Starting phenix.real_space_refine on Sun Oct 25 17:07:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lmt_0919/10_2026/6lmt_0919.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmt_0919/10_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6lmt_0919/10_2026/6lmt_0919.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lmt_0919/10_2026/6lmt_0919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lmt_0919/10_2026/6lmt_0919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmt_0919/10_2026/6lmt_0919.map" model { file = "/net/cci-nas-00/data/ceres_data/6lmt_0919/10_2026/6lmt_0919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmt_0919/10_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-2.3rc1-6221/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: 3.62, per 1000 atoms: 0.21 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=16, 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 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 D 41 " - pdb=" SG CYS D 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.01 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.01 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.01 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.01 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 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: 1.54 Conformation dependent library (CDL) restraints added in 688.2 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: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 91 through 106 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE B 164 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B 250 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.681A pdb=" N LEU C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE C 164 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE C 239 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 91 through 106 Processing helix chain 'D' and resid 107 through 121 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE D 164 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE D 239 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN D 250 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 20 through 37 removed outlier: 3.947A pdb=" N GLY E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 91 through 106 Processing helix chain 'E' and resid 107 through 121 Processing helix chain 'E' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.622A pdb=" N PHE E 164 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 203 Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 209 through 259 removed outlier: 3.759A pdb=" N PHE E 239 " --> pdb=" O HIS E 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 14 Processing helix chain 'F' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 91 through 106 Processing helix chain 'F' and resid 107 through 121 Processing helix chain 'F' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE F 164 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 203 Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE F 239 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 14 Processing helix chain 'G' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 91 through 106 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 132 No H-bonds generated for 'chain 'G' and resid 130 through 132' Processing helix chain 'G' and resid 133 through 137 Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE G 164 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 203 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE G 239 " --> pdb=" O HIS G 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN G 250 " --> pdb=" O GLN G 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN G 257 " --> pdb=" O GLY G 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 14 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY H 24 " --> pdb=" O ASN H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 Processing helix chain 'H' and resid 91 through 106 Processing helix chain 'H' and resid 107 through 121 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'H' and resid 133 through 137 Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE H 164 " --> pdb=" O LYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 203 Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'H' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE H 239 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN H 250 " --> pdb=" O GLN H 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN H 257 " --> pdb=" O GLY H 253 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.02 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: 9872 16.32 - 32.64: 440 32.64 - 48.95: 120 48.95 - 65.27: 48 65.27 - 81.59: 8 Dihedral angle restraints: 10488 sinusoidal: 4504 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 10485 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: 2.41 - 2.91: 6367 2.91 - 3.41: 16743 3.41 - 3.90: 29038 3.90 - 4.40: 34172 4.40 - 4.90: 56210 Nonbonded interactions: 142530 Sorted by model distance: 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 nonbonded pdb=" O ASN B 72 " pdb=" NH2 ARG B 225 " model vdw 2.409 3.120 nonbonded pdb=" O ASN E 72 " pdb=" NH2 ARG E 225 " model vdw 2.409 3.120 ... (remaining 142525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 403) selection = (chain 'B' and resid 7 through 403) selection = (chain 'C' and resid 7 through 403) selection = (chain 'D' and resid 7 through 403) selection = (chain 'E' and resid 7 through 403) selection = (chain 'F' and resid 7 through 403) selection = (chain 'G' and resid 7 through 403) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.980 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- 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 