Starting phenix.real_space_refine on Sat Sep 12 18:59:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lmt_0919/09_2026/6lmt_0919.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmt_0919/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6lmt_0919/09_2026/6lmt_0919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmt_0919/09_2026/6lmt_0919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lmt_0919/09_2026/6lmt_0919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmt_0919/09_2026/6lmt_0919.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6lmt_0919/09_2026/6lmt_0919.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lmt_0919/09_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-2.2.1-6174/lib/python3.11/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: 3.44, per 1000 atoms: 0.20 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: 1.45 Conformation dependent library (CDL) restraints added in 699.2 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: 0.40 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: 3.00 Time building geometry restraints manager: 1.96 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: 9871 16.32 - 32.64: 458 32.64 - 48.95: 119 48.95 - 65.27: 48 65.27 - 81.59: 8 Dihedral angle restraints: 10504 sinusoidal: 4520 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 10501 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.710 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:8.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 11.630 81.587 6552 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/Z covalent geometry : bond 0.01224 / 0.48 (18072) covalent geometry : angle 1.13751 / 0.58 (24568) SS BOND : bond 0.01603 / 0.89 ( 14) SS BOND : angle 2.62644 / 1.72 ( 39) hydrogen bonds : bond 0.22465 / 14.43 ( 1224) hydrogen bonds : angle 8.03212 / 5.56 ( 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 : 0.526 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: 0.8097 time to fit residues: 361.8354 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 : 0.688 ------------------------------------------------------------------------------- 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... ** 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 235 HIS 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 = 0.4132 r_free = 0.4132 target = 0.191858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126640 restraints weight = 17589.063| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.24 r_work: 0.3044 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18086 Z= 0.162 Angle : 0.731 14.440 24607 Z= 0.355 Chirality : 0.041 0.247 2728 Planarity : 0.006 0.048 2904 Dihedral : 9.735 58.120 2612 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 8.65 % Favored : 89.40 % 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: -0.21 (0.17), residues: 2016 helix: 0.32 (0.12), residues: 1512 sheet: None (None), residues: 0 loop : -1.30 (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 B 64 TRP 0.021 0.003 TRP C 217 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (18072) covalent geometry : angle 0.73014 / 0.35 (24568) SS BOND : bond 0.00481 / 0.27 ( 14) SS BOND : angle 0.96475 / 0.60 ( 39) hydrogen bonds : bond 0.06430 / 4.09 ( 1224) hydrogen bonds : angle 4.52180 / 3.12 ( 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 356 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 0.626 Fit side-chains REVERT: A 7 MET cc_start: 0.6375 (mtp) cc_final: 0.6081 (mtp) REVERT: A 228 PHE cc_start: 0.7613 (t80) cc_final: 0.7026 (t80) REVERT: A 241 LYS cc_start: 0.7119 (tptp) cc_final: 0.6608 (mttt) REVERT: B 96 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7318 (ttm110) REVERT: B 105 ARG cc_start: 0.8096 (mtm110) cc_final: 0.7860 (mtp-110) REVERT: B 241 LYS cc_start: 0.7005 (tptp) cc_final: 0.6453 (mtmm) REVERT: C 7 MET cc_start: 0.6367 (mtp) cc_final: 0.6123 (mtp) REVERT: C 228 PHE cc_start: 0.7621 (t80) cc_final: 0.7036 (t80) REVERT: C 237 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6307 (ttmt) REVERT: C 241 LYS cc_start: 0.6994 (tptp) cc_final: 0.6558 (mtmm) REVERT: D 96 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7307 (ttm110) REVERT: D 105 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7868 (mtp-110) REVERT: D 231 THR cc_start: 0.8093 (m) cc_final: 0.7788 (t) REVERT: D 241 LYS cc_start: 0.7028 (tptp) cc_final: 0.6460 (mtmm) REVERT: E 7 MET cc_start: 0.6349 (mtp) cc_final: 0.6046 (mtp) REVERT: E 228 PHE cc_start: 0.7642 (t80) cc_final: 0.7058 (t80) REVERT: E 237 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6309 (ttmt) REVERT: E 241 LYS cc_start: 0.6987 (tptp) cc_final: 0.6553 (mtmm) REVERT: F 96 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7312 (ttm110) REVERT: F 