Starting phenix.real_space_refine on Wed May 6 05:40:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7k_65729/05_2026/9w7k_65729.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7k_65729/05_2026/9w7k_65729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w7k_65729/05_2026/9w7k_65729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7k_65729/05_2026/9w7k_65729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w7k_65729/05_2026/9w7k_65729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7k_65729/05_2026/9w7k_65729.map" } resolution = 2.58 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= 0.001 sd= 0.021 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 85 5.16 5 C 22539 2.51 5 N 6266 2.21 5 O 6972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35862 Number of models: 1 Model: "" Number of chains: 54 Chain: "1" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1574 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 10, 'TRANS': 180} Chain: "2" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2262 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 1 Chain: "3" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 502 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "B" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1212 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 6, 'TRANS': 154} Chain breaks: 1 Chain: "C" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1264 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 4, 'TRANS': 165} Chain breaks: 2 Chain: "D" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "E" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "F" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "G" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1271 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 4, 'TRANS': 166} Chain breaks: 1 Chain: "H" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "I" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1274 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 4, 'TRANS': 166} Chain: "J" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "K" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "L" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "M" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "O" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "P" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Q" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "R" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "S" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "T" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "V" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "W" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "X" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "Y" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1223 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 6, 'TRANS': 155} Chain: "Z" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1278 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "1" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "3" 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: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "C" 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: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "K" 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: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "M" 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: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" 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: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" 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: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "V" 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: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" NB CYC 3 301 " occ=0.94 ... (41 atoms not shown) pdb=" OC CYC 3 301 " occ=0.94 residue: pdb=" NB CYC I 201 " occ=0.98 ... (41 atoms not shown) pdb=" OC CYC I 201 " occ=0.98 residue: pdb=" NB CYC K 201 " occ=0.88 ... (41 atoms not shown) pdb=" OC CYC K 201 " occ=0.88 Time building chain proxies: 8.46, per 1000 atoms: 0.24 Number of scatterers: 35862 At special positions: 0 Unit cell: (130, 124.8, 142.48, 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 85 16.00 O 6972 8.00 N 6266 7.00 C 22539 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=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.4 seconds 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 2 sheets defined 82.