18088 Z= 0.483 Angle : 1.142 15.192 24600 Z= 0.579 Chirality : 0.063 0.280 2728 Planarity : 0.008 0.057 2904 Dihedral : 11.630 81.587 6552 Min Nonbonded Distance : 2.409 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 / 0.88 ( 16) SS BOND : angle 3.10075 / 1.92 ( 32) 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 : 0.656 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: 0.8227 time to fit residues: 368.2149 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 : 0.649 ------------------------------------------------------------------------------- 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: [98, 194, 107, 10, 66, 130, 124, 103, 77, 122, 91] 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 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 HIS ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 235 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 HIS ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 235 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 HIS ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 235 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.192243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119246 restraints weight = 17588.712| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.85 r_work: 0.3051 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18088 Z= 0.161 Angle : 0.732 14.711 24600 Z= 0.354 Chirality : 0.041 0.252 2728 Planarity : 0.006 0.048 2904 Dihedral : 9.731 58.152 2612 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 9.04 % Favored : 89.01 % 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: -0.16 (0.17), residues: 2016 helix: 0.36 (0.12), residues: 1512 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 203 TYR 0.016 0.002 TYR B 216 PHE 0.015 0.002 PHE D 137 TRP 0.021 0.003 TRP E 217 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (18072) covalent geometry : angle 0.73103 / 0.35 (24568) SS BOND : bond 0.00555 / 0.31 ( 16) SS BOND : angle 1.12454 / 0.69 ( 32) hydrogen bonds : bond 0.06335 / 4.03 ( 1224) hydrogen bonds : angle 4.50117 / 3.11 ( 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 353 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 318 time to evaluate : 0.683 Fit side-chains REVERT: A 7 MET cc_start: 0.6383 (mtp) cc_final: 0.6086 (mtp) REVERT: A 228 PHE cc_start: 0.7623 (t80) cc_final: 0.7030 (t80) REVERT: A 241 LYS cc_start: 0.7127 (tptp) cc_final: 0.6605 (mttt) REVERT: B 7 MET cc_start: 0.6217 (mtp) cc_final: 0.5875 (mtp) REVERT: B 96 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7322 (ttm110) REVERT: B 105 ARG cc_start: 0.8079 (mtm110) cc_final: 0.7839 (mtp-110) REVERT: B 241 LYS cc_start: 0.7004 (tptp) cc_final: 0.6413 (mtmm) REVERT: C 7 MET cc_start: 0.6322 (mtp) cc_final: 0.6060 (mtp) REVERT: C 228 PHE cc_start: 0.7626 (t80) cc_final: 0.7029 (t80) REVERT: C 237 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6294 (ttmt) REVERT: C 241 LYS cc_start: 0.7016 (tptp) cc_final: 0.6573 (mtmm) REVERT: D 7 MET cc_start: 0.6250 (mtp) cc_final: 0.5910 (mtp) REVERT: D 96 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7315 (ttm110) REVERT: D 105 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7833 (mtp-110) REVERT: D 241 LYS cc_start: 0.7051 (tptp) cc_final: 0.6476 (mtmm) REVERT: E 7 MET cc_start: 0.6349 (mtp) cc_final: 0.6054 (mtp) REVERT: E 228 PHE cc_start: 0.7643 (t80) cc_final: 0.7052 (t80) REVERT: E 237 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6301 (ttmt) REVERT: E 241 LYS cc_start: 0.7001 (tptp) cc_final: 0.6565 (mtmm) REVERT: F 96 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7317 (ttm110) REVERT: F 105 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7850 (mtp-110) REVERT: F 228 PHE cc_start: 0.7454 (t80) cc_final: 0.7130 (t80) REVERT: F 241 LYS cc_start: 0.6875 (tptp) cc_final: 0.6305 (mtmm) REVERT: G 7 MET cc_start: 0.6363 (mtp) cc_final: 0.6065 (mtp) REVERT: G 228 PHE cc_start: 0.7615 (t80) cc_final: 0.7017 (t80) REVERT: G 241 LYS cc_start: 0.7113 (tptp) cc_final: 0.6590 (mttt) REVERT: H 7 MET cc_start: 0.6217 (mtp) cc_final: 0.5875 (mtp) REVERT: H 96 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7326 (ttm110) REVERT: H 105 ARG cc_start: 0.8085 (mtm110) cc_final: 0.7847 (mtp-110) REVERT: H 228 PHE cc_start: 0.7452 (t80) cc_final: 0.7134 (t80) outliers start: 35 outliers final: 14 residues processed: 333 average time/residue: 0.7277 time to fit residues: 265.0076 Evaluate side-chains 288 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [145, 148, 65, 114, 85, 96, 106, 83, 64, 8, 26] chunk 145 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.190943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123027 restraints weight = 17794.305| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.32 r_work: 0.3035 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18088 Z= 0.165 Angle : 0.661 7.231 24600 Z= 0.323 Chirality : 0.041 0.238 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.242 57.870 2608 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.68 % Allowed : 11.83 % Favored : 85.49 % 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: 1.21 (0.18), residues: 2016 helix: 1.46 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.15 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 83 TYR 0.014 0.002 TYR D 34 PHE 0.019 0.002 PHE H 211 TRP 0.019 0.003 TRP E 217 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (18072) covalent geometry : angle 0.66044 / 0.32 (24568) SS BOND : bond 0.00580 / 0.32 ( 16) SS BOND : angle 1.20828 / 0.73 ( 32) hydrogen bonds : bond 0.05839 / 3.69 ( 1224) hydrogen bonds : angle 4.26164 / 2.94 ( 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: 48 poor density : 287 time to evaluate : 0.646 Fit side-chains REVERT: A 7 MET cc_start: 0.6264 (mtp) cc_final: 0.5877 (mtp) REVERT: A 227 MET cc_start: 0.7644 (mtm) cc_final: 0.7427 (mtm) REVERT: A 228 PHE cc_start: 0.7438 (t80) cc_final: 0.6830 (t80) REVERT: A 237 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6150 (ttmt) REVERT: A 241 LYS cc_start: 0.7041 (tptp) cc_final: 0.6522 (mtmm) REVERT: B 219 HIS cc_start: 0.7661 (m-70) cc_final: 0.7448 (m170) REVERT: B 241 LYS cc_start: 0.6983 (tptp) cc_final: 0.6386 (mtmt) REVERT: C 7 MET cc_start: 0.6180 (mtp) cc_final: 0.5860 (mtp) REVERT: C 38 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: C 228 PHE cc_start: 0.7476 (t80) cc_final: 0.6766 (t80) REVERT: C 237 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6153 (ttmt) REVERT: C 241 LYS cc_start: 0.6998 (tptp) cc_final: 0.6523 (mtmm) REVERT: D 215 LYS cc_start: 0.7856 (ttmm) cc_final: 0.7591 (ttmm) REVERT: D 241 LYS cc_start: 0.6991 (tptp) cc_final: 0.6390 (mtmt) REVERT: E 7 MET cc_start: 0.6219 (mtp) cc_final: 0.5831 (mtp) REVERT: E 38 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: E 228 PHE cc_start: 0.7490 (t80) cc_final: 0.6774 (t80) REVERT: E 237 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6150 (ttmt) REVERT: E 241 LYS cc_start: 0.7026 (tptp) cc_final: 0.6556 (mtmm) REVERT: F 215 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7599 (ttmm) REVERT: F 241 LYS cc_start: 0.6996 (tptp) cc_final: 0.6354 (mtmm) REVERT: G 7 MET cc_start: 0.6263 (mtp) cc_final: 0.5878 (mtp) REVERT: G 228 PHE cc_start: 0.7459 (t80) cc_final: 0.6846 (t80) REVERT: G 237 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6138 (ttmt) REVERT: G 241 LYS cc_start: 0.7040 (tptp) cc_final: 0.6537 (mtmm) REVERT: H 219 HIS cc_start: 0.7641 (m-70) cc_final: 0.7423 (m170) outliers start: 48 outliers final: 23 residues processed: 305 average time/residue: 0.7103 time to fit residues: 237.7005 Evaluate side-chains 311 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain 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 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: [91, 160, 147, 94, 61, 90, 123, 155, 37, 36, 71] chunk 91 optimal weight: 0.3980 chunk 160 optimal weight: 0.1980 chunk 147 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 0.0670 chunk 123 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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** 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** ** 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 = 0.4149 r_free = 0.4149 target = 0.193842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121285 restraints weight = 17744.611| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.84 r_work: 0.3083 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18088 Z= 0.129 Angle : 0.592 7.309 24600 Z= 0.294 Chirality : 0.039 0.232 2728 Planarity : 0.005 0.047 2904 Dihedral : 8.387 56.213 2608 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.85 % Allowed : 13.45 % 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: 2.03 (0.19), residues: 2016 helix: 2.05 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.86 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 83 TYR 0.010 0.002 TYR C 97 PHE 0.010 0.001 PHE F 211 TRP 0.013 0.002 TRP E 217 HIS 0.003 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (18072) covalent geometry : angle 0.59104 / 0.29 (24568) SS BOND : bond 0.00357 / 0.20 ( 16) SS BOND : angle 0.88589 / 0.54 ( 32) hydrogen bonds : bond 0.04939 / 3.11 ( 1224) hydrogen bonds : angle 4.03327 / 2.79 ( 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 339 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.654 Fit side-chains REVERT: A 227 MET cc_start: 0.7454 (mtm) cc_final: 0.7191 (mtm) REVERT: A 228 PHE cc_start: 0.7343 (t80) cc_final: 0.6713 (t80) REVERT: A 237 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5994 (ttmt) REVERT: A 241 LYS cc_start: 0.7022 (tptp) cc_final: 0.6481 (mtmm) REVERT: B 7 MET cc_start: 0.6276 (mtp) cc_final: 0.5697 (mpp) REVERT: B 96 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7355 (ttm110) REVERT: B 219 HIS cc_start: 0.7635 (m-70) cc_final: 0.7419 (m170) REVERT: B 231 THR cc_start: 0.8083 (m) cc_final: 0.7806 (t) REVERT: B 241 LYS cc_start: 0.7037 (tptp) cc_final: 0.6373 (mtmm) REVERT: C 7 MET cc_start: 0.6189 (mtp) cc_final: 0.5916 (mtp) REVERT: C 237 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.5991 (ttmt) REVERT: C 241 LYS cc_start: 0.7003 (tptp) cc_final: 0.6536 (mttt) REVERT: D 7 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5754 (mpp) REVERT: D 96 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7364 (ttm110) REVERT: D 215 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7508 (ttmm) REVERT: D 219 HIS cc_start: 0.7594 (m-70) cc_final: 0.7348 (m170) REVERT: D 241 LYS cc_start: 0.7040 (tptp) cc_final: 0.6373 (mtmm) REVERT: E 237 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5978 (ttmt) REVERT: E 241 LYS cc_start: 0.7025 (tptp) cc_final: 0.6517 (mttp) REVERT: F 7 MET cc_start: 0.6309 (mtp) cc_final: 0.5793 (mpp) REVERT: F 96 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7364 (ttm110) REVERT: F 215 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7521 (ttmm) REVERT: F 219 HIS cc_start: 0.7610 (m-70) cc_final: 0.7366 (m170) REVERT: F 241 LYS cc_start: 0.6973 (tptp) cc_final: 0.6330 (mtmt) REVERT: G 237 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6026 (ttmt) REVERT: G 241 LYS cc_start: 0.7025 (tptp) cc_final: 0.6470 (mtmm) REVERT: H 7 MET cc_start: 0.6301 (mtp) cc_final: 0.5717 (mpp) REVERT: H 96 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7372 (ttm110) REVERT: H 219 HIS cc_start: 0.7636 (m-70) cc_final: 0.7417 (m170) REVERT: H 231 THR cc_start: 0.8092 (m) cc_final: 0.7843 (t) outliers start: 51 outliers final: 25 residues processed: 312 average time/residue: 0.6968 time