Starting phenix.real_space_refine on Sat Feb 7 21:03:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v7l_64817/02_2026/9v7l_64817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v7l_64817/02_2026/9v7l_64817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v7l_64817/02_2026/9v7l_64817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v7l_64817/02_2026/9v7l_64817.map" model { file = "/net/cci-nas-00/data/ceres_data/9v7l_64817/02_2026/9v7l_64817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v7l_64817/02_2026/9v7l_64817.cif" } resolution = 3.76 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= 0.003 sd= 0.031 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 153 5.16 5 C 22964 2.51 5 N 6286 2.21 5 O 7037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36440 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1717 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "Z" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "B" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "D" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "E" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "G" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "H" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "I" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "J" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "K" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "L" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "M" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2173 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain: "N" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "O" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "P" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "Q" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "R" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "S" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "T" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "U" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "V" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "W" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "X" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "Y" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1293 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 167} Chain: "a" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1243 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.22, per 1000 atoms: 0.25 Number of scatterers: 36440 At special positions: 0 Unit cell: (137.5, 130, 147.5, 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 153 16.00 O 7037 8.00 N 6286 7.00 C 22964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=36, symmetry=0 Number of additional bonds: simple=36, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8512 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 2 sheets defined 83.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.845A pdb=" N ALA A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 151 through 162 removed outlier: 4.640A pdb=" N ALA A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.715A pdb=" N ILE A 197 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.522A pdb=" N GLU A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'Z' and resid 49 through 62 removed outlier: 3.944A pdb=" N LEU Z 53 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) Proline residue: Z 54 - end of helix Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 20 through 63 removed outlier: 4.614A pdb=" N ASN B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 153 through 172 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 20 through 63 removed outlier: 3.519A pdb=" N LEU C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 75 through 100 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 123 through 142 removed outlier: 4.103A pdb=" N TYR C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 141 " --> pdb=" O LYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 3.533A pdb=" N LEU C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 20 through 63 removed outlier: 4.598A pdb=" N ASN D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA D 49 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 102 through 109 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 123 through 144 Processing helix chain 'D' and resid 153 through 172 Processing helix chain 'E' and resid 3 through 16 Processing helix chain 'E' and resid 20 through 63 removed outlier: 3.505A pdb=" N LEU E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 75 through 100 removed outlier: 3.501A pdb=" N GLN E 79 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 112 through 121 Processing helix chain 'E' and resid 123 through 142 removed outlier: 4.099A pdb=" N TYR E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 140 " --> pdb=" O GLY E 136 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 162 removed outlier: 3.536A pdb=" N LEU E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 16 Processing helix chain 'F' and resid 20 through 63 removed outlier: 4.642A pdb=" N ASN F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU F 50 " --> pdb=" O GLY F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 75 through 100 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'F' and resid 123 through 144 Processing helix chain 'F' and resid 153 through 172 Processing helix chain 'G' and resid 3 through 16 Processing helix chain 'G' and resid 20 through 63 removed outlier: 3.508A pdb=" N LEU G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP G 49 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N SER G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 75 through 100 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 123 through 142 removed outlier: 4.109A pdb=" N TYR G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 162 removed outlier: 3.538A pdb=" N LEU G 147 " --> pdb=" O SER G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 16 Processing helix chain 'H' and resid 20 through 63 removed outlier: 4.613A pdb=" N ASN H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALA H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU H 50 " --> pdb=" O GLY H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 75 through 100 Processing helix chain 'H' and resid 102 through 109 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'H' and resid 123 through 144 Processing helix chain 'H' and resid 153 through 172 Processing helix chain 'I' and resid 3 through 16 Processing helix chain 'I' and resid 20 through 63 removed outlier: 3.517A pdb=" N LEU I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER I 50 " --> pdb=" O SER I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 75 through 100 Processing helix chain 'I' and resid 102 through 109 Processing helix chain 'I' and resid 112 through 121 Processing helix chain 'I' and resid 123 through 142 removed outlier: 4.102A pdb=" N TYR I 127 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER I 140 " --> pdb=" O GLY I 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN I 141 " --> pdb=" O LYS I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 162 removed outlier: 3.536A pdb=" N LEU I 147 " --> pdb=" O SER I 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 16 Processing helix chain 'J' and resid 20 through 63 removed outlier: 4.606A pdb=" N ASN J 35 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS J 36 " --> pdb=" O LYS J 32 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA J 49 " --> pdb=" O THR J 45 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU J 50 " --> pdb=" O GLY J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 109 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 123 through 144 Processing helix chain 'J' and resid 153 through 172 Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 20 through 63 removed outlier: 3.508A pdb=" N LEU K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA K 26 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR K 35 " --> pdb=" O PHE K 31 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER K 50 " --> pdb=" O SER K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 68 Processing helix chain 'K' and resid 75 through 100 Processing helix