105 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7881 (mtp-110) REVERT: F 228 PHE cc_start: 0.7457 (t80) cc_final: 0.7144 (t80) REVERT: F 241 LYS cc_start: 0.7035 (tptp) cc_final: 0.6483 (mtmm) REVERT: G 7 MET cc_start: 0.6338 (mtp) cc_final: 0.6044 (mtp) REVERT: G 228 PHE cc_start: 0.7608 (t80) cc_final: 0.7018 (t80) REVERT: G 241 LYS cc_start: 0.7108 (tptp) cc_final: 0.6595 (mttt) REVERT: H 96 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7317 (ttm110) REVERT: H 105 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7864 (mtp-110) REVERT: H 228 PHE cc_start: 0.7445 (t80) cc_final: 0.7137 (t80) outliers start: 35 outliers final: 13 residues processed: 336 average time/residue: 0.7186 time to fit residues: 263.8331 Evaluate side-chains 285 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 270 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 2.9990 chunk 148 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.190522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115624 restraints weight = 17751.215| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.18 r_work: 0.3007 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18086 Z= 0.176 Angle : 0.673 7.368 24607 Z= 0.327 Chirality : 0.042 0.245 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.245 55.994 2608 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.12 % Allowed : 11.16 % Favored : 85.71 % 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: 1.19 (0.18), residues: 2016 helix: 1.43 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.11 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.015 0.002 TYR B 34 PHE 0.019 0.002 PHE B 137 TRP 0.018 0.003 TRP E 217 HIS 0.003 0.001 HIS E 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (18072) covalent geometry : angle 0.67193 / 0.33 (24568) SS BOND : bond 0.00563 / 0.32 ( 14) SS BOND : angle 1.07695 / 0.68 ( 39) hydrogen bonds : bond 0.05918 / 3.75 ( 1224) hydrogen bonds : angle 4.29409 / 2.96 ( 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 335 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 279 time to evaluate : 0.644 Fit side-chains REVERT: A 7 MET cc_start: 0.6300 (mtp) cc_final: 0.5925 (mtp) REVERT: A 228 PHE cc_start: 0.7467 (t80) cc_final: 0.6848 (t80) REVERT: A 237 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6162 (ttmt) REVERT: A 241 LYS cc_start: 0.7080 (tptp) cc_final: 0.6540 (mtmm) REVERT: B 241 LYS cc_start: 0.7020 (tptp) cc_final: 0.6398 (mtmm) REVERT: C 228 PHE cc_start: 0.7507 (t80) cc_final: 0.6894 (t80) REVERT: C 237 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6188 (ttmt) REVERT: C 241 LYS cc_start: 0.7063 (tptp) cc_final: 0.6533 (mtmm) REVERT: D 241 LYS cc_start: 0.7005 (tptp) cc_final: 0.6382 (mtmm) REVERT: E 7 MET cc_start: 0.6242 (mtp) cc_final: 0.5865 (mtp) REVERT: E 38 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: E 228 PHE cc_start: 0.7509 (t80) cc_final: 0.6899 (t80) REVERT: E 237 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6176 (ttmt) REVERT: E 241 LYS cc_start: 0.7059 (tptp) cc_final: 0.6533 (mtmm) REVERT: F 7 MET cc_start: 0.6236 (mtp) cc_final: 0.5979 (mtp) REVERT: F 241 LYS cc_start: 0.7014 (tptp) cc_final: 0.6367 (mtmm) REVERT: G 7 MET cc_start: 0.6226 (mtp) cc_final: 0.5851 (mtp) REVERT: G 228 PHE cc_start: 0.7488 (t80) cc_final: 0.6878 (t80) REVERT: G 237 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6162 (ttmt) REVERT: G 241 LYS cc_start: 0.7075 (tptp) cc_final: 0.6543 (mtmm) outliers start: 56 outliers final: 27 residues processed: 294 average time/residue: 0.7289 time to fit residues: 234.6393 Evaluate side-chains 313 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 281 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 83 ARG 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 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: 1.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** E 104 GLN E 219 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.192241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118957 restraints weight = 17755.565| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.84 r_work: 0.3054 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18086 Z= 0.146 Angle : 0.631 7.215 24607 Z= 0.308 Chirality : 0.040 0.242 2728 Planarity : 0.005 0.047 2904 Dihedral : 8.672 55.226 2608 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.52 % Allowed : 12.28 % 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: 1.84 (0.19), residues: 2016 helix: 1.92 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.96 (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 H 34 PHE 0.013 0.001 PHE B 137 TRP 0.014 0.003 TRP E 217 HIS 0.003 0.001 HIS E 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18072) covalent geometry : angle 0.63015 / 0.31 (24568) SS BOND : bond 0.00435 / 0.25 ( 14) SS BOND : angle 0.89339 / 0.56 ( 39) hydrogen bonds : bond 0.05257 / 3.32 ( 1224) hydrogen bonds : angle 4.10978 / 2.84 ( 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 353 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 0.596 Fit side-chains REVERT: A 7 MET cc_start: 0.6174 (mtp) cc_final: 0.5837 (mtp) REVERT: A 38 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: A 227 MET cc_start: 0.7439 (mtm) cc_final: 0.7195 (mtm) REVERT: A 228 PHE cc_start: 0.7342 (t80) cc_final: 0.6686 (t80) REVERT: A 237 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6025 (ttmt) REVERT: A 241 LYS cc_start: 0.7029 (tptp) cc_final: 0.6485 (mtmm) REVERT: B 96 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7238 (ttm110) REVERT: B 215 LYS cc_start: 0.7715 (ttmm) cc_final: 0.7473 (ttmm) REVERT: B 219 HIS cc_start: 0.7598 (m-70) cc_final: 0.7350 (m170) REVERT: B 231 THR cc_start: 0.8068 (m) cc_final: 0.7772 (t) REVERT: B 241 LYS cc_start: 0.7023 (tptp) cc_final: 0.6360 (mtmm) REVERT: C 7 MET cc_start: 0.5994 (mtp) cc_final: 0.5579 (mtp) REVERT: C 237 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6037 (ttmt) REVERT: C 241 LYS cc_start: 0.7015 (tptp) cc_final: 0.6559 (mtmm) REVERT: D 96 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7240 (ttm110) REVERT: D 219 HIS cc_start: 0.7633 (m-70) cc_final: 0.7382 (m170) REVERT: D 231 THR cc_start: 0.8100 (m) cc_final: 0.7793 (t) REVERT: D 241 LYS cc_start: 0.7015 (tptp) cc_final: 0.6360 (mtmm) REVERT: E 7 MET cc_start: 0.6128 (mtp) cc_final: 0.5793 (mtp) REVERT: E 237 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6051 (ttmt) REVERT: E 241 LYS cc_start: 0.7014 (tptp) cc_final: 0.6562 (mtmm) REVERT: F 96 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7263 (ttm110) REVERT: F 219 HIS cc_start: 0.7610 (m-70) cc_final: 0.7392 (m170) REVERT: F 241 LYS cc_start: 0.7011 (tptp) cc_final: 0.6346 (mtmm) REVERT: G 7 MET cc_start: 0.6150 (mtp) cc_final: 0.5811 (mtp) REVERT: G 38 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: G 237 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6021 (ttmt) REVERT: G 241 LYS cc_start: 0.7029 (tptp) cc_final: 0.6481 (mtmm) REVERT: H 96 ARG cc_start: 0.7802 (mtm110) cc_final: 0.7255 (ttm110) REVERT: H 157 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8141 (mtt180) REVERT: H 219 HIS cc_start: 0.7615 (m-70) cc_final: 0.7380 (m170) REVERT: H 231 THR cc_start: 0.8104 (m) cc_final: 0.7806 (t) outliers start: 63 outliers final: 25 residues processed: 318 average time/residue: 0.7310 time to fit residues: 253.8566 Evaluate side-chains 305 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C 219 HIS ** 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 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117678 restraints weight = 17646.471| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.82 r_work: 0.3030 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2805 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= 0.159 Angle : 0.653 7.047 24607 Z= 0.316 Chirality : 0.041 0.235 2728 Planarity : 0.005 0.047 2904 Dihedral : 8.643 55.439 2608 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.85 % Allowed : 13.95 % Favored : 83.20 % 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: 1.91 (0.18), residues: 2016 helix: 1.94 (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 0.012 0.002 TYR H 34 PHE 0.019 0.001 PHE D 211 TRP 0.023 0.003 TRP A 217 HIS 0.004 0.001 HIS F 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (18072) covalent geometry : angle 0.65216 / 0.32 (24568) SS BOND : bond 0.00531 / 0.31 ( 14) SS BOND : angle 0.95558 / 0.60 ( 39) hydrogen bonds : bond 0.05283 / 3.34 ( 1224) hydrogen bonds : angle 4.07941 / 2.82 ( 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 341 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 0.659 Fit side-chains REVERT: A 7 MET cc_start: 0.6036 (mtp) cc_final: 0.5741 (mtp) REVERT: A 38 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: A 228 PHE cc_start: 0.7369 (t80) cc_final: 0.6717 (t80) REVERT: A 237 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6076 (ttmt) REVERT: A 241 LYS cc_start: 0.7059 (tptp) cc_final: 0.6541 (mttp) REVERT: B 7 MET cc_start: 0.6417 (mtp) cc_final: 0.5958 (mpp) REVERT: B 96 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7316 (ttm110) REVERT: B 215 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7477 (ttmm) REVERT: B 219 HIS cc_start: 0.7703 (m-70) cc_final: 0.7492 (m170) REVERT: B 241 LYS cc_start: 0.7041 (tptp) cc_final: 0.6323 (mtmt) REVERT: C 237 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.6082 (ttmt) REVERT: C 241 LYS cc_start: 0.7056 (tptp) cc_final: 0.6549 (mtmm) REVERT: D 7 MET cc_start: 0.6518 (mtp) cc_final: 