to fit residues: 239.0865 Evaluate side-chains 305 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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 7 MET 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 19 MET Chi-restraints excluded: chain G residue 28 LEU 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 162 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [113, 198, 8, 67, 108, 143, 72, 5, 102, 171, 132] chunk 113 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** 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** F 32 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 219 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.192154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118491 restraints weight = 17750.582| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.85 r_work: 0.3044 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18088 Z= 0.152 Angle : 0.640 6.888 24600 Z= 0.311 Chirality : 0.040 0.224 2728 Planarity : 0.005 0.047 2904 Dihedral : 8.395 55.903 2608 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.23 % Allowed : 14.40 % Favored : 83.37 % 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: 2.08 (0.19), residues: 2016 helix: 2.05 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.71 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 105 TYR 0.013 0.002 TYR F 34 PHE 0.018 0.001 PHE G 211 TRP 0.024 0.003 TRP G 217 HIS 0.003 0.000 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (18072) covalent geometry : angle 0.63927 / 0.31 (24568) SS BOND : bond 0.00472 / 0.26 ( 16) SS BOND : angle 1.07748 / 0.66 ( 32) hydrogen bonds : bond 0.05100 / 3.22 ( 1224) hydrogen bonds : angle 4.03831 / 2.79 ( 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 327 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.640 Fit side-chains REVERT: A 38 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: A 227 MET cc_start: 0.7457 (mtm) cc_final: 0.7171 (mtm) REVERT: A 237 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6062 (ttmt) REVERT: A 241 LYS cc_start: 0.7054 (tptp) cc_final: 0.6536 (mtmm) REVERT: B 7 MET cc_start: 0.6276 (mtp) cc_final: 0.5664 (mpp) REVERT: B 33 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8513 (tpt) REVERT: B 96 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7326 (ttm110) REVERT: B 231 THR cc_start: 0.8087 (m) cc_final: 0.7810 (t) REVERT: B 241 LYS cc_start: 0.7031 (tptp) cc_final: 0.6381 (mtmt) REVERT: C 7 MET cc_start: 0.6123 (mtp) cc_final: 0.5855 (mtp) REVERT: C 38 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: C 237 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.6037 (ttmt) REVERT: C 241 LYS cc_start: 0.7011 (tptp) cc_final: 0.6525 (mtmm) REVERT: D 7 MET cc_start: 0.6334 (mtp) cc_final: 0.5819 (mpp) REVERT: D 96 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7332 (ttm110) REVERT: D 215 LYS cc_start: 0.7657 (ttmm) cc_final: 0.7449 (ttmm) REVERT: D 219 HIS cc_start: 0.7605 (m-70) cc_final: 0.7393 (m170) REVERT: D 241 LYS cc_start: 0.7034 (tptp) cc_final: 0.6382 (mtmt) REVERT: E 7 MET cc_start: 0.6116 (mtp) cc_final: 0.5783 (mtp) REVERT: E 38 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: E 83 ARG cc_start: 0.6592 (ptp-110) cc_final: 0.6375 (ptm160) REVERT: E 237 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6014 (ttmt) REVERT: E 241 LYS cc_start: 0.7021 (tptp) cc_final: 0.6537 (mtmm) REVERT: F 7 MET cc_start: 0.6470 (mtp) cc_final: 0.5934 (mpp) REVERT: F 96 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7328 (ttm110) REVERT: F 215 LYS cc_start: 0.7678 (ttmm) cc_final: 0.7471 (ttmm) REVERT: F 219 HIS cc_start: 0.7635 (m-70) cc_final: 0.7423 (m170) REVERT: F 241 LYS cc_start: 0.7014 (tptp) cc_final: 0.6336 (mtmt) REVERT: G 38 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: G 237 LYS cc_start: 0.6514 (OUTLIER) cc_final: 0.6056 (ttmt) REVERT: G 241 LYS cc_start: 0.7100 (tptp) cc_final: 0.6571 (mtmm) REVERT: H 7 MET cc_start: 0.6298 (mtp) cc_final: 0.5684 (mpp) REVERT: H 33 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8527 (tpt) REVERT: H 96 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7336 (ttm110) REVERT: H 231 THR cc_start: 0.8125 (m) cc_final: 0.7842 (t) outliers start: 40 outliers final: 14 residues processed: 305 average time/residue: 0.7403 time to fit residues: 246.9901 Evaluate side-chains 299 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 275 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 33 MET Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [80, 92, 35, 9, 99, 46, 60, 44, 114, 115, 129] chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4133 r_free = 0.4133 target = 0.191914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125117 restraints weight = 17586.231| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.66 r_work: 0.3045 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18088 Z= 0.150 Angle : 0.634 6.733 24600 Z= 0.309 Chirality : 0.040 0.217 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.400 55.419 2608 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.18 % Allowed : 14.45 % Favored : 83.37 % 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: 2.12 (0.19), residues: 2016 helix: 2.03 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.51 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.012 0.002 TYR F 34 PHE 0.016 0.001 PHE A 211 TRP 0.028 0.003 TRP E 217 HIS 0.002 0.000 HIS E 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (18072) covalent geometry : angle 0.63304 / 0.31 (24568) SS BOND : bond 0.00499 / 0.28 ( 16) SS BOND : angle 1.05450 / 0.64 ( 32) hydrogen bonds : bond 0.05050 / 3.19 ( 1224) hydrogen bonds : angle 4.01371 / 2.78 ( 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 328 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 