chain 'K' and resid 102 through 109 Processing helix chain 'K' and resid 112 through 121 Processing helix chain 'K' and resid 123 through 142 removed outlier: 4.113A pdb=" N TYR K 127 " --> pdb=" O SER K 123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER K 140 " --> pdb=" O GLY K 136 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN K 141 " --> pdb=" O LYS K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 162 removed outlier: 3.535A pdb=" N LEU K 147 " --> pdb=" O SER K 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 20 through 63 removed outlier: 4.611A pdb=" N ASN L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS L 36 " --> pdb=" O LYS L 32 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA L 49 " --> pdb=" O THR L 45 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU L 50 " --> pdb=" O GLY L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 75 through 100 Processing helix chain 'L' and resid 102 through 109 Processing helix chain 'L' and resid 112 through 121 Processing helix chain 'L' and resid 123 through 144 Processing helix chain 'L' and resid 153 through 172 Processing helix chain 'M' and resid 48 through 62 removed outlier: 4.458A pdb=" N LEU M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA M 54 " --> pdb=" O ASP M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 87 removed outlier: 4.197A pdb=" N ILE M 87 " --> pdb=" O SER M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 115 Processing helix chain 'M' and resid 125 through 132 Processing helix chain 'M' and resid 138 through 149 Processing helix chain 'M' and resid 149 through 160 removed outlier: 4.439A pdb=" N PHE M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS M 159 " --> pdb=" O ARG M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 174 removed outlier: 4.092A pdb=" N GLU M 167 " --> pdb=" O ASN M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 195 removed outlier: 4.288A pdb=" N ILE M 184 " --> pdb=" O ASN M 180 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR M 193 " --> pdb=" O ASP M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.591A pdb=" N GLU M 199 " --> pdb=" O GLY M 195 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR M 203 " --> pdb=" O GLU M 199 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE M 204 " --> pdb=" O ILE M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 212 Processing helix chain 'M' and resid 231 through 242 removed outlier: 3.825A pdb=" N PHE M 235 " --> pdb=" O THR M 231 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN M 236 " --> pdb=" O VAL M 232 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE M 239 " --> pdb=" O PHE M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 270 removed outlier: 3.651A pdb=" N LEU M 266 " --> pdb=" O ASP M 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 20 through 33 removed outlier: 3.536A pdb=" N LEU N 24 " --> pdb=" O ASN N 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE N 31 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 63 removed outlier: 5.607A pdb=" N ASP N 49 " --> pdb=" O THR N 45 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER N 50 " --> pdb=" O SER N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 68 Processing helix chain 'N' and resid 75 through 100 Processing helix chain 'N' and resid 102 through 109 Processing helix chain 'N' and resid 112 through 121 Processing helix chain 'N' and resid 123 through 142 removed outlier: 4.097A pdb=" N TYR N 127 " --> pdb=" O SER N 123 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER N 140 " --> pdb=" O GLY N 136 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN N 141 " --> pdb=" O LYS N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 162 removed outlier: 3.535A pdb=" N LEU N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 20 through 63 removed outlier: 4.612A pdb=" N ASN O 35 " --> pdb=" O VAL O 31 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS O 36 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA O 49 " --> pdb=" O THR O 45 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU O 50 " --> pdb=" O GLY O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 75 through 100 Processing helix chain 'O' and resid 102 through 109 Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 123 through 144 Processing helix chain 'O' and resid 153 through 172 Processing helix chain 'P' and resid 3 through 16 Processing helix chain 'P' and resid 20 through 63 removed outlier: 3.531A pdb=" N LEU P 24 " --> pdb=" O ASN P 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA P 26 " --> pdb=" O THR P 22 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR P 35 " --> pdb=" O PHE P 31 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP P 49 " --> pdb=" O THR P 45 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER P 50 " --> pdb=" O SER P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 68 Processing helix chain 'P' and resid 75 through 100 Processing helix chain 'P' and resid 102 through 109 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'P' and resid 123 through 142 removed outlier: 4.106A pdb=" N TYR P 127 " --> pdb=" O SER P 123 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER P 140 " --> pdb=" O GLY P 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN P 141 " --> pdb=" O LYS P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 162 removed outlier: 3.533A pdb=" N LEU P 147 " --> pdb=" O SER P 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 Processing helix chain 'Q' and resid 20 through 63 removed outlier: 4.602A pdb=" N ASN Q 35 " --> pdb=" O VAL Q 31 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS Q 36 " --> pdb=" O LYS Q 32 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ALA Q 49 " --> pdb=" O THR Q 45 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU Q 50 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 68 Processing helix chain 'Q' and resid 75 through 100 Processing helix chain 'Q' and resid 102 through 109 Processing helix chain 'Q' and resid 112 through 121 Processing helix chain 'Q' and resid 123 through 144 Processing helix chain 'Q' and resid 153 through 172 Processing helix chain 'R' and resid 3 through 16 Processing helix chain 'R' and resid 20 through 63 removed outlier: 3.522A pdb=" N ALA R 26 " --> pdb=" O THR R 22 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA R 36 " --> pdb=" O GLN R 32 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP R 49 " --> pdb=" O THR R 45 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER R 50 " --> pdb=" O SER R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 68 Processing helix chain 'R' and resid 75 through 100 Processing helix chain 'R' and resid 102 through 109 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'R' and resid 123 through 142 removed outlier: 4.113A pdb=" N TYR R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER R 140 " --> pdb=" O GLY R 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN R 141 " --> pdb=" O LYS R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 162 removed outlier: 3.538A pdb=" N LEU R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 16 Processing helix chain 'S' and resid 20 through 63 removed outlier: 4.623A pdb=" N ASN S 35 " --> pdb=" O VAL S 31 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS S 36 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA S 49 " --> pdb=" O THR S 45 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU S 50 " --> pdb=" O GLY S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 68 Processing helix chain 'S' and resid 75 through 100 Processing helix chain 'S' and resid 102 through 109 Processing helix chain 'S' and resid 112 through 121 Processing helix chain 'S' and resid 123 through 144 Processing helix chain 'S' and resid 153 through 172 Processing helix chain 'T' and resid 3 through 16 Processing helix chain 'T' and resid 20 through 63 removed outlier: 3.513A pdb=" N LEU T 24 " --> pdb=" O ASN T 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA T 36 " --> pdb=" O GLN T 32 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP T 49 " --> pdb=" O THR T 45 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER T 50 " --> pdb=" O SER T 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 