Starting phenix.real_space_refine on Thu Mar 5 00:43:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lmt_0919/03_2026/6lmt_0919.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmt_0919/03_2026/6lmt_0919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lmt_0919/03_2026/6lmt_0919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmt_0919/03_2026/6lmt_0919.map" model { file = "/net/cci-nas-00/data/ceres_data/6lmt_0919/03_2026/6lmt_0919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmt_0919/03_2026/6lmt_0919.cif" } resolution = 2.66 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= 0.003 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 192 5.16 5 C 11688 2.51 5 N 2696 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 17552 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, D, E, F, G Time building chain proxies: 2.83, per 1000 atoms: 0.16 Number of scatterers: 17552 At special positions: 0 Unit cell: (123.67, 123.67, 100.43, 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 192 16.00 O 2976 8.00 N 2696 7.00 C 11688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 160 " distance=2.01 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.01 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 23 " distance=0.00 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 41 " distance=0.00 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.01 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 43 " distance=0.00 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.01 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 100 " distance=0.00 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 41 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 126 " distance=0.00 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 43 " distance=2.01 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 160 " distance=0.00 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 179 " distance=0.00 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 184 " distance=0.00 Simple disulfide: pdb=" SG CYS C 205 " - pdb=" SG CYS C 205 " distance=0.00 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 232 " distance=0.00 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 243 " distance=0.00 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.01 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.01 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.01 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.01 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.01 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: 1.55 Conformation dependent library (CDL) restraints added in 753.3 milliseconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 85.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 91 through 106 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE B 164 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B 250 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.681A pdb=" N LEU C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE C 164 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE C 239 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 91 through 106 Processing helix chain 'D' and resid 107 through 121 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE D 164 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE D 239 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN D 250 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 20 through 37 removed outlier: 3.947A pdb=" N GLY E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 91 through 106 Processing helix chain 'E' and resid 107 through 121 Processing helix chain 'E' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.622A pdb=" N PHE E 164 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 203 Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 209 through 259 removed outlier: 3.759A pdb=" N PHE E 239 " --> pdb=" O HIS E 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 14 Processing helix chain 'F' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 91 through 106 Processing helix chain 'F' and resid 107 through 121 Processing helix chain 'F' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE F 164 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 203 Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE F 239 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 14 Processing helix chain 'G' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 91 through 106 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 132 No H-bonds generated for 'chain 'G' and resid 130 through 132' Processing helix chain 'G' and resid 133 through 137 Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE G 164 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 203 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE G 239 " --> pdb=" O HIS G 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN G 250 " --> pdb=" O GLN G 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN G 257 " --> pdb=" O GLY G 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 14 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY H 24 " --> pdb=" O ASN H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 Processing helix chain 'H' and resid 91 through 106 Processing helix chain 'H' and resid 107 through 121 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'H' and resid 133 through 137 Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE H 164 " --> pdb=" O LYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 203 Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'H' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE H 239 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN H 250 " --> pdb=" O GLN H 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN H 257 " --> pdb=" O GLY H 253 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2847 1.32 - 1.45: 4847 1.45 - 1.57: 10082 1.57 - 1.70: 0 1.70 - 1.82: 296 Bond restraints: 18072 Sorted by residual: bond pdb=" CB MET G 98 " pdb=" CG MET G 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CB MET A 98 " pdb=" CG MET A 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CB