289 time to evaluate : 0.643 Fit side-chains REVERT: A 7 MET cc_start: 0.6223 (mtp) cc_final: 0.5577 (mtt) REVERT: A 38 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: A 227 MET cc_start: 0.7369 (mtm) cc_final: 0.7156 (mtm) REVERT: A 237 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5903 (ttmt) REVERT: A 241 LYS cc_start: 0.7028 (tptp) cc_final: 0.6500 (mtmm) REVERT: B 7 MET cc_start: 0.6241 (mtp) cc_final: 0.5702 (mpp) REVERT: B 33 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8468 (tpt) REVERT: B 80 GLU cc_start: 0.7588 (tp30) cc_final: 0.6877 (mm-30) REVERT: B 96 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7337 (ttm110) REVERT: B 219 HIS cc_start: 0.7581 (m90) cc_final: 0.7375 (m170) REVERT: B 231 THR cc_start: 0.8078 (m) cc_final: 0.7800 (t) REVERT: B 241 LYS cc_start: 0.7010 (tptp) cc_final: 0.6288 (mtmt) REVERT: C 7 MET cc_start: 0.6240 (mtp) cc_final: 0.5980 (mtp) REVERT: C 38 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: C 237 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5937 (ttmt) REVERT: C 241 LYS cc_start: 0.6960 (tptp) cc_final: 0.6434 (mtmm) REVERT: D 7 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5809 (mpp) REVERT: D 96 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7343 (ttm110) REVERT: D 219 HIS cc_start: 0.7518 (m-70) cc_final: 0.7305 (m170) REVERT: D 241 LYS cc_start: 0.7012 (tptp) cc_final: 0.6268 (mtmt) REVERT: E 38 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: E 83 ARG cc_start: 0.6541 (ptp-110) cc_final: 0.6317 (ptm160) REVERT: E 223 ILE cc_start: 0.7793 (mm) cc_final: 0.7556 (mp) REVERT: E 227 MET cc_start: 0.7339 (mtp) cc_final: 0.7115 (mtm) REVERT: E 237 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5928 (ttmt) REVERT: E 241 LYS cc_start: 0.6971 (tptp) cc_final: 0.6438 (mtmm) REVERT: F 7 MET cc_start: 0.6365 (mtp) cc_final: 0.5869 (mpp) REVERT: F 96 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7351 (ttm110) REVERT: F 219 HIS cc_start: 0.7519 (m-70) cc_final: 0.7304 (m170) REVERT: F 241 LYS cc_start: 0.6899 (tptp) cc_final: 0.6126 (mtmt) REVERT: G 7 MET cc_start: 0.6199 (mtp) cc_final: 0.5567 (mtt) REVERT: G 38 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: G 237 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5918 (ttmt) REVERT: G 241 LYS cc_start: 0.7016 (tptp) cc_final: 0.6506 (mtmm) REVERT: H 7 MET cc_start: 0.6254 (mtp) cc_final: 0.5713 (mpp) REVERT: H 33 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8449 (tpt) REVERT: H 96 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7355 (ttm110) REVERT: H 231 THR cc_start: 0.8080 (m) cc_final: 0.7788 (t) outliers start: 39 outliers final: 23 residues processed: 306 average time/residue: 0.7037 time to fit residues: 236.6008 Evaluate side-chains 310 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 A residue 248 PHE Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 MET Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [137, 87, 74, 42, 24, 60, 189, 106, 49, 177, 104] chunk 137 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.4107 r_free = 0.4107 target = 0.189191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121857 restraints weight = 17505.576| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.18 r_work: 0.3019 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 18088 Z= 0.204 Angle : 0.710 7.085 24600 Z= 0.338 Chirality : 0.044 0.222 2728 Planarity : 0.005 0.048 2904 Dihedral : 9.034 58.475 2608 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.96 % Allowed : 14.29 % Favored : 82.76 % 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: 1.83 (0.18), residues: 2016 helix: 1.80 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.57 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 96 TYR 0.014 0.003 TYR D 34 PHE 0.020 0.002 PHE B 137 TRP 0.034 0.003 TRP E 217 HIS 0.002 0.000 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.20 (18072) covalent geometry : angle 0.70881 / 0.34 (24568) SS BOND : bond 0.00648 / 0.36 ( 16) SS BOND : angle 1.32018 / 0.81 ( 32) hydrogen bonds : bond 0.05540 / 3.50 ( 1224) hydrogen bonds : angle 4.14080 / 2.86 ( 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 352 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 0.603 Fit side-chains REVERT: A 38 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: A 98 MET cc_start: 0.8341 (ttp) cc_final: 0.8125 (ttt) REVERT: A 215 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7462 (mtmm) REVERT: A 237 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6120 (ttmt) REVERT: A 241 LYS cc_start: 0.6947 (tptp) cc_final: 0.6291 (mtmm) REVERT: B 7 MET cc_start: 0.6267 (mtp) cc_final: 0.5773 (mpp) REVERT: B 33 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8449 (tpt) REVERT: B 96 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7492 (ttm110) REVERT: B 98 MET cc_start: 0.8431 (ttp) cc_final: 0.8179 (ttt) REVERT: B 241 LYS cc_start: 0.7060 (tptp) cc_final: 0.6345 (mtmt) REVERT: C 38 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: C 80 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: C 237 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6176 (ttmt) REVERT: C 241 LYS cc_start: 0.6961 (tptp) cc_final: 0.6334 (mtmm) REVERT: D 7 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6040 (mpp) REVERT: D 96 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7495 (ttm110) REVERT: D 98 MET cc_start: 0.8412 (ttp) cc_final: 0.8164 (ttt) REVERT: D 219 HIS cc_start: 0.7662 (m-70) cc_final: 0.7455 (m170) REVERT: D 241 LYS cc_start: 0.7054 (tptp) cc_final: 0.6295 (mttt) REVERT: E 38 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: E 83 ARG cc_start: 0.6627 (ptp-110) cc_final: 0.6414 (ptm160) REVERT: E 237 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6129 (ttmt) REVERT: E 241 