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain '1' and resid 13 through 17 removed outlier: 3.738A pdb=" N VAL 1 17 " --> pdb=" O ASN 1 14 " (cutoff:3.500A) Processing helix chain '1' and resid 20 through 25 removed outlier: 3.952A pdb=" N ALA 1 23 " --> pdb=" O PHE 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 34 through 38 Processing helix chain '1' and resid 40 through 57 Processing helix chain '1' and resid 58 through 61 Processing helix chain '1' and resid 67 through 76 Processing helix chain '1' and resid 80 through 90 Processing helix chain '1' and resid 91 through 98 Processing helix chain '1' and resid 103 through 116 Processing helix chain '1' and resid 122 through 147 removed outlier: 3.591A pdb=" N LYS 1 126 " --> pdb=" O ASN 1 122 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE 1 131 " --> pdb=" O ILE 1 127 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN 1 132 " --> pdb=" O ALA 1 128 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE 1 133 " --> pdb=" O TRP 1 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP 1 138 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLY 1 139 " --> pdb=" O SER 1 135 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY 1 140 " --> pdb=" O LYS 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 148 through 155 Processing helix chain '1' and resid 172 through 176 Processing helix chain '1' and resid 180 through 188 Processing helix chain '2' and resid 6 through 11 Processing helix chain '2' and resid 12 through 17 removed outlier: 4.628A pdb=" N ASP 2 17 " --> pdb=" O GLU 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 44 removed outlier: 3.513A pdb=" N LEU 2 44 " --> pdb=" O TYR 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 54 removed outlier: 3.675A pdb=" N ARG 2 54 " --> pdb=" O ALA 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 55 through 64 Processing helix chain '2' and resid 68 through 79 Processing helix chain '2' and resid 79 through 87 Processing helix chain '2' and resid 91 through 105 Processing helix chain '2' and resid 110 through 124 removed outlier: 3.837A pdb=" N VAL 2 114 " --> pdb=" O ASP 2 110 " (cutoff:3.500A) Processing helix chain '2' and resid 125 through 136 Processing helix chain '2' and resid 136 through 143 Processing helix chain '2' and resid 161 through 172 removed outlier: 4.140A pdb=" N PHE 2 165 " --> pdb=" O LYS 2 161 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN 2 166 " --> pdb=" O THR 2 162 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE 2 169 " --> pdb=" O PHE 2 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG 2 170 " --> pdb=" O ASN 2 166 " (cutoff:3.500A) Processing helix chain '2' and resid 190 through 197 Processing helix chain '2' and resid 265 through 277 Processing helix chain '3' and resid 265 through 276 Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.515A pdb=" N ALA B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 removed outlier: 4.022A pdb=" N SER B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.961A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 41' Processing helix chain 'B' and resid 48 through 64 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 78 through 103 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 126 through 141 removed outlier: 4.107A pdb=" N TYR B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.559A pdb=" N TYR B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 48 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 58 through 64 Processing helix chain 'C' and resid 64 through 69 removed outlier: 4.252A pdb=" N ILE C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 101 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 124 through 144 Processing helix chain 'C' and resid 154 through 173 Processing helix chain 'D' and resid 4 through 17 Processing helix chain 'D' and resid 21 through 48 removed outlier: 3.585A pdb=" N SER D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA D 37 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 64 removed outlier: 3.511A pdb=" N TYR D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 78 through 103 Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 126 through 141 removed outlier: 4.333A pdb=" N TYR D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 163 removed outlier: 3.539A pdb=" N TYR D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 17 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 34 through 48 Processing helix chain 'E' and resid 48 through 64 removed outlier: 3.603A pdb=" N GLU E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 101 Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 113 through 122 Processing helix chain 'E' and resid 124 through 144 Processing helix chain 'E' and resid 154 through 173 Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 21 through 48 removed outlier: 3.896A pdb=" N SER F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 36 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 64 Processing helix chain 'F' and resid 65 through 69 Processing helix chain 'F' and resid 78 through 103 Processing helix chain 'F' and resid 105 through 112 Processing helix chain 'F' and resid 115 through 123 Processing helix chain 'F' and resid 126 through 141 removed outlier: 4.292A pdb=" N TYR F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 163 removed outlier: 3.746A pdb=" N TYR F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 34 through 48 Processing helix chain 'G' and resid 48 through 64 removed outlier: 3.538A pdb=" N GLU G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 101 Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 113 through 