MET E 98 " pdb=" CG MET E 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" CB MET C 98 " pdb=" CG MET C 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" CB MET B 98 " pdb=" CG MET B 98 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.31e+00 ... (remaining 18067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 23943 3.04 - 6.08: 545 6.08 - 9.11: 64 9.11 - 12.15: 8 12.15 - 15.19: 8 Bond angle restraints: 24568 Sorted by residual: angle pdb=" C GLN F 208 " pdb=" N ALA F 209 " pdb=" CA ALA F 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN B 208 " pdb=" N ALA B 209 " pdb=" CA ALA B 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN H 208 " pdb=" N ALA H 209 " pdb=" CA ALA H 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN D 208 " pdb=" N ALA D 209 " pdb=" CA ALA D 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN G 208 " pdb=" N ALA G 209 " pdb=" CA ALA G 209 " ideal model delta sigma weight residual 121.54 132.06 -10.52 1.91e+00 2.74e-01 3.03e+01 ... (remaining 24563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 11543 16.32 - 32.64: 554 32.64 - 48.95: 207 48.95 - 65.27: 48 65.27 - 81.59: 8 Dihedral angle restraints: 12360 sinusoidal: 6376 harmonic: 5984 Sorted by residual: dihedral pdb=" CA ALA E 209 " pdb=" C ALA E 209 " pdb=" N ALA E 210 " pdb=" CA ALA E 210 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ALA C 209 " pdb=" C ALA C 209 " pdb=" N ALA C 210 " pdb=" CA ALA C 210 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA G 209 " pdb=" C ALA G 209 " pdb=" N ALA G 210 " pdb=" CA ALA G 210 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 12357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1758 0.056 - 0.112: 779 0.112 - 0.168: 167 0.168 - 0.224: 8 0.224 - 0.280: 16 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CBE Y01 C 402 " pdb=" CAP Y01 C 402 " pdb=" CBB Y01 C 402 " pdb=" CBI Y01 C 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CBE Y01 E 402 " pdb=" CAP Y01 E 402 " pdb=" CBB Y01 E 402 " pdb=" CBI Y01 E 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CBE Y01 G 402 " pdb=" CAP Y01 G 402 " pdb=" CBB Y01 G 402 " pdb=" CBI Y01 G 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2725 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 137 " 0.027 2.00e-02 2.50e+03 2.38e-02 9.95e+00 pdb=" CG PHE C 137 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 137 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 137 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 137 " -0.027 2.00e-02 2.50e+03 2.38e-02 9.92e+00 pdb=" CG PHE G 137 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE G 137 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE G 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 137 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE G 137 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 137 " -0.027 2.00e-02 2.50e+03 2.38e-02 9.92e+00 pdb=" CG PHE A 137 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 137 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 137 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 137 " -0.005 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 65 2.59 - 3.17: 13770 3.17 - 3.74: 26651 3.74 - 4.32: 38671 4.32 - 4.90: 63379 Nonbonded interactions: 142536 Sorted by model distance: nonbonded pdb=" SG CYS H 43 " pdb=" SG CYS H 160 " model vdw 2.010 3.760 nonbonded pdb=" SG CYS H 41 " pdb=" SG CYS H 126 " model vdw 2.039 3.760 nonbonded pdb=" O ASN F 72 " pdb=" NH2 ARG F 225 " model vdw 2.409 3.120 nonbonded pdb=" O ASN H 72 " pdb=" NH2 ARG H 225 " model vdw 2.409 3.120 nonbonded pdb=" O ASN D 72 " pdb=" NH2 ARG D 225 " model vdw 2.409 3.120 ... (remaining 142531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 403) selection = (chain 'B' and resid 7 through 403) selection = (chain 'C' and resid 7 through 403) selection = (chain 'D' and resid 7 through 403) selection = (chain 'E' and resid 7 through 403) selection = (chain 'F' and resid 7 through 403) selection = (chain 'G' and resid 7 through 403) selection = chain 'H' } 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.940 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.125 18086 Z= 0.483 Angle : 1.141 15.192 24607 Z= 0.578 Chirality : 0.063 0.280 2728 Planarity : 0.008 0.057 2904 Dihedral : 11.689 81.587 8408 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -4.48 (0.12), residues: 2016 helix: -2.86 (0.08), residues: 1464 sheet: None (None), residues: 0 loop : -2.61 (0.20), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 225 TYR 0.038 0.006 TYR G 47 PHE 0.055 0.005 PHE C 137 TRP 0.031 0.006 TRP A 62 HIS 0.012 0.003 HIS G 219 Details of bonding type rmsd covalent geometry : bond 0.01224 (18072) covalent geometry : angle 1.13751 (24568) SS BOND : bond 0.01603 ( 14) SS BOND : angle 2.62644 ( 39) hydrogen bonds : bond 0.22465 ( 1224) hydrogen bonds : angle 8.03212 ( 3600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.497 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 80 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6952 (tp30) REVERT: A 148 GLU cc_start: 0.6668 (tp30) cc_final: 0.6332 (tm-30) REVERT: A 157 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6402 (mtp85) REVERT: A 168 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 234 GLU cc_start: 0.7501 (pt0) cc_final: 0.6971 (tp30) REVERT: B 80 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6982 (tp30) REVERT: B 96 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6769 (ttm110) REVERT: B 148 GLU cc_start: 0.6476 (tp30) cc_final: 0.6196 (tm-30) REVERT: B 157 ARG cc_start: 0.6819 (mtm-85) cc_final: 0.6468 (mtt180) REVERT: B 168 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 216 TYR cc_start: 0.7787 (t80) cc_final: 0.7442 (t80) REVERT: B 234 GLU cc_start: 0.7410 (pt0) cc_final: 0.6855 (tp30) REVERT: C 80 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6903 (tp30) REVERT: C 96 ARG cc_start: 0.7010 (mtm-85) cc_final: 0.6700 (ttm110) REVERT: C 148 GLU cc_start: 0.6599 (tp30) cc_final: 0.6275 (tm-30) REVERT: C 157 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.6350 (mtp85) REVERT: C 234 GLU cc_start: 0.7498 (pt0) cc_final: 