LYS cc_start: 0.6942 (tptp) cc_final: 0.6278 (mtmt) REVERT: F 7 MET cc_start: 0.6412 (mtp) cc_final: 0.5935 (mpp) REVERT: F 33 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8384 (tpt) REVERT: F 96 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7501 (ttm110) REVERT: F 98 MET cc_start: 0.8435 (ttp) cc_final: 0.8184 (ttt) REVERT: F 219 HIS cc_start: 0.7678 (m-70) cc_final: 0.7476 (m170) REVERT: F 241 LYS cc_start: 0.6840 (tptp) cc_final: 0.6160 (mtmm) REVERT: G 38 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: G 237 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6098 (ttmt) REVERT: G 241 LYS cc_start: 0.7054 (tptp) cc_final: 0.6526 (mtmm) REVERT: H 7 MET cc_start: 0.6295 (mtp) cc_final: 0.5793 (mpp) REVERT: H 33 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8443 (tpt) REVERT: H 96 ARG cc_start: 0.7826 (mtm110) cc_final: 0.7488 (ttm110) REVERT: H 98 MET cc_start: 0.8420 (ttp) cc_final: 0.8167 (ttt) outliers start: 53 outliers final: 21 residues processed: 311 average time/residue: 0.6712 time to fit residues: 230.4031 Evaluate side-chains 320 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 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 28 LEU Chi-restraints excluded: chain B residue 33 MET 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 80 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 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 80 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 162 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [44, 172, 7, 89, 54, 176, 174, 59, 12, 147, 40] chunk 44 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 147 optimal weight: 5.9990 chunk 40 optimal weight: 0.0060 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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** F 32 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.193410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120351 restraints weight = 17506.488| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.82 r_work: 0.3070 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18088 Z= 0.131 Angle : 0.614 6.716 24600 Z= 0.300 Chirality : 0.039 0.210 2728 Planarity : 0.005 0.048 2904 Dihedral : 8.356 55.590 2608 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.12 % Allowed : 15.90 % 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: 2.32 (0.19), residues: 2016 helix: 2.18 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.45 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 170 TYR 0.012 0.002 TYR G 216 PHE 0.032 0.001 PHE A 211 TRP 0.025 0.003 TRP E 217 HIS 0.002 0.001 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (18072) covalent geometry : angle 0.61327 / 0.30 (24568) SS BOND : bond 0.00342 / 0.19 ( 16) SS BOND : angle 0.90688 / 0.57 ( 32) hydrogen bonds : bond 0.04660 / 2.94 ( 1224) hydrogen bonds : angle 3.97129 / 2.75 ( 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 320 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.483 Fit side-chains REVERT: A 96 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7303 (ttm110) REVERT: A 215 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7419 (mtmm) REVERT: A 237 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5988 (ttmt) REVERT: A 241 LYS cc_start: 0.6885 (tptp) cc_final: 0.6315 (mtmm) REVERT: B 7 MET cc_start: 0.6324 (mtp) cc_final: 0.5906 (mpp) REVERT: B 33 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8468 (tpt) REVERT: B 80 GLU cc_start: 0.7600 (tp30) cc_final: 0.6924 (mm-30) REVERT: B 96 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7348 (ttm110) REVERT: B 241 LYS cc_start: 0.7052 (tptp) cc_final: 0.6314 (ttpp) REVERT: C 7 MET cc_start: 0.6116 (mtp) cc_final: 0.5838 (mtp) REVERT: C 96 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7338 (ttm110) REVERT: C 237 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6005 (ttmt) REVERT: C 241 LYS cc_start: 0.6899 (tptp) cc_final: 0.6346 (mtmm) REVERT: D 7 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.6012 (mpp) REVERT: D 80 GLU cc_start: 0.7600 (tp30) cc_final: 0.6923 (mm-30) REVERT: D 96 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7348 (ttm110) REVERT: D 241 LYS cc_start: 0.7093 (tptp) cc_final: 0.6418 (mtmt) REVERT: E 83 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6406 (ptm160) REVERT: E 96 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7341 (ttm110) REVERT: E 223 ILE cc_start: 0.7723 (mm) cc_final: 0.7491 (mp) REVERT: E 237 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5997 (ttmt) REVERT: E 241 LYS cc_start: 0.6907 (tptp) cc_final: 0.6369 (mtmm) REVERT: F 7 MET cc_start: 0.6343 (mtp) cc_final: 0.5776 (mpp) REVERT: F 80 GLU cc_start: 0.7589 (tp30) cc_final: 0.6906 (mm-30) REVERT: F 96 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7352 (ttm110) REVERT: F 241 LYS cc_start: 0.6865 (tptp) cc_final: 0.6166 (mtmm) REVERT: G 7 MET cc_start: 0.6232 (mtp) cc_final: 0.5622 (mtt) REVERT: G 96 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7345 (ttm110) REVERT: G 231 THR cc_start: 0.8073 (m) cc_final: 0.7837 (t) REVERT: G 237 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5983 (ttmt) REVERT: G 241 LYS cc_start: 0.7030 (tptp) cc_final: 0.6473 (mtmm) REVERT: H 7 MET cc_start: 0.6336 (mtp) cc_final: 0.5914 (mpp) REVERT: H 33 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8366 (tpt) REVERT: H 80 GLU cc_start: 0.7610 (tp30) cc_final: 0.6926 (mm-30) REVERT: H 96 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7354 (ttm110) outliers start: 38 outliers final: 14 residues processed: 302 average time/residue: 0.6888 time to fit residues: 228.7542 Evaluate side-chains 295 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 33 MET Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 83 ARG 