122 Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 154 through 173 Processing helix chain 'H' and resid 4 through 17 Processing helix chain 'H' and resid 21 through 48 removed outlier: 3.669A pdb=" N ALA H 36 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA H 37 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 64 Processing helix chain 'H' and resid 65 through 69 Processing helix chain 'H' and resid 78 through 103 removed outlier: 3.539A pdb=" N LYS H 82 " --> pdb=" O ASP H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 112 Processing helix chain 'H' and resid 115 through 123 Processing helix chain 'H' and resid 126 through 141 removed outlier: 4.078A pdb=" N TYR H 130 " --> pdb=" O SER H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 163 removed outlier: 3.696A pdb=" N TYR H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 161 " --> pdb=" O TYR H 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 removed outlier: 3.524A pdb=" N VAL I 9 " --> pdb=" O VAL I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 34 Processing helix chain 'I' and resid 34 through 48 Processing helix chain 'I' and resid 48 through 64 Processing helix chain 'I' and resid 76 through 101 Processing helix chain 'I' and resid 103 through 110 Processing helix chain 'I' and resid 113 through 122 Processing helix chain 'I' and resid 124 through 144 Processing helix chain 'I' and resid 154 through 172 Processing helix chain 'J' and resid 4 through 17 removed outlier: 3.656A pdb=" N GLN J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 48 removed outlier: 4.094A pdb=" N ALA J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN J 48 " --> pdb=" O GLY J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 64 Processing helix chain 'J' and resid 65 through 69 Processing helix chain 'J' and resid 78 through 103 Processing helix chain 'J' and resid 105 through 112 Processing helix chain 'J' and resid 115 through 123 Processing helix chain 'J' and resid 126 through 141 removed outlier: 4.303A pdb=" N TYR J 130 " --> pdb=" O SER J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 163 removed outlier: 3.624A pdb=" N TYR J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 17 removed outlier: 3.525A pdb=" N VAL K 9 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG K 16 " --> pdb=" O GLN K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 34 Processing helix chain 'K' and resid 35 through 48 Processing helix chain 'K' and resid 48 through 64 Processing helix chain 'K' and resid 65 through 68 Processing helix chain 'K' and resid 76 through 101 Processing helix chain 'K' and resid 103 through 110 Processing helix chain 'K' and resid 113 through 122 removed outlier: 3.854A pdb=" N LEU K 121 " --> pdb=" O THR K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 144 Processing helix chain 'K' and resid 154 through 173 Processing helix chain 'L' and resid 4 through 17 Processing helix chain 'L' and resid 21 through 48 removed outlier: 3.993A pdb=" N SER L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 28 " --> pdb=" O GLU L 24 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA L 36 " --> pdb=" O TYR L 32 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA L 37 " --> pdb=" O GLU L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 64 Processing helix chain 'L' and resid 65 through 69 Processing helix chain 'L' and resid 78 through 103 removed outlier: 3.530A pdb=" N LYS L 82 " --> pdb=" O ASP L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 112 Processing helix chain 'L' and resid 115 through 123 Processing helix chain 'L' and resid 126 through 141 removed outlier: 4.331A pdb=" N TYR L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 163 removed outlier: 3.583A pdb=" N TYR L 154 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 17 removed outlier: 3.590A pdb=" N ARG M 16 " --> pdb=" O GLN M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 34 Processing helix chain 'M' and resid 34 through 48 Processing helix chain 'M' and resid 48 through 64 Processing helix chain 'M' and resid 76 through 101 Processing helix chain 'M' and resid 103 through 110 removed outlier: 3.604A pdb=" N ARG M 109 " --> pdb=" O VAL M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 122 Processing helix chain 'M' and resid 124 through 144 Processing helix chain 'M' and resid 154 through 173 Processing helix chain 'O' and resid 4 through 17 Processing helix chain 'O' and resid 21 through 48 removed outlier: 3.538A pdb=" N SER O 27 " --> pdb=" O THR O 23 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA O 36 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA O 37 " --> pdb=" O GLU O 33 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 64 Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 78 through 103 removed outlier: 3.624A pdb=" N LYS O 82 " --> pdb=" O ASP O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 112 Processing helix chain 'O' and resid 115 through 124 Processing helix chain 'O' and resid 126 through 141 removed outlier: 4.093A pdb=" N TYR O 130 " --> pdb=" O SER