68 Processing helix chain 'T' and resid 75 through 100 Processing helix chain 'T' and resid 102 through 109 Processing helix chain 'T' and resid 112 through 121 Processing helix chain 'T' and resid 123 through 142 removed outlier: 4.103A pdb=" N TYR T 127 " --> pdb=" O SER T 123 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER T 140 " --> pdb=" O GLY T 136 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN T 141 " --> pdb=" O LYS T 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 162 removed outlier: 3.536A pdb=" N LEU T 147 " --> pdb=" O SER T 143 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 16 Processing helix chain 'U' and resid 20 through 63 removed outlier: 4.604A pdb=" N ASN U 35 " --> pdb=" O VAL U 31 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA U 49 " --> pdb=" O THR U 45 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU U 50 " --> pdb=" O GLY U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 68 Processing helix chain 'U' and resid 75 through 100 Processing helix chain 'U' and resid 102 through 109 Processing helix chain 'U' and resid 112 through 121 Processing helix chain 'U' and resid 123 through 144 Processing helix chain 'U' and resid 153 through 172 Processing helix chain 'V' and resid 3 through 16 Processing helix chain 'V' and resid 20 through 63 removed outlier: 3.510A pdb=" N LEU V 24 " --> pdb=" O ASN V 20 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR V 35 " --> pdb=" O PHE V 31 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA V 36 " --> pdb=" O GLN V 32 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP V 49 " --> pdb=" O THR V 45 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER V 50 " --> pdb=" O SER V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 68 Processing helix chain 'V' and resid 75 through 100 Processing helix chain 'V' and resid 102 through 109 Processing helix chain 'V' and resid 112 through 121 Processing helix chain 'V' and resid 123 through 142 removed outlier: 4.103A pdb=" N TYR V 127 " --> pdb=" O SER V 123 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER V 140 " --> pdb=" O GLY V 136 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN V 141 " --> pdb=" O LYS V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 162 removed outlier: 3.537A pdb=" N LEU V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 16 Processing helix chain 'W' and resid 20 through 63 removed outlier: 4.609A pdb=" N ASN W 35 " --> pdb=" O VAL W 31 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS W 36 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA W 49 " --> pdb=" O THR W 45 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU W 50 " --> pdb=" O GLY W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 68 Processing helix chain 'W' and resid 75 through 100 Processing helix chain 'W' and resid 102 through 109 Processing helix chain 'W' and resid 112 through 121 Processing helix chain 'W' and resid 123 through 144 Processing helix chain 'W' and resid 153 through 172 Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 20 through 63 removed outlier: 3.502A pdb=" N LEU X 24 " --> pdb=" O ASN X 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA X 26 " --> pdb=" O THR X 22 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR X 35 " --> pdb=" O PHE X 31 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA X 36 " --> pdb=" O GLN X 32 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP X 49 " --> pdb=" O THR X 45 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER X 50 " --> pdb=" O SER X 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 68 Processing helix chain 'X' and resid 75 through 100 Processing helix chain 'X' and resid 102 through 109 Processing helix chain 'X' and resid 112 through 121 Processing helix chain 'X' and resid 123 through 142 removed outlier: 4.124A pdb=" N TYR X 127 " --> pdb=" O SER X 123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER X 140 " --> pdb=" O GLY X 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN X 141 " --> pdb=" O LYS X 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 162 removed outlier: 3.539A pdb=" N LEU X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 16 Processing helix chain 'Y' and resid 20 through 63 removed outlier: 4.622A pdb=" N ASN Y 35 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS Y 36 " --> pdb=" O LYS Y 32 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA Y 49 " --> pdb=" O THR Y 45 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU Y 50 " --> pdb=" O GLY Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 68 Processing helix chain 'Y' and resid 75 through 100 Processing helix chain 'Y' and resid 102 through 109 Processing helix chain 'Y' and resid 112 through 121 Processing helix chain 'Y' and resid 123 through 144 Processing helix chain 'Y' and resid 153 through 172 Processing helix chain 'a' and resid 3 through 16 Processing helix chain 'a' and resid 20 through 33 removed outlier: 3.514A pdb=" N LEU a 24 " --> pdb=" O ASN a 20 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE a 31 " --> pdb=" O ALA a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 63 removed outlier: 5.609A pdb=" N ASP a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER a 50 " --> pdb=" O SER a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 68 Processing helix chain 'a' and resid 75 through 100 Processing helix chain 'a' and resid 102 through 109 Processing helix chain 'a' and resid 112 through 121 Processing helix chain 'a' and resid 123 through 142 removed outlier: 4.092A pdb=" N TYR a 127 " --> pdb=" O SER a 123 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER a 140 " --> pdb=" O GLY a 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN a 141 " --> pdb=" O LYS a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 162 removed outlier: 3.537A pdb=" N LEU a 147 " --> pdb=" O SER a 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 42 through 48 removed outlier: 6.076A pdb=" N ALA Z 20 " --> pdb=" O ILE Z 66 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE Z 66 " --> pdb=" O ALA Z 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 42 through 47 removed outlier: 6.757A pdb=" N THR M 20 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL M 66 " --> pdb=" O THR M 20 " (cutoff:3.500A) 2807 hydrogen bonds defined for protein. 8274 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: 7.00 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7144 1.33 - 1.45: 10185 1.45 - 1.58: 19497 1.58 - 1.70: 0 1.70 - 1.83: 243 Bond restraints: 37069 Sorted by residual: bond pdb=" C4A CYC X 201 " pdb=" CHB CYC X 201 " ideal model delta sigma weight residual 1.437 1.318 0.119 2.00e-02 2.50e+03 3.51e+01 bond pdb=" C4A CYC T 201 " pdb=" CHB CYC T 201 " ideal model delta sigma weight residual 1.437 1.322 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C4A CYC K 201 " pdb=" CHB CYC K 201 " ideal model delta sigma weight residual 1.437 1.324 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C4A CYC R 201 " pdb=" CHB CYC R 201 " ideal model delta sigma weight residual 1.437 1.328 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4A CYC a 201 " pdb=" CHB CYC a 201 " ideal model delta sigma weight residual 1.437 1.337 0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 37064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 48977 4.39 - 8.78: 1319 8.78 - 13.16: 78 13.16 - 17.55: 7 17.55 - 21.94: 3 Bond angle restraints: 50384 Sorted by residual: angle pdb=" C GLU Y 50 " pdb=" CA GLU Y 50 " pdb=" CB GLU Y 50 " ideal model delta sigma weight residual 110.96 132.90 -21.94 1.54e+00 4.22e-01 2.03e+02 angle pdb=" C GLU L 50 " pdb=" CA GLU L 50 " pdb=" CB GLU L 50 " ideal model delta sigma weight residual 110.96 132.84 -21.88 1.54e+00 4.22e-01 2.02e+02 angle pdb=" CD ARG G 17 " pdb=" NE ARG G 17 " pdb=" CZ ARG G 17 " ideal model delta sigma weight residual 124.40 141.70 -17.30 1.40e+00 5.10e-01 1.53e+02 angle pdb=" C ASN A 147 " pdb=" CA ASN A 147 " pdb=" CB ASN A 147 " ideal model delta sigma weight residual 110.79 93.90 16.89 1.66e+00 3.63e-01 1.04e+02 angle pdb=" CA ASP A 264 " pdb=" CB ASP A 264 " pdb=" CG ASP A 264 " ideal model delta sigma weight residual 112.60 120.94 -8.34 1.00e+00 1.00e+00 6.96e+01 ... (remaining 50379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 19995 17.89 - 35.78: 2317 35.78 - 53.67: 551 53.67 - 71.56: 147 71.56 - 89.45: 68 Dihedral angle restraints: 23078 sinusoidal: 9816 harmonic: 13262 Sorted by residual: dihedral pdb=" C GLU L 50 " pdb=" N GLU L 50 " pdb=" CA GLU L 50 " pdb=" CB GLU L 50 " ideal model delta harmonic sigma weight residual -122.60 -153.16 30.56 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" C GLU Y 50 " pdb=" N GLU Y 50 " pdb=" CA GLU Y 50 " pdb=" CB GLU Y 50 " ideal model delta harmonic sigma weight residual -122.60 -153.05 30.45 0 2.50e+00 1.60e-01 1.48e+02 dihedral pdb=" CD ARG F 84 " pdb=" NE ARG F 84 " pdb=" CZ ARG F 84 " pdb=" NH1 ARG F 84 " ideal model delta sinusoidal sigma weight residual 0.00 78.39 -78.39 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 23075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 5511 0.231 - 0.462: 50 0.462 - 0.693: 2 0.693 - 0.924: 0 0.924 - 1.155: 2 Chirality restraints: 5565 Sorted by residual: chirality pdb=" CA GLU L 50 " pdb=" N GLU L 50 " pdb=" C GLU L 50 " pdb=" CB GLU L 50 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" CA GLU Y 50 " pdb=" N GLU Y 50 " pdb=" C GLU Y 50 " pdb=" CB GLU Y 50 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CA GLN R 32 " pdb=" N GLN R 32 " pdb=" C GLN R 32 " pdb=" CB GLN R 32 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.79e+00 ... (remaining 5562 not shown) Planarity restraints: 6524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CYC X 201 " -0.103 2.00e-02 2.50e+03 2.28e-01 1.17e+03 pdb=" C2A CYC X 201 " -0.004 2.00e-02 2.50e+03 pdb=" C3A CYC X 201 " -0.080 2.00e-02 2.50e+03 pdb=" C4A CYC X 201 " 0.082 2.00e-02 2.50e+03 pdb=" CAA CYC X 201 " 0.420 2.00e-02 2.50e+03 pdb=" CHA CYC X 201 " -0.161 2.00e-02 2.50e+03 pdb=" CHB CYC X 201 " 0.309 2.00e-02 2.50e+03 pdb=" CMA CYC X 201 " -0.371 2.00e-02 2.50e+03 pdb=" NA CYC X 201 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CYC K 201 " -0.116 2.00e-02 2.50e+03 2.23e-01 1.11e+03 pdb=" C2A CYC K 201 " -0.004 2.00e-02 2.50e+03 pdb=" C3A CYC K 201 " -0.046 2.00e-02 2.50e+03 pdb=" C4A CYC K 201 " 0.114 2.00e-02 2.50e+03 pdb=" CAA CYC K 201 " 0.412 2.00e-02 2.50e+03 pdb=" CHA CYC K 201 " -0.275 2.00e-02 2.50e+03 pdb=" CHB CYC K 201 " 0.158 2.00e-02 2.50e+03 pdb=" CMA CYC K 201 " -0.363 2.00e-02 2.50e+03 pdb=" NA CYC K 201 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC F 202 " -0.032 2.00e-02 2.50e+03 2.12e-01 1.01e+03 pdb=" OB CYC F 202 " 0.246 2.00e-02 2.50e+03 pdb=" C1B CYC F 202 " -0.069 2.00e-02 2.50e+03 pdb=" C2B CYC F 202 " 0.068 2.00e-02 2.50e+03 pdb=" C3B CYC F 202 " -0.032 2.00e-02 2.50e+03 pdb=" C4B CYC F 202 " 0.050 2.00e-02 2.50e+03 pdb=" CAB CYC F 202 " -0.374 2.00e-02 2.50e+03 pdb=" CHB CYC F 202 " -0.230 2.00e-02 2.50e+03 pdb=" CMB CYC F 202 " 0.373 2.00e-02 2.50e+03 ... (remaining 6521 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 916 2.60 - 3.17: 39222 3.17 - 3.75: 57852 3.75 - 4.32: 85269 4.32 - 4.90: 132935 Nonbonded interactions: 316194 Sorted by model distance: nonbonded pdb=" O GLY M 135 " pdb=" OG SER M 136 " model vdw 2.020 3.040 nonbonded pdb=" OD1 ASP G 76 " pdb=" N THR G 77 " model vdw 2.126 3.120 nonbonded pdb=" OD1 ASP K 76 " pdb=" N THR K 77 " model vdw 2.126 3.120 nonbonded pdb=" OD1 ASP C 76 " pdb=" N THR C 77 " model vdw 2.126 3.120 nonbonded pdb=" OD1 ASP I 76 " pdb=" N THR I 77 " model vdw 2.127 3.120 ... (remaining 316189 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 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'a' } 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 group one per residue 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: 27.840 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: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.880 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.119 37105 Z= 0.603 Angle : 1.779 21.941 50384 Z= 1.134 Chirality : 0.078 1.155 5565 Planarity : 0.029 0.449 6524 Dihedral : 16.979 89.449 14566 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 2.83 % Allowed : 16.56 % Favored : 80.60 % Rotamer: Outliers : 1.84 % Allowed : 8.66 % Favored : 89.50 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.48 (0.09), residues: 4516 helix: -3.99 (0.05), residues: 3436 sheet: -0.58 (0.73), residues: 45 loop : -1.24 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.006 ARG I 30 TYR 0.061 0.008 TYR Q 117 PHE 0.058 0.008 PHE X 120 TRP 0.013 0.003 TRP Z 30 HIS 0.019 0.004 HIS T 88 Details of bonding type rmsd covalent geometry : bond 0.00950 (37069) covalent geometry : angle 1.77864 (50384) hydrogen bonds : bond 0.22078 ( 2807) hydrogen bonds : angle 9.96677 ( 8274) Misc. bond : bond 0.07147 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 407 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.4772 (ttp80) REVERT: D 162 THR cc_start: 0.8274 (p) cc_final: 0.8032 (p) REVERT: H 9 ILE cc_start: 0.3048 (mm) cc_final: 0.2769 (mm) REVERT: J 25 ASN cc_start: 0.6847 (m-40) cc_final: 0.6634 (m-40) REVERT: M 29 PRO cc_start: 0.8332 (OUTLIER) cc_final: 0.8058 (Cg_endo) REVERT: M 134 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7377 (m-40) REVERT: Q 113 LEU cc_start: 0.6952 (tp) cc_final: 0.6681 (tp) REVERT: a 4 VAL cc_start: 0.6599 (t) cc_final: 0.6379 (t) outliers start: 67 outliers final: 17 residues processed: 463 average time/residue: 0.2902 time to fit residues: 206.1181 Evaluate side-chains 251 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain M residue 29 PRO Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain Q residue 32 LYS Chi-restraints excluded: chain R residue 81 LYS Chi-restraints excluded: chain Y residue 166 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 30.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN Z 9 GLN ** Z 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 62 ASN C 21 ASN E 15 GLN E 61 ASN E 88 HIS F 2 GLN F 111 ASN F 132 GLN F 158 ASN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN J 2 GLN J 111 ASN J 158 ASN L 25 ASN L 26 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 GLN M 41 ASN N 28 ASN N 61 ASN Q 2 GLN Q 25 ASN R 15 GLN R 57 GLN R 61 ASN R 88 HIS S 2 GLN T 15 GLN T 28 ASN T 32 GLN T 88 HIS V 25 GLN W 2 GLN X 68 GLN X 88 HIS Y 25 ASN ** Y 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 111 ASN a 20 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.037281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.030342 restraints weight = 461470.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.031001 restraints weight = 320990.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.031455 restraints weight = 247887.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.031763 restraints weight = 206231.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.031979 restraints weight = 181251.599| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 37105 Z= 0.224 Angle : 0.809 9.792 50384 Z= 0.417 Chirality : 0.040 0.201 5565 Planarity : 0.007 0.175 6524 Dihedral : 11.224 159.086 6687 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.59 % Rotamer: Outliers : 1.65 % Allowed : 13.44 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.48 (0.11), residues: 4516 helix: -0.92 (0.08), residues: 3514 sheet: -0.12 (0.80), residues: 36 loop : -0.46 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 30 TYR 0.041 0.002 TYR Q 117 PHE 0.032 0.003 PHE L 164 TRP 0.012 0.001 TRP K 126 HIS 0.010 0.002 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00469 (37069) covalent geometry : angle 0.80887 (50384) hydrogen bonds : bond 0.05149 ( 2807) hydrogen bonds : angle 4.97878 ( 8274) Misc. bond : bond 0.00079 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 142 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: B 134 MET cc_start: 0.5334 (mmm) cc_final: 0.4971 (tpt) REVERT: D 86 MET cc_start: 0.9343 (mtp) cc_final: 0.9084 (mtm) REVERT: D 125 ARG cc_start: 0.8599 (ptm160) cc_final: 0.8376 (ptt180) REVERT: I 68 GLN cc_start: 0.8078 (pt0) cc_final: 0.7841 (pp30) REVERT: J 25 ASN cc_start: 0.9054 (m-40) cc_final: 0.8809 (m-40) REVERT: J 78 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7697 (mmm-85) REVERT: J 118 VAL cc_start: 0.7882 (t) cc_final: 0.7677 (t) REVERT: L 22 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8781 (pp30) REVERT: L 111 ASN cc_start: 0.9103 (t0) cc_final: 0.8536 (p0) REVERT: L 113 LEU cc_start: 0.8729 (tp) cc_final: 0.8334 (mt) REVERT: L 165 ASP cc_start: 0.9543 (m-30) cc_final: 0.9247 (m-30) REVERT: M 163 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8077 (p0) REVERT: P 72 MET cc_start: 0.0598 (tpp) cc_final: 0.0335 (ttp) REVERT: Q 79 MET cc_start: 0.7999 (tpp) cc_final: 0.7674 (tpp) REVERT: T 72 MET cc_start: 0.7152 (mtp) cc_final: 0.6891 (ttt) REVERT: U 86 MET cc_start: 0.9444 (mtt) cc_final: 0.9166 (ptp) REVERT: a 1 MET cc_start: 0.6858 (tmm) cc_final: 0.6250 (tmm) outliers start: 60 outliers final: 22 residues processed: 300 average time/residue: 0.2617 time to fit residues: 125.1965 Evaluate side-chains 219 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 133 HIS Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain Q residue 32 LYS Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain Y residue 111 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 393 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 448 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 398 optimal weight: 2.9990 chunk 418 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 129 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN Z 9 GLN C 133 HIS E 133 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 HIS ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 GLN K 61 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN M 192 GLN N 68 GLN N 133 HIS O 26 GLN O 132 GLN P 57 GLN P 61 ASN ** P 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 132 GLN T 151 ASN V 68 GLN ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 GLN X 61 ASN X 133 HIS Y 2 GLN Y 72 ASN a 68 GLN a 133 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.034996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.028145 restraints weight = 476388.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.028777 restraints weight = 327535.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.029181 restraints weight = 252409.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.029465 restraints weight = 211140.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.029651 restraints weight = 185934.079| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 37105 Z= 0.235 Angle : 0.760 16.879 50384 Z= 0.380 Chirality : 0.039 0.240 5565 Planarity : 0.006 0.073 6524 Dihedral : 10.799 172.674 6648 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Rotamer: Outliers : 2.28 % Allowed : 15.08 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.98 (0.12), residues: 4516 helix: 1.09 (0.08), residues: 3517 sheet: -0.12 (0.80), residues: 35 loop : -0.74 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 78 TYR 0.031 0.002 TYR A 123 PHE 0.023 0.003 PHE H 60 TRP 0.016 0.002 TRP a 126 HIS 0.007 0.002 HIS N 133 Details of bonding type rmsd covalent geometry : bond 0.00509 (37069) covalent geometry : angle 0.76034 (50384) hydrogen bonds : bond 0.04614 ( 2807) hydrogen bonds : angle 4.58319 ( 8274) Misc. bond : bond 0.00069 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 197 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: Z 9 GLN cc_start: 0.5574 (OUTLIER) cc_final: 0.4534 (mm110) REVERT: Z 52 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9340 (mt) REVERT: B 79 MET cc_start: 0.8118 (ttm) cc_final: 0.7587 (ptm) REVERT: D 1 MET cc_start: 0.6716 (mpp) cc_final: 0.6467 (mpp) REVERT: I 38 MET cc_start: 0.7634 (mtp) cc_final: 0.6928 (mtp) REVERT: J 25 ASN cc_start: 0.9198 (m-40) cc_final: 0.8955 (m-40) REVERT: J 60 PHE cc_start: 0.7965 (m-80) cc_final: 0.7692 (m-10) REVERT: J 134 MET cc_start: 0.8843 (mmm) cc_final: 0.7964 (tmm) REVERT: K 155 ASP cc_start: 0.9489 (m-30) cc_final: 0.9278 (t0) REVERT: L 86 MET cc_start: 0.9432 (ttt) cc_final: 0.9087 (ttt) REVERT: L 111 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8918 (t0) REVERT: L 165 ASP cc_start: 0.9461 (m-30) cc_final: 0.9234 (m-30) REVERT: a 1 MET cc_start: 0.6912 (tmm) cc_final: 0.5699 (tmm) REVERT: a 155 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8700 (m-30) outliers start: 83 outliers final: 41 residues processed: 263 average time/residue: 0.2395 time to fit residues: 103.9887 Evaluate side-chains 219 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 9 GLN Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 111 ASN Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 133 HIS Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 125 ARG Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 111 ASN Chi-restraints excluded: chain L residue 125 ARG Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain Q residue 114 LYS Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 61 ASN Chi-restraints excluded: chain a residue 155 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 101 optimal weight: 0.5980 chunk 359 optimal weight: 0.9980 chunk 365 optimal weight: 10.0000 chunk 333 optimal weight: 4.9990 chunk 421 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 197 optimal weight: 40.0000 chunk 157 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 257 GLN N 68 GLN O 111 ASN ** P 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 GLN X 57 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.034926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.028054 restraints weight = 473927.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.028699 restraints weight = 325486.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.029122 restraints weight = 248212.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.029398 restraints weight = 206902.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.029591 restraints weight = 182478.484| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 37105 Z= 0.156 Angle : 0.658 16.729 50384 Z= 0.322 Chirality : 0.036 0.211 5565 Planarity : 0.004 0.057 6524 Dihedral : 10.644 173.305 6638 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.86 % Favored : 98.05 % Rotamer: Outliers : 1.54 % Allowed : 16.31 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.21 (0.12), residues: 4516 helix: 2.02 (0.08), residues: 3531 sheet: 0.52 (0.90), residues: 28 loop : -0.56 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 30 TYR 0.019 0.001 TYR A 209 PHE 0.016 0.002 PHE O 60 TRP 0.010 0.001 TRP T 126 HIS 0.006 0.001 HIS Q 57 Details of bonding type rmsd covalent geometry : bond 0.00346 (37069) covalent geometry : angle 0.65834 (50384) hydrogen bonds : bond 0.03777 ( 2807) hydrogen bonds : angle 4.19803 ( 8274) Misc. bond : bond 0.00053 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 79 MET cc_start: 0.7747 (ttm) cc_final: 0.7072 (ptm) REVERT: B 134 MET cc_start: 0.6958 (tpp) cc_final: 0.6367 (mmt) REVERT: D 1 MET cc_start: 0.6624 (mpp) cc_final: 0.6408 (mpp) REVERT: D 52 ILE cc_start: 0.8903 (mt) cc_final: 0.8687 (mm) REVERT: F 86 MET cc_start: 0.8875 (ptp) cc_final: 0.8419 (mpp) REVERT: G 1 MET cc_start: 0.6772 (mmt) cc_final: 0.6358 (mmt) REVERT: H 134 MET cc_start: 0.8855 (mtp) cc_final: 0.8623 (mtp) REVERT: I 38 MET cc_start: 0.7678 (mtp) cc_final: 0.7101 (mtp) REVERT: J 25 ASN cc_start: 0.9184 (m-40) cc_final: 0.8944 (m-40) REVERT: J 134 MET cc_start: 0.8727 (mmm) cc_final: 0.8121 (tmm) REVERT: K 39 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9140 (mp0) REVERT: K 155 ASP cc_start: 0.9420 (m-30) cc_final: 0.9176 (t0) REVERT: L 1 MET cc_start: 0.3664 (mpp) cc_final: 0.3393 (pmm) REVERT: L 22 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8702 (pp30) REVERT: L 86 MET cc_start: 0.9268 (ttt) cc_final: 0.9007 (ttt) REVERT: L 165 ASP cc_start: 0.9460 (m-30) cc_final: 0.9230 (m-30) REVERT: M 245 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: P 38 MET cc_start: 0.9344 (ptp) cc_final: 0.9143 (ptp) REVERT: W 1 MET cc_start: 0.7263 (tpt) cc_final: 0.6026 (tmm) REVERT: Y 1 MET cc_start: 0.7808 (ppp) cc_final: 0.7589 (ppp) REVERT: a 1 MET cc_start: 0.6573 (tmm) cc_final: 0.5404 (tmm) outliers start: 56 outliers final: 28 residues processed: 243 average time/residue: 0.2424 time to fit residues: 96.7095 Evaluate side-chains 198 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain Q residue 114 LYS Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain V residue 5 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 186 optimal weight: 0.0980 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 439 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 334 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN F 2 GLN F 63 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 ASN T 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.034011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.027235 restraints weight = 479572.