0.6073 (mpp) REVERT: D 96 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7333 (ttm110) REVERT: D 241 LYS cc_start: 0.7027 (tptp) cc_final: 0.6393 (mtmm) REVERT: E 7 MET cc_start: 0.6062 (mtp) cc_final: 0.5788 (mtp) REVERT: E 38 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: E 237 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6090 (ttmt) REVERT: E 241 LYS cc_start: 0.7038 (tptp) cc_final: 0.6536 (mtmm) REVERT: F 96 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7341 (ttm110) REVERT: F 241 LYS cc_start: 0.7020 (tptp) cc_final: 0.6320 (mtmt) REVERT: G 7 MET cc_start: 0.6027 (mtp) cc_final: 0.5755 (mtp) REVERT: G 38 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: G 237 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6052 (ttmt) REVERT: G 241 LYS cc_start: 0.7053 (tptp) cc_final: 0.6512 (mttt) REVERT: H 7 MET cc_start: 0.6404 (mtp) cc_final: 0.5951 (mpp) REVERT: H 96 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7334 (ttm110) REVERT: H 219 HIS cc_start: 0.7699 (m-70) cc_final: 0.7485 (m170) REVERT: H 231 THR cc_start: 0.8125 (m) cc_final: 0.7813 (t) outliers start: 51 outliers final: 25 residues processed: 305 average time/residue: 0.6973 time to fit residues: 233.4707 Evaluate side-chains 310 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 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 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 223 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 33 MET Chi-restraints excluded: chain H residue 38 GLU 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: 0.5980 chunk 35 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** 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 104 GLN ** 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 104 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN H 219 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.192993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127328 restraints weight = 17590.629| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.17 r_work: 0.3085 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3070 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= 0.132 Angle : 0.617 6.786 24607 Z= 0.301 Chirality : 0.039 0.220 2728 Planarity : 0.004 0.048 2904 Dihedral : 8.300 55.950 2608 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.12 % Allowed : 14.17 % Favored : 83.71 % 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 (0.19), residues: 2016 helix: 2.10 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.67 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.011 0.002 TYR C 97 PHE 0.019 0.001 PHE E 211 TRP 0.028 0.003 TRP C 217 HIS 0.003 0.000 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (18072) covalent geometry : angle 0.61682 / 0.30 (24568) SS BOND : bond 0.00407 / 0.23 ( 14) SS BOND : angle 0.77837 / 0.48 ( 39) hydrogen bonds : bond 0.04823 / 3.04 ( 1224) hydrogen bonds : angle 3.96268 / 2.75 ( 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 324 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 0.576 Fit side-chains REVERT: A 228 PHE cc_start: 0.7268 (t80) cc_final: 0.6703 (t80) REVERT: A 237 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.5902 (ttmt) REVERT: A 241 LYS cc_start: 0.7046 (tptp) cc_final: 0.6508 (mtmm) REVERT: B 7 MET cc_start: 0.6433 (mtp) cc_final: 0.5869 (mpp) REVERT: B 96 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7338 (ttm110) REVERT: B 215 LYS cc_start: 0.7581 (ttmm) cc_final: 0.7328 (mtpm) REVERT: B 241 LYS cc_start: 0.7027 (tptp) cc_final: 0.6301 (mttt) REVERT: C 38 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: C 223 ILE cc_start: 0.7756 (mm) cc_final: 0.7555 (mp) REVERT: C 237 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5918 (ttmt) REVERT: C 241 LYS cc_start: 0.6991 (tptp) cc_final: 0.6458 (mtmm) REVERT: D 7 MET cc_start: 0.6556 (mtp) cc_final: 0.5975 (mpp) REVERT: D 96 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7328 (ttm110) REVERT: D 219 HIS cc_start: 0.7653 (m90) cc_final: 0.7448 (m170) REVERT: D 241 LYS cc_start: 0.7018 (tptp) cc_final: 0.6367 (mtmm) REVERT: E 7 MET cc_start: 0.6145 (mtp) cc_final: 0.5935 (mtp) REVERT: E 223 ILE cc_start: 0.7804 (mm) cc_final: 0.7591 (mp) REVERT: E 237 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5917 (ttmt) REVERT: E 241 LYS cc_start: 0.6982 (tptp) cc_final: 0.6480 (mttp) REVERT: F 7 MET cc_start: 0.6421 (mtp) cc_final: 0.5881 (mpp) REVERT: F 96 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7354 (ttm110) REVERT: F 219 HIS cc_start: 0.7649 (m90) cc_final: 0.7423 (m170) REVERT: F 241 LYS cc_start: 0.6898 (tptp) cc_final: 0.6151 (mtmm) REVERT: G 7 MET cc_start: 0.6147 (mtp) cc_final: 0.5937 (mtp) REVERT: G 237 LYS cc_start: 0.6376 (OUTLIER) cc_final: 0.5883 (ttmt) REVERT: G 241 LYS cc_start: 0.7001 (tptp) cc_final: 0.6483 (mtmm) REVERT: H 7 MET cc_start: 0.6417 (mtp) cc_final: 0.5820 (mpp) REVERT: H 96 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7344 (ttm110) REVERT: H 231 THR cc_start: 0.8108 (m) cc_final: 0.7824 (t) outliers start: 38 outliers final: 26 residues processed: 303 average time/residue: 0.7004 time to fit residues: 232.4378 Evaluate side-chains 304 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 134 ILE Chi-restraints excluded: chain C residue 237 LYS 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 134 ILE 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 33 MET 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 G residue 248 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 137 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115333 restraints weight = 17540.107| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.83 r_work: 0.2999 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 18086 Z= 0.201 Angle : 0.703 6.831 24607 Z= 0.337 Chirality : 0.044 0.222 2728 Planarity : 0.005 0.048 2904 Dihedral : 9.002 57.368 2608 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.68 % Allowed : 14.01 % Favored : 83.31 % 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: 1.85 (0.18), residues: 2016 helix: 1.86 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.72 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.014 0.002 TYR F 34 PHE 0.020 0.002 PHE B 137 TRP 0.037 0.003 TRP C 217 HIS 0.002 0.000 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (18072) covalent geometry : angle 0.70227 / 0.34 (24568) SS BOND : bond 0.00757 / 0.43 ( 14) SS BOND : angle 1.07940 / 0.68 ( 39) hydrogen bonds : bond 0.05481 / 3.47 ( 1224) hydrogen bonds : angle 4.11357 / 2.84 ( 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 345 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 297 time to evaluate : 0.627 Fit side-chains REVERT: A 38 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: A 227 MET cc_start: 0.7467 (mtm) cc_final: 0.7121 (ptp) REVERT: A 228 PHE cc_start: 0.7404 (t80) cc_final: 0.6910 (t80) REVERT: A 237 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6094 (ttmt) REVERT: A 241 LYS cc_start: 0.7090 (tptp) cc_final: 0.6534 (mtmm) REVERT: B 7 MET cc_start: 0.6374 (mtp) cc_final: 0.5793 (mpp) REVERT: B 96 ARG cc_start: 0.7870 (mtm110) cc_final: 0.7375 (ttm110) REVERT: B 98 MET cc_start: 0.8457 (ttp) cc_final: 0.8240 (ttt) REVERT: B 215 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7659 (ttmm) REVERT: B 219 HIS cc_start: 0.7663 (m-70) cc_final: 0.7451 (m170) REVERT: B 241 LYS cc_start: 0.7015 (tptp) cc_final: 0.6307 (ttpp) REVERT: C 38 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: C 237 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6168 (ttmt) REVERT: C 241 LYS cc_start: 0.6949 (tptp) cc_final: 0.6322 (mtmm) REVERT: D 7 MET cc_start: 0.6467 (mtp) cc_final: 0.5865 (mpp) REVERT: D 33 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8438 (tpt) REVERT: D 96 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7354 (ttm110) REVERT: D 98 MET cc_start: 0.8464 (ttp) cc_final: 0.8249 (ttt) REVERT: D 219 HIS cc_start: 0.7770 (m90) cc_final: 0.7566 (m170) REVERT: D 241 LYS cc_start: 0.6956 (tptp) cc_final: 0.6192 (mtmt) REVERT: E 7 MET cc_start: 0.6245 (mtp) cc_final: 0.5959 (mtp) REVERT: E 38 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: E 237 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6156 (ttmt) REVERT: E 241 LYS cc_start: 0.6967 (tptp) cc_final: 0.6327 (mtmm) REVERT: F 7 MET cc_start: 0.6498 (mtp) cc_final: 0.5993 (mpp) REVERT: F 96 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7386 (ttm110) REVERT: F 98 MET cc_start: 0.8471 (ttp) cc_final: 0.8258 (ttt) REVERT: F 241 LYS cc_start: 0.6841 (tptp) cc_final: 0.6170 (mtmm) REVERT: G 7 MET cc_start: 0.6243 (mtp) cc_final: 0.5959 (mtp) REVERT: G 38 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: G 237 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.6079 (ttmt) REVERT: G 241 LYS cc_start: 0.7083 (tptp) cc_final: 0.6527 (mtmm) REVERT: H 7 MET cc_start: 0.6366 (mtp) cc_final: 0.5786 (mpp) REVERT: H 96 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7366 (ttm110) REVERT: H 98 MET cc_start: 0.8448 (ttp) cc_final: 0.8232 (ttt) REVERT: H 161 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8525 (mttp) outliers start: 48 outliers final: 22 residues processed: 310 average time/residue: 0.6756 time to fit residues: 230.1100 Evaluate side-chains 311 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 19 MET 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 28 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP 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 28 LEU Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 38 GLU 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: 0.8980 chunk 172 optimal weight: 0.8980 chunk 7 optimal weight: 0.0770 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 40 optimal weight: 0.0010 overall best weight: 0.