0.6978 (tp30) REVERT: D 80 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6981 (tp30) REVERT: D 96 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6769 (ttm110) REVERT: D 148 GLU cc_start: 0.6476 (tp30) cc_final: 0.6198 (tm-30) REVERT: D 157 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6471 (mtt180) REVERT: D 168 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7114 (tm-30) REVERT: D 216 TYR cc_start: 0.7793 (t80) cc_final: 0.7505 (t80) REVERT: D 234 GLU cc_start: 0.7411 (pt0) cc_final: 0.6857 (tp30) REVERT: E 80 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6893 (tp30) REVERT: E 148 GLU cc_start: 0.6567 (tp30) cc_final: 0.6265 (tm-30) REVERT: E 157 ARG cc_start: 0.6780 (mtm-85) cc_final: 0.6362 (mtp85) REVERT: E 168 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7267 (tm-30) REVERT: E 234 GLU cc_start: 0.7489 (pt0) cc_final: 0.6983 (tp30) REVERT: F 80 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6983 (tp30) REVERT: F 96 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6772 (ttm110) REVERT: F 148 GLU cc_start: 0.6476 (tp30) cc_final: 0.6199 (tm-30) REVERT: F 157 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6472 (mtt180) REVERT: F 168 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7111 (tm-30) REVERT: F 216 TYR cc_start: 0.7795 (t80) cc_final: 0.7505 (t80) REVERT: F 234 GLU cc_start: 0.7412 (pt0) cc_final: 0.6858 (tp30) REVERT: G 80 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6951 (tp30) REVERT: G 148 GLU cc_start: 0.6669 (tp30) cc_final: 0.6333 (tm-30) REVERT: G 157 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6400 (mtp85) REVERT: G 168 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7242 (tm-30) REVERT: G 234 GLU cc_start: 0.7501 (pt0) cc_final: 0.6972 (tp30) REVERT: H 80 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6981 (tp30) REVERT: H 96 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6770 (ttm110) REVERT: H 148 GLU cc_start: 0.6477 (tp30) cc_final: 0.6199 (tm-30) REVERT: H 157 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6473 (mtt180) REVERT: H 168 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7115 (tm-30) REVERT: H 216 TYR cc_start: 0.7786 (t80) cc_final: 0.7503 (t80) REVERT: H 234 GLU cc_start: 0.7413 (pt0) cc_final: 0.6857 (tp30) REVERT: H 241 LYS cc_start: 0.6237 (ttpt) cc_final: 0.6032 (mtmt) outliers start: 0 outliers final: 2 residues processed: 413 average time/residue: 0.8697 time to fit residues: 386.9463 Evaluate side-chains 324 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain E residue 162 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0050 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 235 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 HIS ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 235 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 HIS ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 235 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 HIS ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 235 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.192287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119226 restraints weight = 17580.001| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.86 r_work: 0.3049 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18086 Z= 0.167 Angle : 0.729 14.643 24607 Z= 0.355 Chirality : 0.042 0.280 2728 Planarity : 0.006 0.047 2904 Dihedral : 9.921 57.358 4468 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 8.87 % Favored : 89.17 % 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: -0.22 (0.17), residues: 2016 helix: 0.32 (0.12), residues: 1512 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.016 0.002 TYR B 216 PHE 0.015 0.002 PHE D 137 TRP 0.023 0.003 TRP C 217 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00366 (18072) covalent geometry : angle 0.72880 (24568) SS BOND : bond 0.00487 ( 14) SS BOND : angle 0.97668 ( 39) hydrogen bonds : bond 0.06501 ( 1224) hydrogen bonds : angle 4.52630 ( 3600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 327 time to evaluate : 0.594 Fit side-chains REVERT: A 228 PHE cc_start: 0.7606 (t80) cc_final: 0.7019 (t80) REVERT: A 241 LYS cc_start: 0.7098 (tptp) cc_final: 0.6574 (mtmm) REVERT: B 96 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7274 (ttm110) REVERT: B 105 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7838 (mtp-110) REVERT: B 241 LYS cc_start: 0.6936 (tptp) cc_final: 0.6346 (mtmt) REVERT: C 7 MET cc_start: 0.6342 (mtp) cc_final: 0.6112 (mtp) REVERT: C 228 PHE cc_start: 0.7613 (t80) cc_final: 0.7025 (t80) REVERT: C 237 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6311 (ttmt) REVERT: C 241 LYS cc_start: 0.7034 (tptp) cc_final: 0.6579 (mtmm) REVERT: D 96 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7271 (ttm110) REVERT: D 105 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7847 (mtp-110) REVERT: D 241 LYS cc_start: 0.6930 (tptp) cc_final: 0.6353 (mtmt) REVERT: E 228 PHE cc_start: 0.7637 (t80) cc_final: 0.7049 (t80) REVERT: E 241 LYS cc_start: 0.6992 (tptp) cc_final: 0.6556 (mtmm) REVERT: F 96 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7276 (ttm110) REVERT: F 105 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7859 (mtp-110) REVERT: F 228 PHE cc_start: 0.7462 (t80) cc_final: 0.7143 (t80) REVERT: F 241 LYS cc_start: 0.6888 (tptp) cc_final: 0.6305 (mtmt) REVERT: G 228 PHE cc_start: 0.7599 (t80) cc_final: 0.7012 (t80) REVERT: G 241 LYS cc_start: 0.7090 (tptp) cc_final: 0.6565 (mtmm) REVERT: H 96 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7280 (ttm110) REVERT: H 105 ARG cc_start: 0.8083 (mtm110) cc_final: 0.7843 (mtp-110) REVERT: H 228 PHE cc_start: 0.7453 (t80) cc_final: 0.7141 (t80) outliers start: 35 outliers final: 14 residues processed: 339 average time/residue: 0.7749 time to fit residues: 286.0406 Evaluate side-chains 294 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 279 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.190134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114851 restraints weight = 17689.294| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.19 r_work: 0.2996 