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.027868 restraints weight = 321730.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.028276 restraints weight = 245007.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.028530 restraints weight = 203264.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.028693 restraints weight = 180143.818| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.8824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 37105 Z= 0.184 Angle : 0.682 16.152 50384 Z= 0.335 Chirality : 0.037 0.171 5565 Planarity : 0.004 0.043 6524 Dihedral : 10.611 175.678 6638 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 1.81 % Allowed : 16.34 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.30 (0.12), residues: 4516 helix: 2.09 (0.08), residues: 3519 sheet: 0.23 (0.94), residues: 28 loop : -0.53 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 129 TYR 0.021 0.002 TYR G 65 PHE 0.026 0.002 PHE K 63 TRP 0.012 0.001 TRP R 126 HIS 0.005 0.001 HIS W 57 Details of bonding type rmsd covalent geometry : bond 0.00404 (37069) covalent geometry : angle 0.68209 (50384) hydrogen bonds : bond 0.03754 ( 2807) hydrogen bonds : angle 4.20468 ( 8274) Misc. bond : bond 0.00064 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 79 MET cc_start: 0.7751 (ttm) cc_final: 0.7181 (ptm) REVERT: B 134 MET cc_start: 0.7677 (tpp) cc_final: 0.7228 (mmm) REVERT: D 86 MET cc_start: 0.9227 (mtp) cc_final: 0.9015 (ptp) REVERT: F 86 MET cc_start: 0.8916 (ptp) cc_final: 0.8669 (mpp) REVERT: H 134 MET cc_start: 0.9180 (mtp) cc_final: 0.8829 (mtp) REVERT: I 38 MET cc_start: 0.8020 (mtp) cc_final: 0.7505 (mtp) REVERT: J 25 ASN cc_start: 0.9129 (m-40) cc_final: 0.8890 (m-40) REVERT: J 134 MET cc_start: 0.9140 (mmm) cc_final: 0.8616 (tmm) REVERT: K 39 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9168 (mp0) REVERT: L 1 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.5582 (pmm) REVERT: L 22 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9013 (pp30) REVERT: L 79 MET cc_start: 0.9461 (ttm) cc_final: 0.9237 (mtm) REVERT: L 86 MET cc_start: 0.9338 (ttt) cc_final: 0.8923 (ttm) REVERT: L 165 ASP cc_start: 0.9463 (m-30) cc_final: 0.9232 (m-30) REVERT: M 81 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6737 (p0) REVERT: P 38 MET cc_start: 0.9451 (ptp) cc_final: 0.9249 (ptp) REVERT: R 1 MET cc_start: 0.8796 (tpp) cc_final: 0.8594 (tpp) REVERT: U 86 MET cc_start: 0.9197 (mtp) cc_final: 0.8793 (mtp) REVERT: V 72 MET cc_start: 0.3855 (mmt) cc_final: 0.3539 (mmm) REVERT: Y 1 MET cc_start: 0.7722 (ppp) cc_final: 0.7470 (ppp) REVERT: a 1 MET cc_start: 0.6472 (tmm) cc_final: 0.5809 (tmm) outliers start: 66 outliers final: 43 residues processed: 238 average time/residue: 0.2296 time to fit residues: 90.5395 Evaluate side-chains 207 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain K residue 81 LYS Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 134 MET Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain Q residue 114 LYS Chi-restraints excluded: chain S residue 135 LYS Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain X residue 141 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 442 optimal weight: 10.0000 chunk 415 optimal weight: 3.9990 chunk 360 optimal weight: 0.0370 chunk 41 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 418 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 178 optimal weight: 0.0070 chunk 151 optimal weight: 30.0000 chunk 9 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN Q 63 GLN ** Q 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 25 GLN W 2 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.034904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.027957 restraints weight = 465103.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.028629 restraints weight = 312253.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.029075 restraints weight = 236525.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.029371 restraints weight = 195167.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.029569 restraints weight = 170950.949| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.8915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 37105 Z= 0.110 Angle : 0.634 15.235 50384 Z= 0.303 Chirality : 0.036 0.337 5565 Planarity : 0.003 0.040 6524 Dihedral : 10.390 176.843 6636 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 1.37 % Allowed : 16.89 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.84 (0.12), residues: 4516 helix: 2.43 (0.08), residues: 3531 sheet: -0.25 (0.85), residues: 28 loop : -0.17 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 125 TYR 0.023 0.001 TYR E 74 PHE 0.014 0.001 PHE O 60 TRP 0.009 0.001 TRP R 126 HIS 0.006 0.001 HIS W 57 Details of bonding type rmsd covalent geometry : bond 0.00241 (37069) covalent geometry : angle 0.63383 (50384) hydrogen bonds : bond 0.03241 ( 2807) hydrogen bonds : angle 3.98179 ( 8274) Misc. bond : bond 0.00029 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 MET cc_start: 0.7801 (ttm) cc_final: 0.7285 (ptm) REVERT: B 134 MET cc_start: 0.7525 (tpp) cc_final: 0.7020 (mmt) REVERT: D 79 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8122 (mmt) REVERT: E 68 GLN cc_start: 0.9517 (pm20) cc_final: 0.9311 (pm20) REVERT: F 78 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8469 (mmm-85) REVERT: F 79 MET cc_start: 0.8769 (tpp) cc_final: 0.8459 (mtt) REVERT: F 106 GLU cc_start: 0.8825 (pt0) cc_final: 0.8619 (tm-30) REVERT: G 156 TYR cc_start: 0.8675 (t80) cc_final: 0.8317 (t80) REVERT: H 134 MET cc_start: 0.9099 (mtp) cc_final: 0.8733 (mtp) REVERT: I 38 MET cc_start: 0.7922 (mtp) cc_final: 0.7437 (mtp) REVERT: J 25 ASN cc_start: 0.9246 (m-40) cc_final: 0.9027 (m-40) REVERT: J 78 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7757 (mmm-85) REVERT: J 134 MET cc_start: 0.9032 (mmm) cc_final: 0.8599 (tmm) REVERT: L 22 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9114 (pp30) REVERT: L 79 MET cc_start: 0.9425 (ttm) cc_final: 0.9214 (mtm) REVERT: L 86 MET cc_start: 0.9340 (ttt) cc_final: 0.9034 (ttm) REVERT: L 165 ASP cc_start: 0.9436 (m-30) cc_final: 0.9164 (m-30) REVERT: M 153 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9102 (mtmm) REVERT: M 238 MET cc_start: 0.8735 (tpp) cc_final: 0.8433 (tmm) REVERT: N 74 TYR cc_start: 0.9168 (t80) cc_final: 0.8957 (t80) REVERT: R 1 MET cc_start: 0.8865 (tpp) cc_final: 0.8640 (tpp) REVERT: S 79 MET cc_start: 0.8523 (ppp) cc_final: 0.8035 (ppp) REVERT: U 79 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8129 (mtt) REVERT: U 86 MET cc_start: 0.9079 (mtp) cc_final: 0.8616 (mtp) REVERT: V 72 MET cc_start: 0.3865 (mmt) cc_final: 0.3594 (mmm) REVERT: W 1 MET cc_start: 0.7272 (tpt) cc_final: 0.7039 (tmm) REVERT: W 134 MET cc_start: 0.8877 (mmm) cc_final: 0.8400 (mmm) REVERT: Y 1 MET cc_start: 0.7610 (ppp) cc_final: 0.7389 (ppp) REVERT: a 1 MET cc_start: 0.6392 (tmm) cc_final: 0.5539 (tmm) REVERT: a 155 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8560 (m-30) outliers start: 50 outliers final: 27 residues processed: 226 average time/residue: 0.2288 time to fit residues: 86.3693 Evaluate side-chains 201 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 79 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain U residue 26 GLN Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain a residue 155 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 79 optimal weight: 4.9990 chunk 314 optimal weight: 7.9990 chunk 369 optimal weight: 4.9990 chunk 212 optimal weight: 0.3980 chunk 406 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 373 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN C 21 ASN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** 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 = 0.3503 r_free = 0.3503 target = 0.033872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.027102 restraints weight = 482275.