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 G residue 28 LEU 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 33 MET 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: [74, 120, 131, 16, 85, 152, 69, 83, 54, 62, 167] chunk 74 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** 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** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.192249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124802 restraints weight = 17552.624| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.65 r_work: 0.3043 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18088 Z= 0.148 Angle : 0.651 6.521 24600 Z= 0.315 Chirality : 0.040 0.207 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.473 55.913 2608 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.84 % Allowed : 16.41 % Favored : 81.75 % 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: 2.28 (0.18), residues: 2016 helix: 2.13 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.38 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.012 0.002 TYR D 34 PHE 0.025 0.001 PHE A 211 TRP 0.039 0.003 TRP E 217 HIS 0.002 0.000 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (18072) covalent geometry : angle 0.65041 / 0.32 (24568) SS BOND : bond 0.00545 / 0.30 ( 16) SS BOND : angle 0.99232 / 0.60 ( 32) hydrogen bonds : bond 0.04855 / 3.07 ( 1224) hydrogen bonds : angle 4.01512 / 2.78 ( 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 322 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.634 Fit side-chains REVERT: A 7 MET cc_start: 0.6288 (mtp) cc_final: 0.5604 (mtt) REVERT: A 38 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 161 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8303 (tttm) REVERT: A 215 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7398 (mtmm) REVERT: A 237 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5955 (ttmt) REVERT: A 241 LYS cc_start: 0.6768 (tptp) cc_final: 0.6174 (mtmt) REVERT: B 7 MET cc_start: 0.6142 (mtp) cc_final: 0.5747 (mpp) REVERT: B 33 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8456 (tpt) REVERT: B 80 GLU cc_start: 0.7562 (tp30) cc_final: 0.6895 (mm-30) REVERT: B 96 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7477 (ttm110) REVERT: B 241 LYS cc_start: 0.6923 (tptp) cc_final: 0.6189 (ttpp) REVERT: C 80 GLU cc_start: 0.7717 (tp30) cc_final: 0.6873 (mm-30) REVERT: C 215 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7459 (mtmt) REVERT: C 237 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5776 (tmtt) REVERT: C 241 LYS cc_start: 0.6765 (tptp) cc_final: 0.6188 (ttpp) REVERT: D 7 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5885 (mpp) REVERT: D 80 GLU cc_start: 0.7543 (tp30) cc_final: 0.6873 (mm-30) REVERT: D 96 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7478 (ttm110) REVERT: D 241 LYS cc_start: 0.6948 (tptp) cc_final: 0.6220 (ttpp) REVERT: E 83 ARG cc_start: 0.6589 (ptp-110) cc_final: 0.6369 (ptm160) REVERT: E 161 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8277 (tttm) REVERT: E 237 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5937 (ttmt) REVERT: E 241 LYS cc_start: 0.6872 (tptp) cc_final: 0.6236 (mtmt) REVERT: F 7 MET cc_start: 0.6344 (mtp) cc_final: 0.5745 (mpp) REVERT: F 80 GLU cc_start: 0.7550 (tp30) cc_final: 0.6881 (mm-30) REVERT: F 96 ARG cc_start: 0.7830 (mtm110) cc_final: 0.7486 (ttm110) REVERT: F 241 LYS cc_start: 0.6784 (tptp) cc_final: 0.6072 (mtmt) REVERT: G 7 MET cc_start: 0.6315 (mtp) cc_final: 0.5654 (mtt) REVERT: G 38 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: G 96 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7327 (ttm110) REVERT: G 161 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8304 (tttm) REVERT: G 215 LYS cc_start: 0.7540 (mtmt) cc_final: 0.7268 (mtmm) REVERT: G 237 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5947 (ttmt) REVERT: G 241 LYS cc_start: 0.6930 (tptp) cc_final: 0.6320 (mtmm) REVERT: H 7 MET cc_start: 0.6134 (mtp) cc_final: 0.5738 (mpp) REVERT: H 33 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8504 (tpt) REVERT: H 80 GLU cc_start: 0.7567 (tp30) cc_final: 0.6892 (mm-30) REVERT: H 96 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7485 (ttm110) REVERT: H 231 THR cc_start: 0.8066 (m) cc_final: 0.7806 (t) outliers start: 33 outliers final: 24 residues processed: 303 average time/residue: 0.6974 time to fit residues: 232.5414 Evaluate side-chains 320 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 33 MET 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 237 LYS Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 162 ASP 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 162 ASP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain G residue 248 PHE 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 Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [198, 89, 80, 99, 177, 96, 144, 183, 112, 40, 27] chunk 198 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 27 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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** ** 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** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 219 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126223 restraints weight = 17359.198| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.18 r_work: 0.3035 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18088 Z= 0.144 Angle : 0.641 6.588 24600 Z= 0.310 Chirality : 0.039 0.206 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.461 56.025 2608 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.45 % Allowed : 16.80 % Favored : 81.75 % 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: 2.38 (0.18), residues: 2016 helix: 2.17 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.26 