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.192959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120045 restraints weight = 17528.539| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.29 r_work: 0.3042 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18086 Z= 0.135 Angle : 0.624 6.656 24607 Z= 0.304 Chirality : 0.039 0.214 2728 Planarity : 0.004 0.048 2904 Dihedral : 8.460 55.539 2608 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 11.05 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: 2.25 (0.19), residues: 2016 helix: 2.15 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.58 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.011 0.002 TYR A 97 PHE 0.031 0.001 PHE E 211 TRP 0.028 0.003 TRP C 217 HIS 0.001 0.000 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (18072) covalent geometry : angle 0.62337 / 0.30 (24568) SS BOND : bond 0.00421 / 0.24 ( 14) SS BOND : angle 0.79124 / 0.49 ( 39) hydrogen bonds : bond 0.04747 / 3.00 ( 1224) hydrogen bonds : angle 3.99924 / 2.77 ( 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 326 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 0.485 Fit side-chains REVERT: A 38 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: A 96 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7340 (ttm110) REVERT: A 227 MET cc_start: 0.7299 (mtm) cc_final: 0.7041 (ptp) REVERT: A 237 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5889 (ttmt) REVERT: A 241 LYS cc_start: 0.6949 (tptp) cc_final: 0.6296 (mtmm) REVERT: B 7 MET cc_start: 0.6345 (mtp) cc_final: 0.5791 (mpp) REVERT: B 80 GLU cc_start: 0.7543 (tp30) cc_final: 0.6841 (mm-30) REVERT: B 96 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7278 (ttm110) REVERT: B 215 LYS cc_start: 0.7604 (ttmm) cc_final: 0.7399 (ttmm) REVERT: B 241 LYS cc_start: 0.6989 (tptp) cc_final: 0.6225 (ttpp) REVERT: C 38 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: C 96 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7300 (ttm110) REVERT: C 237 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5989 (ttmt) REVERT: C 241 LYS cc_start: 0.6845 (tptp) cc_final: 0.6316 (mtmm) REVERT: D 7 MET cc_start: 0.6356 (mtp) cc_final: 0.5801 (mpp) REVERT: D 33 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8303 (tpt) REVERT: D 80 GLU cc_start: 0.7555 (tp30) cc_final: 0.6869 (mm-30) REVERT: D 96 ARG cc_start: 0.7760 (mtm110) cc_final: 0.7267 (ttm110) REVERT: D 241 LYS cc_start: 0.6859 (tptp) cc_final: 0.6200 (mtmt) REVERT: E 7 MET cc_start: 0.6192 (mtp) cc_final: 0.5981 (mtp) REVERT: E 38 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: E 96 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7303 (ttm110) REVERT: E 237 LYS cc_start: 0.6360 (OUTLIER) cc_final: 0.5965 (ttmt) REVERT: E 241 LYS cc_start: 0.6873 (tptp) cc_final: 0.6325 (mtmm) REVERT: F 7 MET cc_start: 0.6421 (mtp) cc_final: 0.5944 (mpp) REVERT: F 80 GLU cc_start: 0.7536 (tp30) cc_final: 0.6837 (mm-30) REVERT: F 96 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7276 (ttm110) REVERT: F 241 LYS cc_start: 0.6769 (tptp) cc_final: 0.6034 (mtmm) REVERT: G 7 MET cc_start: 0.6196 (mtp) cc_final: 0.5973 (mtp) REVERT: G 38 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: G 96 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7346 (ttm110) REVERT: G 237 LYS cc_start: 0.6382 (OUTLIER) cc_final: 0.5934 (ttmt) REVERT: G 241 LYS cc_start: 0.6949 (tptp) cc_final: 0.6292 (mtmm) REVERT: H 7 MET cc_start: 0.6322 (mtp) cc_final: 0.5777 (mpp) REVERT: H 80 GLU cc_start: 0.7572 (tp30) cc_final: 0.6878 (mm-30) REVERT: H 96 ARG cc_start: 0.7762 (mtm110) cc_final: 0.7274 (ttm110) outliers start: 36 outliers final: 16 residues processed: 310 average time/residue: 0.6814 time to fit residues: 231.8521 Evaluate side-chains 303 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 278 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP 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 28 LEU Chi-restraints excluded: chain H residue 38 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117246 restraints weight = 17529.801| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.84 r_work: 0.3025 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18086 Z= 0.165 Angle : 0.670 6.665 24607 Z= 0.324 Chirality : 0.041 0.211 2728 Planarity : 0.005 0.048 2904 Dihedral : 8.747 55.942 2608 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.90 % Allowed : 16.02 % Favored : 82.09 % 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: 2.10 (0.18), residues: 2016 helix: 2.03 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.56 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.013 0.002 TYR F 34 PHE 0.024 0.001 PHE E 211 TRP 0.046 0.003 TRP C 217 HIS 0.002 0.000 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (18072) covalent geometry : angle 0.66974 / 0.32 (24568) SS BOND : bond 0.00604 / 0.34 ( 14) SS BOND : angle 0.92664 / 0.58 ( 39) hydrogen bonds : bond 0.05049 / 3.20 ( 1224) hydrogen bonds : angle 4.06076 / 2.81 ( 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: 34 poor density : 296 time to evaluate : 0.571 Fit side-chains REVERT: A 38 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: A 161 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8320 (tttm) REVERT: A 227 MET cc_start: 0.7331 (mtm) cc_final: 0.7098 (ptp) REVERT: A 237 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.6066 (ttmt) REVERT: A 241 LYS cc_start: 0.6873 (tptp) cc_final: 0.6274 (mtmt) REVERT: B 7 MET cc_start: 0.6449 (mtp) cc_final: 0.5905 (mpp) REVERT: B 80 GLU cc_start: 0.7622 (tp30) cc_final: 0.6940 (mm-30) REVERT: B 96 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7504 (ttm110) REVERT: B 215 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7500 (mtpp) REVERT: B 241 LYS cc_start: 0.6879 (tptp) cc_final: 0.6145 (mtmm) REVERT: C 38 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: C 237 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.6027 (ttmt) REVERT: C 241 LYS cc_start: 0.6888 (tptp) cc_final: 0.6233 (mtmt) REVERT: D 7 MET cc_start: 0.6427 (mtp) cc_final: 0.5886 (mpp) REVERT: D 33 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8383 (tpt) REVERT: D 80 GLU cc_start: 0.7649 (tp30) cc_final: 0.6939 (mm-30) REVERT: D 96 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7498 (ttm110) REVERT: D 241 LYS cc_start: 0.6854 (tptp) cc_final: 0.6351 (tppt) REVERT: E 7 MET cc_start: 0.6257 (mtp) cc_final: 0.6015 (mtp) REVERT: E 38 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: E 96 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7404 (ttm110) REVERT: E 237 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.6023 (ttmt) REVERT: E 241 LYS cc_start: 0.6905 (tptp) cc_final: 0.6302 (mtmm) REVERT: F 7 MET cc_start: 0.6479 (mtp) cc_final: 0.6009 (mpp) REVERT: F 33 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8345 (tpt) REVERT: F 80 GLU cc_start: 0.7645 (tp30) cc_final: 0.6930 (mm-30) REVERT: F 96 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7522 (ttm110) REVERT: F 241 LYS cc_start: 0.6782 (tptp) cc_final: 0.6047 (mtmm) REVERT: G 7 MET cc_start: 0.6262 (mtp) cc_final: 0.6021 (mtp) REVERT: G 38 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: G 161 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8327 (tttm) REVERT: G 237 LYS cc_start: 0.6465 (OUTLIER) cc_final: 0.6057 (ttmt) REVERT: G 241 LYS cc_start: 0.6864 (tptp) cc_final: 0.6262 (mtmm) REVERT: H 7 MET cc_start: 0.6445 (mtp) cc_final: 0.5907 (mpp) REVERT: H 80 GLU cc_start: 0.7663 (tp30) cc_final: 0.6946 (mm-30) REVERT: H 96 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7513 (ttm110) REVERT: H 161 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8411 (mttp) outliers start: 34 outliers final: 15 residues processed: 310 average time/residue: 0.6609 time to fit residues: 225.1764 Evaluate side-chains 318 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 162 ASP 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 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 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 28 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 38 GLU 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: 0.5980 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 219 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126466 restraints weight = 17304.438| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.40 r_work: 0.3016 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18086 Z= 0.145 Angle : 0.645 6.684 24607 Z= 0.312 Chirality : 0.039 0.200 2728 Planarity : 0.005 0.048 2904 Dihedral : 8.577 55.866 2608 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.56 % Allowed : 16.18 % Favored : 82.25 % 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: 2.29 (0.19), residues: 2016 helix: 2.17 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.49 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 200 TYR 0.011 0.002 TYR F 34 PHE 0.024 0.001 PHE E 211 TRP 0.040 0.003 TRP C 217 HIS 0.002 0.000 HIS F 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (18072) covalent geometry : angle 0.64418 / 0.31 (24568) SS BOND : bond 0.00506 / 0.29 ( 14) SS BOND : angle 0.82258 / 0.51 ( 39) hydrogen bonds : bond 0.04757 / 3.01 ( 1224) hydrogen bonds : angle 4.01835 / 2.78 ( 