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.027729 restraints weight = 322361.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.028148 restraints weight = 244895.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.028420 restraints weight = 202533.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.028605 restraints weight = 178404.902| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.9388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 37105 Z= 0.170 Angle : 0.670 13.728 50384 Z= 0.326 Chirality : 0.037 0.265 5565 Planarity : 0.004 0.041 6524 Dihedral : 10.304 177.494 6634 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 1.37 % Allowed : 17.55 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.65 (0.12), residues: 4516 helix: 2.29 (0.08), residues: 3543 sheet: -0.05 (0.88), residues: 26 loop : -0.27 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 30 TYR 0.036 0.001 TYR M 179 PHE 0.036 0.002 PHE S 164 TRP 0.008 0.001 TRP R 126 HIS 0.004 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00373 (37069) covalent geometry : angle 0.67040 (50384) hydrogen bonds : bond 0.03483 ( 2807) hydrogen bonds : angle 4.10571 ( 8274) Misc. bond : bond 0.00053 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 9 GLN cc_start: 0.5809 (OUTLIER) cc_final: 0.5163 (mm110) REVERT: Z 56 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.9111 (pmm) REVERT: B 79 MET cc_start: 0.7909 (ttm) cc_final: 0.7240 (ptm) REVERT: B 134 MET cc_start: 0.7761 (tpp) cc_final: 0.7372 (mmt) REVERT: F 78 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8467 (mmm-85) REVERT: H 79 MET cc_start: 0.9311 (ttm) cc_final: 0.8859 (tmm) REVERT: H 134 MET cc_start: 0.9176 (mtp) cc_final: 0.8834 (mtp) REVERT: I 38 MET cc_start: 0.8079 (mtp) cc_final: 0.7563 (mtp) REVERT: J 1 MET cc_start: 0.7346 (tmm) cc_final: 0.7016 (tmm) REVERT: J 25 ASN cc_start: 0.9150 (m-40) cc_final: 0.8926 (m-40) REVERT: J 78 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7892 (mmm-85) REVERT: J 134 MET cc_start: 0.9130 (mmm) cc_final: 0.8616 (tmm) REVERT: L 22 GLN cc_start: 0.9398 (tm-30) cc_final: 0.9151 (pp30) REVERT: L 79 MET cc_start: 0.9457 (ttm) cc_final: 0.9194 (mtt) REVERT: L 86 MET cc_start: 0.9308 (ttt) cc_final: 0.9028 (ttm) REVERT: L 165 ASP cc_start: 0.9457 (m-30) cc_final: 0.9190 (m-30) REVERT: M 81 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6690 (p0) REVERT: N 74 TYR cc_start: 0.8967 (t80) cc_final: 0.8721 (t80) REVERT: S 79 MET cc_start: 0.8507 (ppp) cc_final: 0.8034 (ppp) REVERT: U 86 MET cc_start: 0.9126 (mtp) cc_final: 0.8687 (mtp) REVERT: W 134 MET cc_start: 0.8994 (mmm) cc_final: 0.8500 (mmm) REVERT: X 1 MET cc_start: 0.6795 (mmm) cc_final: 0.6576 (mmm) REVERT: X 72 MET cc_start: 0.7534 (mmm) cc_final: 0.7208 (tpt) REVERT: a 1 MET cc_start: 0.6454 (tmm) cc_final: 0.5661 (tmm) outliers start: 50 outliers final: 34 residues processed: 205 average time/residue: 0.2133 time to fit residues: 73.4062 Evaluate side-chains 195 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 9 GLN Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 56 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 21 ASN Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain Q residue 114 LYS Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain W residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 428 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS M 103 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN ** P 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 25 GLN W 2 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.033069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.026451 restraints weight = 484198.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.027067 restraints weight = 325472.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.027463 restraints weight = 246163.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.027682 restraints weight = 204239.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.027866 restraints weight = 182773.830| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 1.0257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 37105 Z= 0.207 Angle : 0.725 14.191 50384 Z= 0.358 Chirality : 0.038 0.232 5565 Planarity : 0.004 0.050 6524 Dihedral : 10.564 178.315 6634 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 1.62 % Allowed : 18.01 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.17 (0.12), residues: 4516 helix: 1.94 (0.08), residues: 3567 sheet: -0.80 (0.81), residues: 35 loop : -0.43 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 10 TYR 0.040 0.002 TYR M 179 PHE 0.021 0.002 PHE J 60 TRP 0.007 0.001 TRP X 126 HIS 0.006 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00450 (37069) covalent geometry : angle 0.72546 (50384) hydrogen bonds : bond 0.03764 ( 2807) hydrogen bonds : angle 4.28990 ( 8274) Misc. bond : bond 0.00069 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 56 MET cc_start: 0.9400 (pmm) cc_final: 0.9094 (pmm) REVERT: B 79 MET cc_start: 0.7844 (ttm) cc_final: 0.7355 (ptm) REVERT: B 134 MET cc_start: 0.8203 (tpp) cc_final: 0.7742 (tpt) REVERT: F 78 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8558 (mmm-85) REVERT: H 63 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: H 79 MET cc_start: 0.9408 (ttm) cc_final: 0.8964 (tmm) REVERT: H 134 MET cc_start: 0.9296 (mtp) cc_final: 0.9060 (mtp) REVERT: I 38 MET cc_start: 0.8228 (mtp) cc_final: 0.7708 (mtp) REVERT: J 1 MET cc_start: 0.7956 (tmm) cc_final: 0.7656 (tmm) REVERT: J 25 ASN cc_start: 0.9208 (m-40) cc_final: 0.8984 (m-40) REVERT: J 78 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7939 (mmm-85) REVERT: J 134 MET cc_start: 0.9180 (mmm) cc_final: 0.8722 (tmm) REVERT: L 23 GLU cc_start: 0.9452 (OUTLIER) cc_final: 0.9180 (mt-10) REVERT: L 79 MET cc_start: 0.9496 (ttm) cc_final: 0.9287 (mtm) REVERT: L 165 ASP cc_start: 0.9444 (m-30) cc_final: 0.9172 (m-30) REVERT: M 153 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.8984 (mtmm) REVERT: N 74 TYR cc_start: 0.8985 (t80) cc_final: 0.8666 (t80) REVERT: Q 1 MET cc_start: 0.8531 (tmm) cc_final: 0.8167 (tmm) REVERT: R 1 MET cc_start: 0.8614 (tpp) cc_final: 0.8062 (tpp) REVERT: S 79 MET cc_start: 0.8702 (ppp) cc_final: 0.8368 (ppp) REVERT: X 72 MET cc_start: 0.7693 (mmm) cc_final: 0.7406 (tpt) outliers start: 59 outliers final: 39 residues processed: 210 average time/residue: 0.2180 time to fit residues: 76.4847 Evaluate side-chains 197 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain N residue 68 GLN Chi-restraints excluded: chain O residue 32 LYS Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain Q residue 114 LYS Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain U residue 116 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain W residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 316 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 100 optimal weight: 40.0000 chunk 335 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 9 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.032916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.026301 restraints weight = 485063.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.026920 restraints weight = 323087.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.027318 restraints weight = 244343.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.027571 restraints weight = 202355.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.027746 restraints weight = 178683.399| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 1.