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18086 Z= 0.190 Angle : 0.685 7.377 24607 Z= 0.335 Chirality : 0.044 0.253 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.865 55.264 4464 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.29 % Allowed : 10.55 % Favored : 86.16 % 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: 1.10 (0.18), residues: 2016 helix: 1.35 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.015 0.003 TYR B 34 PHE 0.022 0.002 PHE B 137 TRP 0.015 0.003 TRP C 217 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00449 (18072) covalent geometry : angle 0.68443 (24568) SS BOND : bond 0.00620 ( 14) SS BOND : angle 1.16434 ( 39) hydrogen bonds : bond 0.06059 ( 1224) hydrogen bonds : angle 4.33446 ( 3600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 282 time to evaluate : 0.560 Fit side-chains REVERT: A 228 PHE cc_start: 0.7470 (t80) cc_final: 0.6910 (t80) REVERT: A 237 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.6141 (ttmt) REVERT: A 241 LYS cc_start: 0.7050 (tptp) cc_final: 0.6487 (mtmm) REVERT: B 7 MET cc_start: 0.6268 (mtp) cc_final: 0.6019 (mtp) REVERT: B 105 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7938 (mtp-110) REVERT: B 241 LYS cc_start: 0.7029 (tptp) cc_final: 0.6376 (mtmm) REVERT: C 38 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: C 228 PHE cc_start: 0.7512 (t80) cc_final: 0.6956 (t80) REVERT: C 237 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6168 (ttmt) REVERT: C 241 LYS cc_start: 0.7035 (tptp) cc_final: 0.6481 (mtmm) REVERT: D 7 MET cc_start: 0.6297 (mtp) cc_final: 0.6041 (mtp) REVERT: D 105 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7942 (mtp-110) REVERT: D 241 LYS cc_start: 0.7007 (tptp) cc_final: 0.6370 (mtmm) REVERT: E 38 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: E 83 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6327 (ptm160) REVERT: E 228 PHE cc_start: 0.7531 (t80) cc_final: 0.6930 (t80) REVERT: E 237 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6194 (ttmt) REVERT: E 241 LYS cc_start: 0.7042 (tptp) cc_final: 0.6492 (mtmm) REVERT: F 105 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7929 (mtp-110) REVERT: F 241 LYS cc_start: 0.7022 (tptp) cc_final: 0.6365 (mtmm) REVERT: G 228 PHE cc_start: 0.7500 (t80) cc_final: 0.6911 (t80) REVERT: G 237 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6145 (ttmt) REVERT: G 241 LYS cc_start: 0.7054 (tptp) cc_final: 0.6489 (mtmm) REVERT: H 7 MET cc_start: 0.6243 (mtp) cc_final: 0.5995 (mtp) REVERT: H 105 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7933 (mtp-110) REVERT: H 228 PHE cc_start: 0.7456 (t80) cc_final: 0.7104 (t80) outliers start: 59 outliers final: 26 residues processed: 295 average time/residue: 0.7509 time to fit residues: 241.8733 Evaluate side-chains 310 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 91 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 147 optimal weight: 0.0010 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN E 219 HIS ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.192903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118713 restraints weight = 17753.085| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.18 r_work: 0.3047 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18086 Z= 0.138 Angle : 0.613 6.997 24607 Z= 0.302 Chirality : 0.040 0.237 2728 Planarity : 0.005 0.046 2904 Dihedral : 9.157 54.294 4464 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.79 % Allowed : 13.00 % Favored : 84.21 % 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: 1.88 (0.19), residues: 2016 helix: 1.95 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.92 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.012 0.002 TYR B 97 PHE 0.011 0.001 PHE B 137 TRP 0.014 0.002 TRP E 217 HIS 0.003 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00303 (18072) covalent geometry : angle 0.61308 (24568) SS BOND : bond 0.00389 ( 14) SS BOND : angle 0.83284 ( 39) hydrogen bonds : bond 0.05150 ( 1224) hydrogen bonds : angle 4.08672 ( 3600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 292 time to evaluate : 0.587 Fit side-chains REVERT: A 7 MET cc_start: 0.6095 (mtp) cc_final: 0.5444 (mpp) REVERT: A 38 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: A 227 MET cc_start: 0.7449 (mtm) cc_final: 0.7223 (mtm) REVERT: A 228 PHE cc_start: 0.7344 (t80) cc_final: 0.6755 (t80) REVERT: A 237 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.5999 (ttmt) REVERT: A 241 LYS cc_start: 0.7058 (tptp) cc_final: 0.6548 (mttp) REVERT: B 96 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7250 (ttm110) REVERT: B 215 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7515 (ttmm) REVERT: B 219 HIS cc_start: 0.7628 (m-70) cc_final: 0.7391 (m170) REVERT: B 231 THR cc_start: 0.8081 (m) cc_final: 0.7800 (t) REVERT: B 241 LYS cc_start: 0.7021 (tptp) cc_final: 0.6366 (mtmm) REVERT: C 228 PHE cc_start: 0.7463 (t80) cc_final: 0.6933 (t80) REVERT: C 237 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.5999 (ttmt) REVERT: C 241 LYS cc_start: 0.6999 (tptp) cc_final: 0.6542 (mtmm) REVERT: D 96 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7254 (ttm110) REVERT: D 219 HIS cc_start: 0.7670 (m-70) cc_final: 0.7465 (m170) REVERT: D 241 LYS cc_start: 0.7022 (tptp) cc_final: 0.6369 (mtmt) REVERT: E 7 MET cc_start: 0.6106 (mtp) cc_final: 0.5451 (mpp) REVERT: E 237 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5985 (ttmt) REVERT: E 241 LYS cc_start: 0.7002 (tptp) cc_final: 0.6532 (mtmm) REVERT: F 7 MET cc_start: 0.6287 (mtp) cc_final: 0.5736 (mpp) REVERT: F 96 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7267 (ttm110) REVERT: F 219 HIS cc_start: 0.7647 (m-70) cc_final: 0.7446 (m170) REVERT: F 241 LYS cc_start: 0.7005 (tptp) cc_final: 0.6335 (mtmm) REVERT: G 7 MET cc_start: 0.6066 (mtp) cc_final: 0.5418 (mpp) REVERT: G 228 PHE cc_start: 0.7461 (t80) cc_final: 0.6927 (t80) REVERT: G 237 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6000 (ttmt) REVERT: G 241 LYS cc_start: 0.7042 (tptp) cc_final: 0.6533 (mttp) REVERT: H 96 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7272 (ttm110) REVERT: H 157 