight = 24835.323| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.64 r_work: 0.3726 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23089 Z= 0.124 Angle : 0.643 8.468 31570 Z= 0.315 Chirality : 0.040 0.132 3520 Planarity : 0.005 0.052 4048 Dihedral : 4.777 36.975 3219 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.50 % Allowed : 23.05 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2871 helix: 1.68 (0.12), residues: 1903 sheet: None (None), residues: 0 loop : -2.56 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 179 TYR 0.018 0.001 TYR C 285 PHE 0.008 0.001 PHE D 200 TRP 0.012 0.001 TRP H 189 HIS 0.017 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00287 (23067) covalent geometry : angle 0.64195 (31526) SS BOND : bond 0.00254 ( 22) SS BOND : angle 1.10121 ( 44) hydrogen bonds : bond 0.04016 ( 1307) hydrogen bonds : angle 3.69738 ( 3855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5716.77 seconds wall clock time: 98 minutes 13.19 seconds (5893.19 seconds total)