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 37105 Z= 0.191 Angle : 0.720 13.468 50384 Z= 0.353 Chirality : 0.038 0.297 5565 Planarity : 0.004 0.041 6524 Dihedral : 10.569 177.586 6634 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 1.43 % Allowed : 18.34 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.20 (0.12), residues: 4516 helix: 1.95 (0.08), residues: 3579 sheet: -0.55 (0.89), residues: 28 loop : -0.37 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 77 TYR 0.039 0.002 TYR E 74 PHE 0.021 0.002 PHE J 60 TRP 0.011 0.001 TRP T 126 HIS 0.006 0.001 HIS I 133 Details of bonding type rmsd covalent geometry : bond 0.00424 (37069) covalent geometry : angle 0.71999 (50384) hydrogen bonds : bond 0.03636 ( 2807) hydrogen bonds : angle 4.27536 ( 8274) Misc. bond : bond 0.00059 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: Z 56 MET cc_start: 0.9442 (pmm) cc_final: 0.9083 (pmm) REVERT: B 79 MET cc_start: 0.7829 (ttm) cc_final: 0.7327 (ptm) REVERT: B 134 MET cc_start: 0.8273 (tpp) cc_final: 0.7849 (tpt) REVERT: F 78 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8450 (mmm-85) REVERT: H 63 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: H 132 GLN cc_start: 0.9676 (mt0) cc_final: 0.9387 (mm110) REVERT: H 134 MET cc_start: 0.9271 (mtp) cc_final: 0.9069 (mtp) REVERT: I 38 MET cc_start: 0.8274 (mtp) cc_final: 0.7793 (mtp) REVERT: J 25 ASN cc_start: 0.9219 (m-40) cc_final: 0.8999 (m-40) REVERT: J 78 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7934 (mmm-85) REVERT: J 134 MET cc_start: 0.9207 (mmm) cc_final: 0.8791 (tmm) REVERT: K 72 MET cc_start: 0.9067 (mtm) cc_final: 0.8811 (ppp) REVERT: L 1 MET cc_start: 0.6372 (pmm) cc_final: 0.5895 (pmm) REVERT: L 22 GLN cc_start: 0.9565 (tm-30) cc_final: 0.9271 (pp30) REVERT: L 165 ASP cc_start: 0.9444 (m-30) cc_final: 0.9191 (m-30) REVERT: M 153 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8958 (mtmm) REVERT: N 74 TYR cc_start: 0.8989 (t80) cc_final: 0.8657 (t80) REVERT: R 1 MET cc_start: 0.8611 (tpp) cc_final: 0.8357 (tpp) REVERT: S 79 MET cc_start: 0.8770 (ppp) cc_final: 0.8394 (ppp) REVERT: U 86 MET cc_start: 0.9126 (mtp) cc_final: 0.8810 (mmm) REVERT: W 134 MET cc_start: 0.8979 (mmm) cc_final: 0.8500 (mmm) REVERT: a 1 MET cc_start: 0.6461 (tmm) cc_final: 0.6213 (tmm) outliers start: 52 outliers final: 37 residues processed: 203 average time/residue: 0.2312 time to fit residues: 77.1488 Evaluate side-chains 194 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain N residue 68 GLN Chi-restraints excluded: chain O residue 32 LYS Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain Q residue 114 LYS Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain W residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 362 optimal weight: 6.9990 chunk 148 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 340 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 GLN ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 133 HIS ** 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 = 0.3464 r_free = 0.3464 target = 0.032891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.026292 restraints weight = 483870.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.026900 restraints weight = 324260.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.027304 restraints weight = 246024.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.027559 restraints weight = 203359.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.027729 restraints weight = 179526.614| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 1.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 37105 Z= 0.168 Angle : 0.716 13.763 50384 Z= 0.349 Chirality : 0.038 0.315 5565 Planarity : 0.004 0.041 6524 Dihedral : 10.496 177.368 6634 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 1.37 % Allowed : 18.54 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.30 (0.12), residues: 4516 helix: 2.01 (0.08), residues: 3579 sheet: -0.63 (0.88), residues: 28 loop : -0.32 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 77 TYR 0.037 0.001 TYR M 179 PHE 0.017 0.002 PHE O 60 TRP 0.013 0.001 TRP T 126 HIS 0.005 0.001 HIS I 133 Details of bonding type rmsd covalent geometry : bond 0.00373 (37069) covalent geometry : angle 0.71567 (50384) hydrogen bonds : bond 0.03530 ( 2807) hydrogen bonds : angle 4.24285 ( 8274) Misc. bond : bond 0.00050 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9032 Ramachandran restraints generated. 4516 Oldfield, 0 Emsley, 4516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 56 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9023 (pmm) REVERT: B 79 MET cc_start: 0.7821 (ttm) cc_final: 0.7299 (ptm) REVERT: B 134 MET cc_start: 0.8293 (tpp) cc_final: 0.7844 (tpt) REVERT: C 72 MET cc_start: 0.3870 (tmm) cc_final: 0.3497 (tmm) REVERT: F 78 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8284 (mmm-85) REVERT: H 132 GLN cc_start: 0.9654 (mt0) cc_final: 0.9371 (mm110) REVERT: I 1 MET cc_start: 0.6205 (pmm) cc_final: 0.5931 (pmm) REVERT: I 38 MET cc_start: 0.8287 (mtp) cc_final: 0.7828 (mtp) REVERT: J 1 MET cc_start: 0.8171 (tmm) cc_final: 0.7708 (tmm) REVERT: J 25 ASN cc_start: 0.9213 (m-40) cc_final: 0.8991 (m-40) REVERT: J 78 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8029 (mmm-85) REVERT: J 134 MET cc_start: 0.9203 (mmm) cc_final: 0.8777 (tmm) REVERT: L 1 MET cc_start: 0.6827 (pmm) cc_final: 0.6457 (pmm) REVERT: L 22 GLN cc_start: 0.9595 (tm-30) cc_final: 0.9313 (pp30) REVERT: L 79 MET cc_start: 0.9207 (mtm) cc_final: 0.8993 (mpp) REVERT: L 165 ASP cc_start: 0.9451 (m-30) cc_final: 0.9174 (m-30) REVERT: M 116 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8431 (t0) REVERT: M 153 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9007 (mtmm) REVERT: N 74 TYR cc_start: 0.8859 (t80) cc_final: 0.8566 (t80) REVERT: R 1 MET cc_start: 0.8550 (tpp) cc_final: 0.8307 (tpp) REVERT: S 79 MET cc_start: 0.8824 (ppp) cc_final: 0.8471 (ppp) REVERT: T 17 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7505 (ptt-90) REVERT: W 1 MET cc_start: 0.8811 (ppp) cc_final: 0.8467 (ppp) REVERT: W 134 MET cc_start: 0.8960 (mmm) cc_final: 0.8699 (mtt) REVERT: X 72 MET cc_start: 0.8009 (mmm) cc_final: 0.7616 (tpt) outliers start: 50 outliers final: 39 residues processed: 202 average time/residue: 0.2377 time to fit residues: 79.4474 Evaluate side-chains 199 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 56 MET Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain I residue 74 TYR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 143 ASN Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 153 LYS Chi-restraints excluded: chain M residue 179 TYR Chi-restraints excluded: chain O residue 32 LYS Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 109 CYS Chi-restraints excluded: chain Q residue 114 LYS Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain U residue 79 MET Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 113 LEU Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain W residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 451 random chunks: chunk 22 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 442 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 189 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 142 optimal weight: 30.0000 chunk 446 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 428 optimal weight: 2.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN W 2 GLN a 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.033180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.026559 restraints weight = 475438.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.027173 restraints weight = 318843.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.027582 restraints weight = 242467.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.027849 restraints weight = 200583.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.028008 restraints weight = 176511.306| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 1.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 37105 Z= 0.135 Angle : 0.714 16.593 50384 Z= 0.346 Chirality : 0.038 0.302 5565 Planarity : 0.004 0.043 6524 Dihedral : 10.408 177.266 6634 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % Rotamer: Outliers : 1.12 % Allowed : 18.86 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.13), residues: 4516 helix: 2.12 (0.08), residues: 3602 sheet: -0.66 (0.87), residues: 28 loop : -0.13 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 78 TYR 0.035 0.001 TYR M 179 PHE 0.016 0.001 PHE O 60 TRP 0.021 0.001 TRP T 126 HIS 0.005 0.001 HIS W 57 Details of bonding type rmsd covalent geometry : bond 0.00303 (37069) covalent geometry : angle 0.71381 (50384) hydrogen bonds : bond 0.03424 ( 2807) hydrogen bonds : angle 4.19407 ( 8274) Misc. bond : bond 0.00040 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7510.12 seconds wall clock time: 131 minutes 0.15 seconds (7860.15 seconds total)