O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 163 removed outlier: 3.839A pdb=" N TYR O 154 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 17 removed outlier: 3.707A pdb=" N VAL P 9 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG P 16 " --> pdb=" O GLN P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 34 Processing helix chain 'P' and resid 35 through 48 Processing helix chain 'P' and resid 48 through 64 Processing helix chain 'P' and resid 64 through 69 removed outlier: 4.335A pdb=" N ILE P 68 " --> pdb=" O GLN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 101 Processing helix chain 'P' and resid 103 through 109 Processing helix chain 'P' and resid 113 through 122 Processing helix chain 'P' and resid 124 through 144 Processing helix chain 'P' and resid 154 through 173 Processing helix chain 'Q' and resid 4 through 17 Processing helix chain 'Q' and resid 21 through 48 removed outlier: 3.593A pdb=" N SER Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA Q 36 " --> pdb=" O TYR Q 32 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 64 Processing helix chain 'Q' and resid 65 through 69 Processing helix chain 'Q' and resid 78 through 103 Processing helix chain 'Q' and resid 105 through 112 Processing helix chain 'Q' and resid 115 through 123 Processing helix chain 'Q' and resid 126 through 141 removed outlier: 4.269A pdb=" N TYR Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 163 removed outlier: 3.600A pdb=" N TYR Q 154 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 17 Processing helix chain 'R' and resid 21 through 34 Processing helix chain 'R' and resid 34 through 48 Processing helix chain 'R' and resid 48 through 64 Processing helix chain 'R' and resid 76 through 101 Processing helix chain 'R' and resid 103 through 110 Processing helix chain 'R' and resid 113 through 122 Processing helix chain 'R' and resid 124 through 145 Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'S' and resid 4 through 17 Processing helix chain 'S' and resid 21 through 48 removed outlier: 3.634A pdb=" N SER S 27 " --> pdb=" O THR S 23 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 64 removed outlier: 3.922A pdb=" N LEU S 52 " --> pdb=" O ASN S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'S' and resid 78 through 103 Processing helix chain 'S' and resid 105 through 112 Processing helix chain 'S' and resid 115 through 123 Processing helix chain 'S' and resid 126 through 141 removed outlier: 4.162A pdb=" N TYR S 130 " --> pdb=" O SER S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 163 removed outlier: 3.764A pdb=" N TYR S 154 " --> pdb=" O GLU S 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 17 removed outlier: 3.514A pdb=" N VAL T 9 " --> pdb=" O VAL T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 34 Processing helix chain 'T' and resid 34 through 48 Processing helix chain 'T' and resid 48 through 64 Processing helix chain 'T' and resid 76 through 101 Processing helix chain 'T' and resid 103 through 110 Processing helix chain 'T' and resid 113 through 122 Processing helix chain 'T' and resid 124 through 144 Processing helix chain 'T' and resid 154 through 173 Processing helix chain 'U' and resid 4 through 17 removed outlier: 3.790A pdb=" N GLN U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 48 removed outlier: 3.575A pdb=" N SER U 27 " --> pdb=" O THR U 23 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA U 36 " --> pdb=" O TYR U 32 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA U 37 " --> pdb=" O GLU U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 64 Processing helix chain 'U' and resid 65 through 69 Processing helix chain 'U' and resid 78 through 103 Processing helix chain 'U' and resid 105 through 112 Processing helix chain 'U' and resid 115 through 124 Processing helix chain 'U' and resid 126 through 141 removed outlier: 4.246A pdb=" N TYR U 130 " --> pdb=" O SER U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 163 removed outlier: 3.661A pdb=" N TYR U 154 " --> pdb=" O GLU U 150 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR U 157 " --> pdb=" O THR U 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 17 removed outlier: 3.956A pdb=" N VAL V 9 " --> pdb=" O VAL V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 21 through 34 Processing helix chain 'V' and resid 34 through 48 Processing helix chain 'V' and resid 48 through 64 Processing helix chain 'V' and resid 64 through 69 removed outlier: 4.338A pdb=" N ILE V 68 " --> pdb=" O GLN V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 101 Processing helix chain 'V' and resid 103 through 110 Processing helix chain 'V' and resid 113 through 122 Processing helix chain 'V' and resid 124 through 144 Processing helix chain 'V' and resid 154 through 173 Processing helix chain 'W' and resid 4 through 17 removed outlier: 3.704A pdb=" N GLN W 16 " --> pdb=" O ALA W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 48 removed outlier: 3.647A pdb=" N SER W 27 " --> pdb=" O THR W 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA W 36 " --> pdb=" O TYR W 32 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA W 37 " --> pdb=" O GLU W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 64 Processing helix chain 'W' and resid 65 through 69 Processing helix chain 'W' and resid 78 through 103 Processing helix chain 'W' and resid 105 through 112 Processing helix chain 'W' and resid 115 through 123 Processing helix chain 'W' and resid 126 through 141 removed outlier: 4.285A pdb=" N TYR W 130 " --> pdb=" O SER W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 163 removed outlier: 3.770A pdb=" N TYR W 154 " --> pdb=" O GLU W 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 17 Processing helix chain 'X' and resid 21 through 34 Processing helix chain 'X' and resid 34 through 48 Processing helix chain 'X' and resid 48 through 64 Processing helix chain 'X' and resid 76 through 101 Processing helix chain 'X' and resid 103 through 110 Processing helix chain 'X' and resid 113 through 122 Processing helix chain 'X' and resid 124 through 144 Processing helix chain 'X' and resid 154 through 173 Processing helix chain 'Y' and resid 4 through 16 removed outlier: 3.510A pdb=" N GLN Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 48 removed outlier: 3.621A pdb=" N ARG Y 31 " --> pdb=" O SER Y 27 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR Y 32 " --> pdb=" O ALA Y 28 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Y 36 " --> pdb=" O TYR Y 32 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA Y 37 " --> pdb=" O GLU Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 64 Processing helix chain 'Y' and resid 65 through 69 Processing helix chain 'Y' and resid 78 through 103 Processing helix chain 'Y' and resid 105 through 112 Processing helix chain 'Y' and resid 115 through 124 Processing helix chain 'Y' and resid 126 through 139 removed outlier: 4.190A pdb=" N TYR Y 130 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 163 removed outlier: 3.577A pdb=" N TYR Y 154 " --> pdb=" O GLU Y 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 17 Processing helix chain 'Z' and resid 21 through 34 Processing helix chain 'Z' and resid 35 through 48 Processing helix chain 'Z' and resid 48 through 64 Processing helix chain 'Z' and resid 64 through 69 removed outlier: 4.319A pdb=" N ILE Z 68 " --> pdb=" O GLN Z 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 101 Processing helix chain 'Z' and resid 103 through 110 Processing helix chain 'Z' and resid 113 through 122 Processing helix chain 'Z' and resid 124 through 144 removed outlier: 3.532A pdb=" N ASP Z 137 " --> pdb=" O GLN Z 133 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Z 138 " --> pdb=" O LYS Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 154 through 173 removed outlier: 3.522A pdb=" N GLY Z 173 " --> pdb=" O ALA Z 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 257 through 262 removed outlier: 7.439A pdb=" N VAL 2 236 " --> pdb=" O SER 2 285 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER 2 285 " --> pdb=" O VAL 2 236 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG 2 238 " --> pdb=" O VAL 2 283 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL 2 283 " --> pdb=" O ARG 2 238 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU 2 240 " --> pdb=" O VAL 2 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 256 through 262 removed outlier: 6.917A pdb=" N VAL 3 236 " --> pdb=" O SER 3 285 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER 3 285 " --> pdb=" O VAL 3 236 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG 3 238 " --> pdb=" O VAL 3 283 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL 3 283 " --> pdb=" O ARG 3 238 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU 3 240 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) 2653 hydrogen bonds defined for protein. 7851 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: 6.61 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6598 1.32 - 1.44: 9244 1.44 - 1.57: 20510 1.57 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 36474 Sorted by residual: bond pdb=" N TYR 3 249 " pdb=" CA TYR 3 249 " ideal model delta sigma weight residual 1.463 1.493 -0.029 6.90e-03 2.10e+04 1.83e+01 bond pdb=" C4A CYC R 202 " pdb=" CHB CYC R 202 " ideal model delta sigma weight residual 1.437 1.367 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4A CYC C 201 " pdb=" CHB CYC C 201 " ideal model delta sigma weight residual 1.437 1.370 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C4C CYC T 201 " pdb=" CHD CYC T 201 " ideal model delta sigma weight residual 1.346 1.409 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" C4A CYC D 201 " pdb=" CHB CYC D 201 " ideal model delta sigma weight residual 1.437 1.374 0.063 2.00e-02 2.50e+03 9.93e+00 ... (remaining 36469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 48972 2.92 - 5.83: 571 5.83 - 8.75: 29 8.75 - 11.67: 42 11.67 - 14.59: 12 Bond angle restraints: 49626 Sorted by residual: angle pdb=" C1B CYC M 201 " pdb=" CHB CYC M 201 " pdb=" C4A CYC M 201 " ideal model delta sigma weight residual 126.10 140.69 -14.59 3.00e+00 1.11e-01 2.36e+01 angle pdb=" C1B CYC Y 201 " pdb=" CHB CYC Y 201 " pdb=" C4A CYC Y 201 " ideal model delta sigma weight residual 126.10 139.89 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C1B CYC E 201 " pdb=" CHB CYC E 201 " pdb=" C4A CYC E 201 " ideal model delta sigma weight residual 126.10 139.83 -13.73 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N ARG R 16 " pdb=" CA ARG R 16 " pdb=" C ARG R 16 " ideal model delta sigma weight residual 113.38 107.86 5.52 1.23e+00 6.61e-01 2.02e+01 angle pdb=" C1B CYC T 201 " pdb=" CHB CYC T 201 " pdb=" C4A CYC T 201 " ideal model delta sigma weight residual 126.10 139.49 -13.39 3.00e+00 1.11e-01 1.99e+01 ... (remaining 49621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.56: 19761 18.56 - 37.11: 2038 37.11 - 55.67: 599 55.67 - 74.23: 170 74.23 - 92.78: 38 Dihedral angle restraints: 22606 sinusoidal: 9531 harmonic: 13075 Sorted by residual: dihedral pdb=" CD ARG 3 245 " pdb=" NE ARG 3 245 " pdb=" CZ ARG 3 245 " pdb=" NH1 ARG 3 245 " ideal model delta sinusoidal sigma weight residual 0.00 -63.28 63.28 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" CD ARG R 78 " pdb=" NE ARG R 78 " pdb=" CZ ARG R 78 " pdb=" NH1 ARG R 78 " ideal model delta sinusoidal sigma weight residual 0.00 -52.82 52.82 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CD ARG 3 254 " pdb=" NE ARG 3 254 " pdb=" CZ ARG 3 254 " pdb=" NH1 ARG 3 254 " ideal model delta sinusoidal sigma weight residual 0.00 -46.87 46.87 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 22603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4231 0.044 - 0.088: 995 0.088 - 0.132: 194 0.132 - 0.175: 56 0.175 - 0.219: 10 Chirality restraints: 5486 Sorted by residual: chirality pdb=" CA VAL 3 258 " pdb=" N VAL 3 258 " pdb=" C VAL 3 258 " pdb=" CB VAL 3 258 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL 3 273 " pdb=" N VAL 3 273 " pdb=" C VAL 3 273 " pdb=" CB VAL 3 273 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL 3 283 " pdb=" N VAL 3 283 " pdb=" C VAL 3 283 " pdb=" CB VAL 3 283 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 5483 not shown) Planarity restraints: 6460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CYC R 202 " 0.006 2.00e-02 2.50e+03 2.31e-01 1.20e+03 pdb=" C2A CYC R 202 " -0.099 2.00e-02 2.50e+03 pdb=" C3A CYC R 202 " 0.036 2.00e-02 2.50e+03 pdb=" C4A CYC R 202 " -0.094 2.00e-02 2.50e+03 pdb=" CAA CYC R 202 " -0.285 2.00e-02 2.50e+03 pdb=" CHA CYC R 202 " 0.427 2.00e-02 2.50e+03 pdb=" CHB CYC R 202 " 0.034 2.00e-02 2.50e+03 pdb=" CMA CYC R 202 " 0.302 2.00e-02 2.50e+03 pdb=" NA CYC R 202 " -0.326 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC C 201 " -0.333 2.00e-02 2.50e+03 1.93e-01 8.35e+02 pdb=" OB CYC C 201 " 0.082 2.00e-02 2.50e+03 pdb=" C1B CYC C 201 " -0.000 2.00e-02 2.50e+03 pdb=" C2B CYC C 201 " -0.065 2.00e-02 2.50e+03 pdb=" C3B CYC C 201 " 0.032 2.00e-02 2.50e+03 pdb=" C4B CYC C 201 " -0.061 2.00e-02 2.50e+03 pdb=" CAB CYC C 201 " 0.200 2.00e-02 2.50e+03 pdb=" CHB CYC C 201 " 0.353 2.00e-02 2.50e+03 pdb=" CMB CYC C 201 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC R 202 " -0.331 2.00e-02 2.50e+03 1.85e-01 7.67e+02 pdb=" OB CYC R 202 " 0.095 2.00e-02 2.50e+03 pdb=" C1B CYC R 202 " -0.006 2.00e-02 2.50e+03 pdb=" C2B CYC R 202 " -0.061 2.00e-02 2.50e+03 pdb=" C3B CYC R 202 " 0.028 2.00e-02 2.50e+03 pdb=" C4B CYC R 202 " -0.057 2.00e-02 2.50e+03 pdb=" CAB CYC R 202 " 0.178 2.00e-02 2.50e+03 pdb=" CHB CYC R 202 " 0.338 2.00e-02 2.50e+03 pdb=" CMB CYC R 202 " -0.184 2.00e-02 2.50e+03 ... (remaining 6457 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 12711 2.86 - 3.37: 38049 3.37 - 3.88: 65608 3.88 - 4.39: 76578 4.39 - 4.90: 126999 Nonbonded interactions: 319945 Sorted by model distance: nonbonded pdb=" O ARG R 44 " pdb=" ND2 ASN R 48 " model vdw 2.347 3.120 nonbonded pdb=" N ASP 3 268 " pdb=" OD1 ASP 3 268 " model vdw 2.448 3.120 nonbonded pdb=" O TYR 3 249 " pdb=" C PRO 3 250 " model vdw 2.455 3.270 nonbonded pdb=" O GLY 3 248 " pdb=" N VAL 3 252 " model vdw 2.470 3.120 nonbonded pdb=" N GLN P 66 " pdb=" OE1 GLN P 66 " model vdw 2.474 3.120 ... (remaining 319940 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' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'F' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'H' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'J' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'L' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'O' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'Q' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'S' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'U' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'W' and (resid 2 through 42 or resid 44 through 201)) selection = (chain 'Y' and (resid 2 through 42 or resid 44 through 201)) } ncs_group { reference = (chain 'C' and (resid 2 through 129 or resid 131 through 172 or resid 201)) selection = (chain 'E' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'G' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 17 \ 2 or resid 201)) selection = (chain 'I' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 201)) selection = (chain 