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8184 (mtt180) REVERT: H 219 HIS cc_start: 0.7636 (m-70) cc_final: 0.7417 (m170) REVERT: H 228 PHE cc_start: 0.7379 (t80) cc_final: 0.7072 (t80) REVERT: H 231 THR cc_start: 0.8099 (m) cc_final: 0.7830 (t) outliers start: 50 outliers final: 25 residues processed: 320 average time/residue: 0.7610 time to fit residues: 265.5361 Evaluate side-chains 306 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117829 restraints weight = 17620.718| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.83 r_work: 0.3029 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18086 Z= 0.159 Angle : 0.650 7.851 24607 Z= 0.315 Chirality : 0.041 0.236 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.233 54.729 4464 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.73 % Allowed : 14.29 % Favored : 82.98 % 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: 1.90 (0.19), residues: 2016 helix: 1.93 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.81 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.013 0.002 TYR F 34 PHE 0.025 0.001 PHE D 211 TRP 0.024 0.003 TRP E 217 HIS 0.004 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00377 (18072) covalent geometry : angle 0.64891 (24568) SS BOND : bond 0.00548 ( 14) SS BOND : angle 0.96535 ( 39) hydrogen bonds : bond 0.05247 ( 1224) hydrogen bonds : angle 4.08676 ( 3600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 293 time to evaluate : 0.665 Fit side-chains REVERT: A 7 MET cc_start: 0.6061 (mtp) cc_final: 0.5475 (mpp) REVERT: A 38 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: A 228 PHE cc_start: 0.7368 (t80) cc_final: 0.6726 (t80) REVERT: A 237 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6042 (ttmt) REVERT: A 241 LYS cc_start: 0.7074 (tptp) cc_final: 0.6491 (mtmm) REVERT: B 7 MET cc_start: 0.6532 (mtp) cc_final: 0.6188 (mpp) REVERT: B 215 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7471 (ttmm) REVERT: B 219 HIS cc_start: 0.7675 (m-70) cc_final: 0.7467 (m170) REVERT: B 241 LYS cc_start: 0.7042 (tptp) cc_final: 0.6335 (mtmt) REVERT: C 38 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: C 237 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6068 (ttmt) REVERT: C 241 LYS cc_start: 0.7061 (tptp) cc_final: 0.6534 (mtmm) REVERT: D 7 MET cc_start: 0.6500 (mtp) cc_final: 0.6146 (mpp) REVERT: D 215 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7616 (mtpp) REVERT: D 219 HIS cc_start: 0.7733 (m-70) cc_final: 0.7508 (m170) REVERT: D 241 LYS cc_start: 0.7034 (tptp) cc_final: 0.6391 (mtmm) REVERT: E 7 MET cc_start: 0.6050 (mtp) cc_final: 0.5467 (mpp) REVERT: E 38 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: E 237 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6082 (ttmt) REVERT: E 241 LYS cc_start: 0.7034 (tptp) cc_final: 0.6541 (mtmm) REVERT: F 7 MET cc_start: 0.6378 (mtp) cc_final: 0.5797 (mpp) REVERT: F 215 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7618 (mtpp) REVERT: F 241 LYS cc_start: 0.7021 (tptp) cc_final: 0.6316 (mtmt) REVERT: G 7 MET cc_start: 0.6030 (mtp) cc_final: 0.5446 (mpp) REVERT: G 38 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: G 237 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6073 (ttmt) REVERT: G 241 LYS cc_start: 0.7068 (tptp) cc_final: 0.6535 (mttp) REVERT: H 7 MET cc_start: 0.6540 (mtp) cc_final: 0.6196 (mpp) REVERT: H 161 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: H 219 HIS cc_start: 0.7650 (m-70) cc_final: 0.7436 (m170) REVERT: H 228 PHE cc_start: 0.7426 (t80) cc_final: 0.7162 (t80) REVERT: H 231 THR cc_start: 0.8109 (m) cc_final: 0.7811 (t) outliers start: 49 outliers final: 28 residues processed: 310 average time/residue: 0.7484 time to fit residues: 253.3846 Evaluate side-chains 327 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 161 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.191036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117165 restraints weight = 17661.641| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.84 r_work: 0.3025 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18086 Z= 0.162 Angle : 0.650 6.977 24607 Z= 0.317 Chirality : 0.041 0.235 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.192 54.591 4464 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.12 % Allowed : 14.29 % Favored : 83.59 % 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: 1.96 (0.18), residues: 2016 helix: 1.97 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.76 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.013 0.002 TYR D 34 PHE 0.017 0.001 PHE B 211 TRP 0.029 0.003 TRP C 217 HIS 0.003 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00390 (18072) covalent geometry : angle 0.64959 (24568) SS BOND : bond 0.00561 ( 14) SS BOND : angle 0.97304 ( 39) hydrogen bonds : bond 0.05207 ( 1224) hydrogen bonds : angle 4.06310 ( 3600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.577 Fit side-chains REVERT: A 38 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: A 228 PHE cc_start: 0.7338 (t80) cc_final: 0.6766 (t80) REVERT: A 237 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.5981 (ttmt) REVERT: A 241 LYS cc_start: 0.7062 (tptp) cc_final: 0.6514 (mtmm) REVERT: B 7 MET cc_start: 0.6399 (mtp) cc_final: 0.5689 (mpp) REVERT: B 219 HIS cc_start: 0.7721 (m-70) cc_final: 0.7520 (m170) REVERT: B 241 LYS cc_start: 0.6949 (tptp) cc_final: 0.6162 (mtmt) REVERT: C 7 MET cc_start: 0.6111 (mtp) cc_final: 0.5457 (mpp) REVERT: C 38 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: C 215 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7655 (mtpp) REVERT: C 228 PHE cc_start: 0.7326 (t80) cc_final: 0.6734 (t80) REVERT: C 237 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6053 (ttmt) REVERT: C 241 LYS cc_start: 0.7054 (tptp) cc_final: 0.6403 (mtmt) REVERT: D 7 MET cc_start: 0.6359 (mtp) cc_final: 0.5620 (mpp) REVERT: D 215 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7517 (mtpp) REVERT: D 219 HIS cc_start: 0.7710 (m-70) cc_final: 0.7495 (m170) REVERT: D 241 LYS cc_start: 0.7031 (tptp) cc_final: 0.6291 (mttt) REVERT: E 38 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: E 223 ILE cc_start: 0.7783 (mm) cc_final: 0.7563 (mp) REVERT: E 227 MET cc_start: 0.7459 (mtp) cc_final: 0.7198 (mtp) REVERT: E 237 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6016 (ttmt) REVERT: E 241 LYS cc_start: 0.7005 (tptp) cc_final: 0.6450 (mtmm) REVERT: F 7 MET cc_start: 0.6373 (mtp) cc_final: 0.5773 (mpp) REVERT: F 215 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7580 (mtpp) REVERT: F 219 HIS cc_start: 0.7696 (m-70) cc_final: 0.7474 (m90) REVERT: F 241 LYS cc_start: 0.6919 (tptp) cc_final: 0.6147 (mtmt) REVERT: G 38 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: G 237 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.5985 (ttmt) REVERT: G 241 LYS cc_start: 0.7043 (tptp) cc_final: 0.6511 (mtmm) REVERT: H 7 MET cc_start: 0.6400 (mtp) cc_final: 0.5691 (mpp) REVERT: H 161 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8409 (mttp) REVERT: H 231 THR cc_start: 0.8122 (m) cc_final: 0.7820 (t) outliers start: 38 outliers final: 25 residues processed: 306 average time/residue: 0.7494 time to fit residues: 249.8602 Evaluate side-chains 310 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 161 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 137 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.192142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126495 restraints weight = 17523.200| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.28 r_work: 0.3059 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18086 Z= 0.146 Angle : 0.638 9.361 24607 Z= 0.309 Chirality : 0.040 0.227 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.959 54.624 4464 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.46 % Allowed : 14.62 % Favored : 82.92 % 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: 2.15 (0.18), residues: 2016 helix: 2.08 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.61 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.012 0.002 TYR G 97 PHE 0.028 0.001 PHE F 211 TRP 0.027 0.003 TRP E 217 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00343 (18072) covalent geometry : angle 0.63778 (24568) SS BOND : bond 0.00507 ( 14) SS BOND : angle 0.87167 ( 39) hydrogen bonds : bond 0.04921 ( 1224) hydrogen bonds : angle 4.00036 ( 3600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.6085 (mtp) cc_final: 0.5585 (mpp) REVERT: A 38 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: A 161 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8253 (tttm) REVERT: A 227 MET cc_start: 0.7335 (mtm) cc_final: 0.7053 (ptp) REVERT: A 237 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.5902 (ttmt) REVERT: A 241 LYS cc_start: 0.6925 (tptp) cc_final: 0.6265 (mtmm) REVERT: B 7 MET cc_start: 0.6352 (mtp) cc_final: 0.5766 (mpp) REVERT: B 98 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7787 (ttp) REVERT: B 241 LYS cc_start: 0.6855 (tptp) cc_final: 0.6141 (mtmm) REVERT: C 38 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: C 96 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7312 (ttm110) REVERT: C 237 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.6030 (ttmt) REVERT: C 241 LYS cc_start: 0.6831 (tptp) cc_final: 0.6256 (mtmm) REVERT: D 7 MET cc_start: 0.6322 (mtp) cc_final: 0.5735 (mpp) REVERT: D 33 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8423 (tpt) REVERT: D 98 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7784 (ttp) REVERT: D 215 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7470 (mtpp) REVERT: D 241 LYS cc_start: 0.7005 (tptp) cc_final: 0.6247 (ttpp) REVERT: E 38 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: E 227 MET cc_start: 0.7394 (mtp) cc_final: 0.7188 (mtp) REVERT: E 237 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5946 (ttmt) REVERT: E 241 LYS cc_start: 0.6904 (tptp) cc_final: 0.6259 (mtmm) REVERT: F 7 MET cc_start: 0.6261 (mtp) cc_final: 0.5752 (mpp) REVERT: F 215 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7478 (mtpp) REVERT: F 219 HIS cc_start: 0.7509 (m-70) cc_final: 0.7286 (m170) REVERT: F 241 LYS cc_start: 0.6841 (tptp) cc_final: 0.6124 (mtmm) REVERT: G 7 MET cc_start: 0.6046 (mtp) cc_final: 0.5545 (mpp) REVERT: G 38 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: G 96 ARG cc_start: 0.7767 (mtt90) cc_final: 0.7289 (ttm110) REVERT: G 237 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.5859 (ttmt) REVERT: G 241 LYS cc_start: 0.7015 (tptp) cc_final: 0.6451 (mtmm) REVERT: H 7 MET cc_start: 0.6370 (mtp) cc_final: 0.5783 (mpp) REVERT: H 98 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: H 161 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8363 (mttp) REVERT: H 231 THR cc_start: 0.8096 (m) cc_final: 0.7821 (t) outliers start: 44 outliers final: 22 residues processed: 313 average time/residue: 0.7459 time to fit residues: 254.7811 Evaluate side-chains 315 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 161 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 44 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 176 optimal weight: 0.0980 chunk 174 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 219 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125243 restraints weight = 17504.432| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.21 r_work: 0.3054 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18086 Z= 0.156 Angle : 0.653 9.457 24607 Z= 0.315 Chirality : 0.041 0.224 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.041 54.885 4464 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.18 % Allowed : 15.29 % Favored : 82.53 % 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: 2.14 (0.18), residues: 2016 helix: 2.06 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.55 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.012 0.002 TYR F 34 PHE 0.024 0.001 PHE F 211 TRP 0.037 0.003 TRP E 217 HIS 0.002 0.000 HIS H 219 Details of bonding type rmsd covalent geometry : bond 0.00373 (18072) covalent geometry : angle 0.65232 (24568) SS BOND : bond 0.00580 ( 14) SS BOND : angle 0.90011 ( 39) hydrogen bonds : bond 0.05010 ( 1224) hydrogen bonds : angle 4.01791 ( 3600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: A 227 MET cc_start: 0.7348 (mtm) cc_final: 0.7058 (ptp) REVERT: A 237 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.6010 (ttmt) REVERT: A 241 LYS cc_start: 0.6770 (tptp) cc_final: 0.6209 (mtmt) REVERT: B 7 MET cc_start: 0.6394 (mtp) cc_final: 0.5825 (mpp) REVERT: B 80 GLU cc_start: 0.7595 (tp30) cc_final: 0.6885 (mm-30) REVERT: B 241 LYS cc_start: 0.6835 (tptp) cc_final: 0.6137 (mtmm) REVERT: C 7 MET cc_start: 0.6214 (mtp) cc_final: 0.5633 (mpp) REVERT: C 38 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: C 237 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5981 (ttmt) REVERT: C 241 LYS cc_start: 0.6837 (tptp) cc_final: 0.6201 (mtmt) REVERT: D 7 MET cc_start: 0.6365 (mtp) cc_final: 0.5796 (mpp) REVERT: D 33 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8438 (tpt) REVERT: D 80 GLU cc_start: 0.7609 (tp30) cc_final: 0.6902 (mm-30) REVERT: D 215 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7495 (mtpp) REVERT: D 241 LYS cc_start: 0.7056 (tptp) cc_final: 0.6307 (ttpp) REVERT: E 7 MET cc_start: 0.6164 (mtp) cc_final: 0.5553 (mpp) REVERT: E 38 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: E 223 ILE cc_start: 0.7750 (mm) cc_final: 0.7512 (mp) REVERT: E 237 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.6003 (ttmt) REVERT: E 241 LYS cc_start: 0.6868 (tptp) cc_final: 0.6321 (mtmm) REVERT: F 7 MET cc_start: 0.6295 (mtp) cc_final: 0.5773 (mpp) REVERT: F 80 GLU cc_start: 0.7600 (tp30) cc_final: 0.6886 (mm-30) REVERT: F 215 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7484 (mtpp) REVERT: F 241 LYS cc_start: 0.6848 (tptp) cc_final: 0.6158 (mtmt) REVERT: G 38 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: G 237 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5963 (ttmt) REVERT: G 241 LYS cc_start: 0.6945 (tptp) cc_final: 0.6278 (mtmm) REVERT: H 7 MET cc_start: 0.6386 (mtp) cc_final: 0.5824 (mpp) REVERT: H 80 GLU cc_start: 0.7621 (tp30) cc_final: 0.6913 (mm-30) REVERT: H 161 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8360 (mttp) REVERT: H 231 THR cc_start: 0.8077 (m) cc_final: 0.7809 (t) outliers start: 39 outliers final: 18 residues processed: 313 average time/residue: 0.7030 time to fit residues: 240.9614 Evaluate side-chains 301 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 161 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 73 ASN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 219 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 73 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123175 restraints weight = 17552.046| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.53 r_work: 0.3040 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18086 Z= 0.148 Angle : 0.644 7.954 24607 Z= 0.314 Chirality : 0.040 0.220 2728 Planarity : 0.005 0.047 2904 Dihedral : 8.930 55.004 4464 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.01 % Allowed : 15.85 % Favored : 82.14 % 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: 2.22 (0.18), residues: 2016 helix: 2.11 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.52 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 105 TYR 0.012 0.002 TYR F 34 PHE 0.025 0.001 PHE F 211 TRP 0.035 0.003 TRP E 217 HIS 0.002 0.000 HIS H 219 Details of bonding type rmsd covalent geometry : bond 0.00348 (18072) covalent geometry : angle 0.64403 (24568) SS BOND : bond 0.00525 ( 14) SS BOND : angle 0.85882 ( 39) hydrogen bonds : bond 0.04868 ( 1224) hydrogen bonds : angle 4.00515 ( 3600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 294 time to evaluate : 0.635 Fit side-chains REVERT: A 38 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: A 96 ARG cc_start: 0.7784 (mtt90) cc_final: 0.7332 (ttm110) REVERT: A 161 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8260 (tttm) REVERT: A 227 MET cc_start: 0.7326 (mtm) cc_final: 0.7062 (ptp) REVERT: A 237 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5945 (ttmt) REVERT: A 241 LYS cc_start: 0.6762 (tptp) cc_final: 0.6182 (mtmm) REVERT: B 7 MET cc_start: 0.6319 (mtp) cc_final: 0.5689 (mpp) REVERT: B 80 GLU cc_start: 0.7558 (tp30) cc_final: 0.6867 (mm-30) REVERT: B 96 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7418 (ttm110) REVERT: B 241 LYS cc_start: 0.6797 (tptp) cc_final: 0.6103 (mtmt) REVERT: C 7 MET cc_start: 0.6170 (mtp) cc_final: 0.5589 (mpp) REVERT: C 38 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: C 96 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7324 (ttm110) REVERT: C 215 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7275 (mtmm) REVERT: C 237 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5898 (ttmt) REVERT: C 241 LYS cc_start: 0.6888 (tptp) cc_final: 0.6201 (mtmt) REVERT: D 7 MET cc_start: 0.6320 (mtp) cc_final: 0.5690 (mpp) REVERT: D 33 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8464 (tpt) REVERT: D 80 GLU cc_start: 0.7578 (tp30) cc_final: 0.6885 (mm-30) REVERT: D 96 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7383 (ttm110) REVERT: D 215 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7468 (mtpp) REVERT: D 241 LYS cc_start: 0.6997 (tptp) cc_final: 0.6279 (ttpp) REVERT: E 38 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: E 96 ARG cc_start: 0.7783 (mtt90) cc_final: 0.7319 (ttm110) REVERT: E 237 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.5937 (ttmt) REVERT: E 241 LYS cc_start: 0.6831 (tptp) cc_final: 0.6178 (mtmt) REVERT: F 7 MET cc_start: 0.6236 (mtp) cc_final: 0.5760 (mpp) REVERT: F 80 GLU cc_start: 0.7583 (tp30) cc_final: 0.6879 (mm-30) REVERT: F 215 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7473 (mtpp) REVERT: F 241 LYS cc_start: 0.6799 (tptp) cc_final: 0.6111 (mtmt) REVERT: G 38 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: G 96 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7345 (ttm110) REVERT: G 98 MET cc_start: 0.8303 (ttp) cc_final: 0.8067 (ttt) REVERT: G 215 LYS cc_start: 0.7567 (mtmt) cc_final: 0.7293 (mtmm) REVERT: G 237 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5962 (ttmt) REVERT: G 241 LYS cc_start: 0.6826 (tptp) cc_final: 0.6259 (mtmt) REVERT: H 7 MET cc_start: 0.6331 (mtp) cc_final: 0.5705 (mpp) REVERT: H 80 GLU cc_start: 0.7584 (tp30) cc_final: 0.6883 (mm-30) REVERT: H 96 