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 320 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.581 Fit side-chains REVERT: A 7 MET cc_start: 0.6326 (mtp) cc_final: 0.5647 (mtt) REVERT: A 38 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: A 96 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7323 (ttm110) REVERT: A 161 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8344 (tttm) REVERT: A 215 LYS cc_start: 0.7818 (mtpp) cc_final: 0.7602 (mtmt) REVERT: A 237 LYS cc_start: 0.6463 (OUTLIER) cc_final: 0.6132 (ttmt) REVERT: A 241 LYS cc_start: 0.6886 (tptp) cc_final: 0.6268 (mtmm) REVERT: B 7 MET cc_start: 0.6356 (mtp) cc_final: 0.5819 (mpp) REVERT: B 80 GLU cc_start: 0.7603 (tp30) cc_final: 0.6929 (mm-30) REVERT: B 96 ARG cc_start: 0.7808 (mtm110) cc_final: 0.7477 (ttm110) REVERT: B 215 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7384 (mtpp) REVERT: B 241 LYS cc_start: 0.6820 (tptp) cc_final: 0.6092 (mtmt) REVERT: C 38 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: C 96 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7288 (ttm110) REVERT: C 237 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.6031 (ttmt) REVERT: C 241 LYS cc_start: 0.6953 (tptp) cc_final: 0.6257 (mtmt) REVERT: D 7 MET cc_start: 0.6340 (mtp) cc_final: 0.5806 (mpp) REVERT: D 33 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8426 (tpt) REVERT: D 80 GLU cc_start: 0.7614 (tp30) cc_final: 0.6929 (mm-30) REVERT: D 96 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7452 (ttm110) REVERT: D 98 MET cc_start: 0.8367 (ttp) cc_final: 0.8071 (ttt) REVERT: D 241 LYS cc_start: 0.6899 (tptp) cc_final: 0.6138 (mtmt) REVERT: E 7 MET cc_start: 0.6203 (mtp) cc_final: 0.5954 (mtp) REVERT: E 38 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: E 96 ARG cc_start: 0.7735 (mtt90) cc_final: 0.7305 (ttm110) REVERT: E 215 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7375 (mtmm) REVERT: E 234 GLU cc_start: 0.7272 (pt0) cc_final: 0.6538 (tp30) REVERT: E 237 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5751 (tmtt) REVERT: E 241 LYS cc_start: 0.6925 (tptp) cc_final: 0.6302 (ttpp) REVERT: F 7 MET cc_start: 0.6286 (mtp) cc_final: 0.5823 (mpp) REVERT: F 33 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8381 (tpt) REVERT: F 80 GLU cc_start: 0.7629 (tp30) cc_final: 0.6941 (mm-30) REVERT: F 96 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7475 (ttm110) REVERT: F 241 LYS cc_start: 0.6858 (tptp) cc_final: 0.6090 (mtmt) REVERT: G 7 MET cc_start: 0.6203 (mtp) cc_final: 0.5960 (mtp) REVERT: G 38 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: G 96 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7326 (ttm110) REVERT: G 161 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8354 (tttm) REVERT: G 237 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6125 (ttmt) REVERT: G 241 LYS cc_start: 0.6863 (tptp) cc_final: 0.6244 (mtmm) REVERT: H 7 MET cc_start: 0.6349 (mtp) cc_final: 0.5820 (mpp) REVERT: H 80 GLU cc_start: 0.7623 (tp30) cc_final: 0.6936 (mm-30) REVERT: H 96 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7482 (ttm110) REVERT: H 161 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8451 (mttp) outliers start: 28 outliers final: 21 residues processed: 307 average time/residue: 0.7014 time to fit residues: 235.6008 Evaluate side-chains 312 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 162 ASP 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 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 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 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 219 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.192178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118832 restraints weight = 17540.555| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.85 r_work: 0.3036 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18086 Z= 0.144 Angle : 0.642 6.403 24607 Z= 0.311 Chirality : 0.039 0.196 2728 Planarity : 0.005 0.048 2904 Dihedral : 8.559 56.113 2608 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.84 % Allowed : 16.18 % Favored : 81.98 % 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: 2.35 (0.19), residues: 2016 helix: 2.16 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 105 TYR 0.011 0.002 TYR F 34 PHE 0.024 0.001 PHE E 211 TRP 0.053 0.003 TRP C 217 HIS 0.003 0.001 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (18072) covalent geometry : angle 0.64162 / 0.31 (24568) SS BOND : bond 0.00531 / 0.30 ( 14) SS BOND : angle 0.82724 / 0.51 ( 39) hydrogen bonds : bond 0.04743 / 3.00 ( 1224) hydrogen bonds : angle 4.00403 / 2.77 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7827.88 seconds wall clock time: 133 minutes 41.75 seconds (8021.75 seconds total)