'K' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'M' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'P' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'R' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'T' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'V' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'X' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) selection = (chain 'Z' and (resid 2 through 17 or resid 19 through 56 or resid 58 through 12 \ 9 or resid 131 through 172 or resid 201)) } 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=0.88 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.700 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.140 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.005 0.070 36474 Z= 0.300 Angle : 0.775 14.586 49626 Z= 0.397 Chirality : 0.040 0.219 5486 Planarity : 0.015 0.441 6460 Dihedral : 17.036 92.782 14242 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 2.09 % Allowed : 21.47 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.12), residues: 4479 helix: 1.38 (0.08), residues: 3478 sheet: 0.88 (1.00), residues: 28 loop : 0.09 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 16 TYR 0.011 0.001 TYR 3 237 PHE 0.016 0.001 PHE R 19 TRP 0.005 0.001 TRP 2 137 HIS 0.005 0.001 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00544 (36474) covalent geometry : angle 0.77464 (49626) hydrogen bonds : bond 0.19798 ( 2653) hydrogen bonds : angle 6.59644 ( 7851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 695 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9075 (ptpt) cc_final: 0.8683 (ptmt) REVERT: 1 15 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.9002 (pp30) REVERT: 1 147 ASP cc_start: 0.9217 (m-30) cc_final: 0.8984 (m-30) REVERT: 2 271 GLN cc_start: 0.8520 (mt0) cc_final: 0.8295 (mm-40) REVERT: 2 279 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8275 (mttt) REVERT: 3 235 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8271 (mtm180) REVERT: 3 249 TYR cc_start: 0.5372 (OUTLIER) cc_final: 0.4204 (t80) REVERT: 3 265 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7662 (mtp-110) REVERT: 3 275 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8614 (tptm) REVERT: 3 276 GLN cc_start: 0.9074 (mt0) cc_final: 0.8798 (mt0) REVERT: B 156 ASP cc_start: 0.9241 (m-30) cc_final: 0.9034 (m-30) REVERT: C 80 MET cc_start: 0.9411 (tpp) cc_final: 0.9165 (tpp) REVERT: D 50 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8320 (tp40) REVERT: D 54 ASP cc_start: 0.8707 (m-30) cc_final: 0.8438 (m-30) REVERT: D 132 GLU cc_start: 0.9245 (tp30) cc_final: 0.8891 (tp30) REVERT: E 135 MET cc_start: 0.8798 (mtm) cc_final: 0.8481 (mtp) REVERT: F 3 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8930 (tttt) REVERT: F 48 ASN cc_start: 0.8543 (m110) cc_final: 0.8290 (m-40) REVERT: F 154 TYR cc_start: 0.9072 (m-80) cc_final: 0.8791 (m-80) REVERT: G 12 GLN cc_start: 0.9037 (mt0) cc_final: 0.8793 (mt0) REVERT: H 48 ASN cc_start: 0.8718 (m-40) cc_final: 0.8433 (m-40) REVERT: I 62 GLU cc_start: 0.8975 (tt0) cc_final: 0.8656 (mt-10) REVERT: I 88 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8448 (mt-10) REVERT: I 151 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8814 (tppt) REVERT: J 132 GLU cc_start: 0.8817 (tp30) cc_final: 0.8521 (tp30) REVERT: J 156 ASP cc_start: 0.8929 (m-30) cc_final: 0.8726 (m-30) REVERT: L 24 GLU cc_start: 0.9078 (mp0) cc_final: 0.8850 (mp0) REVERT: L 50 GLN cc_start: 0.9295 (tp-100) cc_final: 0.8825 (tp40) REVERT: L 54 ASP cc_start: 0.9046 (m-30) cc_final: 0.8806 (m-30) REVERT: L 124 ASP cc_start: 0.9060 (t70) cc_final: 0.8575 (t0) REVERT: L 156 ASP cc_start: 0.8733 (m-30) cc_final: 0.8490 (m-30) REVERT: M 134 LYS cc_start: 0.9266 (mttp) cc_final: 0.9006 (mttt) REVERT: O 58 GLN cc_start: 0.8614 (tp40) cc_final: 0.8378 (tp-100) REVERT: P 133 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8092 (tp40) REVERT: Q 8 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7680 (mm-30) REVERT: Q 140 ASN cc_start: 0.8747 (m110) cc_final: 0.8385 (m110) REVERT: R 135 MET cc_start: 0.9418 (mtm) cc_final: 0.9101 (mtm) REVERT: S 26 GLN cc_start: 0.9105 (mt0) cc_final: 0.8792 (mt0) REVERT: S 48 ASN cc_start: 0.8321 (t160) cc_final: 0.7622 (t160) REVERT: S 51 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8225 (ttp80) REVERT: S 149 ASN cc_start: 0.9144 (t0) cc_final: 0.8889 (t0) REVERT: U 110 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8236 (mm-30) REVERT: V 166 ASP cc_start: 0.6682 (m-30) cc_final: 0.6289 (m-30) REVERT: W 16 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8533 (mm-40) REVERT: W 69 GLN cc_start: 0.8369 (mt0) cc_final: 0.8091 (mm-40) REVERT: Y 109 ASP cc_start: 0.8327 (m-30) cc_final: 0.7907 (m-30) outliers start: 74 outliers final: 17 residues processed: 737 average time/residue: 0.9389 time to fit residues: 794.3486 Evaluate side-chains 516 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 491 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 15 GLN Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 279 LYS Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 3 residue 235 ARG Chi-restraints