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7407 (ttm110) REVERT: H 161 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8323 (mttp) REVERT: H 231 THR cc_start: 0.8042 (m) cc_final: 0.7796 (t) outliers start: 36 outliers final: 21 residues processed: 312 average time/residue: 0.7461 time to fit residues: 253.8749 Evaluate side-chains 314 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 161 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 198 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 219 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.192452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.118947 restraints weight = 17408.967| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.84 r_work: 0.3037 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18086 Z= 0.143 Angle : 0.634 6.679 24607 Z= 0.311 Chirality : 0.040 0.212 2728 Planarity : 0.005 0.047 2904 Dihedral : 8.837 55.103 4464 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.73 % Allowed : 16.35 % Favored : 81.92 % 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: 2.31 (0.18), residues: 2016 helix: 2.18 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.48 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 96 TYR 0.012 0.002 TYR H 34 PHE 0.025 0.001 PHE F 211 TRP 0.052 0.003 TRP C 217 HIS 0.002 0.000 HIS H 219 Details of bonding type rmsd covalent geometry : bond 0.00334 (18072) covalent geometry : angle 0.63402 (24568) SS BOND : bond 0.00511 ( 14) SS BOND : angle 0.83035 ( 39) hydrogen bonds : bond 0.04756 ( 1224) hydrogen bonds : angle 4.00235 ( 3600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.644 Fit side-chains REVERT: A 38 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: A 96 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7371 (ttm110) REVERT: A 227 MET cc_start: 0.7371 (mtm) cc_final: 0.7137 (ptp) REVERT: A 237 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.5833 (tmtt) REVERT: A 241 LYS cc_start: 0.6902 (tptp) cc_final: 0.6343 (ttpp) REVERT: B 7 MET cc_start: 0.6357 (mtp) cc_final: 0.5966 (mpp) REVERT: B 80 GLU cc_start: 0.7662 (tp30) cc_final: 0.6976 (mm-30) REVERT: B 96 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7473 (ttm110) REVERT: B 241 LYS cc_start: 0.6942 (tptp) cc_final: 0.6208 (mtmt) REVERT: C 38 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: C 96 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7356 (ttm110) REVERT: C 215 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7285 (mtmm) REVERT: C 237 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5900 (tmtt) REVERT: C 241 LYS cc_start: 0.6947 (tptp) cc_final: 0.6304 (ttpp) REVERT: D 7 MET cc_start: 0.6349 (mtp) cc_final: 0.5957 (mpp) REVERT: D 33 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8453 (tpt) REVERT: D 80 GLU cc_start: 0.7671 (tp30) cc_final: 0.6986 (mm-30) REVERT: D 96 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7448 (ttm110) REVERT: D 215 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7510 (mtpp) REVERT: D 241 LYS cc_start: 0.6962 (tptp) cc_final: 0.6248 (ttpp) REVERT: E 7 MET cc_start: 0.6295 (mtp) cc_final: 0.5743 (mpp) REVERT: E 38 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: E 234 GLU cc_start: 0.7300 (pt0) cc_final: 0.6604 (tp30) REVERT: E 237 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5849 (tmtt) REVERT: E 241 LYS cc_start: 0.7027 (tptp) cc_final: 0.6393 (ttpp) REVERT: F 7 MET cc_start: 0.6263 (mtp) cc_final: 0.5959 (mpp) REVERT: F 80 GLU cc_start: 0.7685 (tp30) cc_final: 0.6987 (mm-30) REVERT: F 98 MET cc_start: 0.8393 (ttp) cc_final: 0.8175 (ttt) REVERT: F 215 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7520 (mtpp) REVERT: F 241 LYS cc_start: 0.6935 (tptp) cc_final: 0.6219 (mtmt) REVERT: G 38 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: G 96 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7323 (ttm110) REVERT: G 98 MET cc_start: 0.8333 (ttp) cc_final: 0.8104 (ttt) REVERT: G 161 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8351 (tttp) REVERT: G 215 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7352 (mtmm) REVERT: G 237 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6130 (ttmt) REVERT: G 241 LYS cc_start: 0.6889 (tptp) cc_final: 0.6293 (mtmm) REVERT: H 7 MET cc_start: 0.6375 (mtp) cc_final: 0.5999 (mpp) REVERT: H 80 GLU cc_start: 0.7682 (tp30) cc_final: 0.6998 (mm-30) REVERT: H 96 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7486 (ttm110) REVERT: H 161 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8379 (mttp) REVERT: H 231 THR cc_start: 0.8108 (m) cc_final: 0.7876 (t) outliers start: 31 outliers final: 21 residues processed: 319 average time/residue: 0.7374 time to fit residues: 257.0298 Evaluate side-chains 317 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 CYS Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 179 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 182 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 219 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.193156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119473 restraints weight = 17550.326| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.85 r_work: 0.3042 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18086 Z= 0.138 Angle : 0.629 7.044 24607 Z= 0.307 Chirality : 0.039 0.210 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.740 55.359 4464 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.73 % Allowed : 16.69 % Favored : 81.58 % 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: 2.40 (0.19), residues: 2016 helix: 2.25 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.45 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 200 TYR 0.011 0.002 TYR B 34 PHE 0.025 0.001 PHE F 211 TRP 0.044 0.003 TRP E 217 HIS 0.003 0.000 HIS H 219 Details of bonding type rmsd covalent geometry : bond 0.00321 (18072) covalent geometry : angle 0.62836 (24568) SS BOND : bond 0.00494 ( 14) SS BOND : angle 0.79600 ( 39) hydrogen bonds : bond 0.04643 ( 1224) hydrogen bonds : angle 3.97490 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8266.17 seconds wall clock time: 140 minutes 54.75 seconds (8454.75 seconds total)