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 200 TYR 0.012 0.002 TYR F 34 PHE 0.026 0.001 PHE A 211 TRP 0.033 0.003 TRP E 217 HIS 0.002 0.001 HIS H 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (18072) covalent geometry : angle 0.64073 / 0.31 (24568) SS BOND : bond 0.00538 / 0.29 ( 16) SS BOND : angle 0.95836 / 0.58 ( 32) hydrogen bonds : bond 0.04748 / 3.01 ( 1224) hydrogen bonds : angle 4.00700 / 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 331 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 305 time to evaluate : 0.687 Fit side-chains REVERT: A 7 MET cc_start: 0.6254 (mtp) cc_final: 0.5531 (mtt) REVERT: A 38 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: A 80 GLU cc_start: 0.7857 (tp30) cc_final: 0.6959 (mm-30) REVERT: A 96 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7312 (ttm110) REVERT: A 161 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8359 (tttm) REVERT: A 215 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7422 (mtmm) REVERT: A 234 GLU cc_start: 0.7244 (pt0) cc_final: 0.6560 (tp30) REVERT: A 237 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.6079 (ttmt) REVERT: A 241 LYS cc_start: 0.6887 (tptp) cc_final: 0.6287 (mtmm) REVERT: B 7 MET cc_start: 0.6152 (mtp) cc_final: 0.5810 (mpp) REVERT: B 33 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8562 (ttt) REVERT: B 80 GLU cc_start: 0.7631 (tp30) cc_final: 0.6998 (mm-30) REVERT: B 96 ARG cc_start: 0.7826 (mtm110) cc_final: 0.7497 (ttm110) REVERT: B 98 MET cc_start: 0.8308 (ttp) cc_final: 0.8061 (ttt) REVERT: B 241 LYS cc_start: 0.6910 (tptp) cc_final: 0.6279 (tmmt) REVERT: C 80 GLU cc_start: 0.7793 (tp30) cc_final: 0.6951 (mm-30) REVERT: C 96 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7305 (ttm110) REVERT: C 237 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.6148 (ttmt) REVERT: C 241 LYS cc_start: 0.6945 (tptp) cc_final: 0.6245 (mtmm) REVERT: D 7 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5799 (mpp) REVERT: D 80 GLU cc_start: 0.7654 (tp30) cc_final: 0.7017 (mm-30) REVERT: D 96 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7492 (ttm110) REVERT: D 98 MET cc_start: 0.8279 (ttp) cc_final: 0.8034 (ttt) REVERT: D 241 LYS cc_start: 0.7006 (tptp) cc_final: 0.6267 (ttpp) REVERT: E 80 GLU cc_start: 0.7775 (tp30) cc_final: 0.6827 (mm-30) REVERT: E 96 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7289 (ttm110) REVERT: E 234 GLU cc_start: 0.7224 (pt0) cc_final: 0.6529 (tp30) REVERT: E 237 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6053 (ttmt) REVERT: E 241 LYS cc_start: 0.7038 (tptp) cc_final: 0.6375 (mtmt) REVERT: F 7 MET cc_start: 0.6361 (mtp) cc_final: 0.5795 (mpp) REVERT: F 80 GLU cc_start: 0.7637 (tp30) cc_final: 0.6995 (mm-30) REVERT: F 96 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7492 (ttm110) REVERT: F 241 LYS cc_start: 0.6907 (tptp) cc_final: 0.6163 (mtmm) REVERT: G 7 MET cc_start: 0.6268 (mtp) cc_final: 0.5632 (mtt) REVERT: G 38 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: G 96 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7328 (ttm110) REVERT: G 161 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8351 (tttm) REVERT: G 215 LYS cc_start: 0.7537 (mtmt) cc_final: 0.7263 (mtmm) REVERT: G 237 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6094 (ttmt) REVERT: G 241 LYS cc_start: 0.6956 (tptp) cc_final: 0.6351 (mtmm) REVERT: H 7 MET cc_start: 0.6141 (mtp) cc_final: 0.5799 (mpp) REVERT: H 33 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8549 (tpt) REVERT: H 80 GLU cc_start: 0.7623 (tp30) cc_final: 0.6975 (mm-30) REVERT: H 96 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7503 (ttm110) REVERT: H 98 MET cc_start: 0.8305 (ttp) cc_final: 0.8057 (ttt) REVERT: H 231 THR cc_start: 0.8110 (m) cc_final: 0.7871 (t) outliers start: 26 outliers final: 24 residues processed: 318 average time/residue: 0.7150 time to fit residues: 249.1338 Evaluate side-chains 329 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 296 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 33 MET 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 162 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 162 ASP 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 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 33 MET Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: [107, 65, 38, 62, 143, 2, 55, 159, 136, 182, 94] chunk 107 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** C 104 GLN ** 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** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 219 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.191865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118171 restraints weight = 17537.970| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.85 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18088 Z= 0.151 Angle : 0.654 6.608 24600 Z= 0.316 Chirality : 0.040 0.205 2728 Planarity : 0.004 0.048 2904 Dihedral : 8.539 56.059 2608 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.51 % Allowed : 17.35 % Favored : 81.14 % 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: 2.39 (0.18), residues: 2016 helix: 2.16 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.22 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.013 0.002 TYR D 34 PHE 0.025 0.001 PHE A 211 TRP 0.038 0.003 TRP E 217 HIS 0.002 0.001 HIS D 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (18072) covalent geometry : angle 0.65354 / 0.32 (24568) SS BOND : bond 0.00570 / 0.31 ( 16) SS BOND : angle 0.98888 / 0.60 ( 32) hydrogen bonds : bond 0.04817 / 3.05 ( 1224) hydrogen bonds : angle 4.02115 / 2.78 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7848.57 seconds wall clock time: 133 minutes 59.32 seconds (8039.32 seconds total)