excluded: chain 3 residue 236 VAL Chi-restraints excluded: chain 3 residue 238 ARG Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 249 TYR Chi-restraints excluded: chain 3 residue 265 ARG Chi-restraints excluded: chain 3 residue 275 LYS Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain X residue 23 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 96 GLN 2 271 GLN 3 228 ASN B 16 GLN C 119 GLN D 26 GLN H 120 ASN J 50 GLN J 62 GLN ** J 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 ASN K 112 ASN K 119 GLN K 147 ASN L 26 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 GLN R 147 ASN T 66 GLN U 69 GLN U 149 ASN W 26 GLN X 12 GLN Y 136 HIS ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.065880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.058258 restraints weight = 76576.093| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.11 r_work: 0.2703 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36474 Z= 0.152 Angle : 0.605 9.941 49626 Z= 0.289 Chirality : 0.037 0.131 5486 Planarity : 0.004 0.056 6460 Dihedral : 10.859 138.003 6637 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 3.17 % Allowed : 18.50 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.12), residues: 4479 helix: 2.12 (0.08), residues: 3515 sheet: 0.44 (0.97), residues: 32 loop : 0.08 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 18 TYR 0.014 0.001 TYR 1 105 PHE 0.012 0.001 PHE Y 123 TRP 0.009 0.001 TRP B 129 HIS 0.008 0.002 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00343 (36474) covalent geometry : angle 0.60534 (49626) hydrogen bonds : bond 0.03891 ( 2653) hydrogen bonds : angle 4.20325 ( 7851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 561 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9059 (ptpt) cc_final: 0.8598 (ptmt) REVERT: 1 147 ASP cc_start: 0.9069 (m-30) cc_final: 0.8824 (m-30) REVERT: 2 31 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: 2 179 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8150 (t0) REVERT: 2 271 GLN cc_start: 0.8164 (mt0) cc_final: 0.7841 (mm-40) REVERT: 3 244 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7307 (pt) REVERT: 3 253 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7736 (mmt-90) REVERT: 3 265 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7306 (mtp85) REVERT: 3 269 LYS cc_start: 0.8325 (tptt) cc_final: 0.8123 (tptt) REVERT: 3 275 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8206 (tttt) REVERT: B 26 GLN cc_start: 0.8941 (mt0) cc_final: 0.8703 (pt0) REVERT: B 33 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 62 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: C 34 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: C 80 MET cc_start: 0.9359 (tpp) cc_final: 0.8750 (tpp) REVERT: C 167 ARG cc_start: 0.8894 (ttm-80) cc_final: 0.8599 (ttm170) REVERT: D 50 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8587 (tp-100) REVERT: D 54 ASP cc_start: 0.8900 (m-30) cc_final: 0.8693 (m-30) REVERT: D 132 GLU cc_start: 0.8969 (tp30) cc_final: 0.8439 (tp30) REVERT: D 150 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8846 (mm-30) REVERT: F 3 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8504 (tttt) REVERT: F 154 TYR cc_start: 0.9034 (m-80) cc_final: 0.8715 (m-80) REVERT: G 7 THR cc_start: 0.9124 (m) cc_final: 0.8724 (p) REVERT: G 33 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8548 (mtmm) REVERT: G 34 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8155 (mm-30) REVERT: H 48 ASN cc_start: 0.8462 (m-40) cc_final: 0.8128 (m-40) REVERT: H 138 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8403 (ttmt) REVERT: I 88 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: I 149 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8688 (pp) REVERT: I 151 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8731 (tppt) REVERT: J 132 GLU cc_start: 0.8788 (tp30) cc_final: 0.8393 (tp30) REVERT: J 150 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8638 (mm-30) REVERT: K 18 GLU cc_start: 0.8596 (pm20) cc_final: 0.8368 (pm20) REVERT: K 23 GLU cc_start: 0.8898 (mp0) cc_final: 0.8665 (mp0) REVERT: K 63 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8628 (mt-10) REVERT: L 24 GLU cc_start: 0.9058 (mp0) cc_final: 0.8792 (mp0) REVERT: L 54 ASP cc_start: 0.8844 (m-30) cc_final: 0.8567 (m-30) REVERT: L 156 ASP cc_start: 0.9006 (m-30) cc_final: 0.8708 (m-30) REVERT: M 7 THR cc_start: 0.9140 (m) cc_final: 0.8680 (p) REVERT: M 12 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8384 (mt0) REVERT: M 134 LYS cc_start: 0.8967 (mttp) cc_final: 0.8732 (mttm) REVERT: O 109 ASP cc_start: 0.8871 (m-30) cc_final: 0.8510 (m-30) REVERT: P 80 MET cc_start: 0.9145 (tpp) cc_final: 0.8903 (tpp) REVERT: P 133 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7886 (tp40) REVERT: P 151 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8747 (tptt) REVERT: Q 110 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8842 (mm-30) REVERT: Q 156 ASP cc_start: 0.8776 (m-30) cc_final: 0.8410 (m-30) REVERT: R 40 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8924 (m-30) REVERT: R 88 GLU cc_start: 0.8828 (tt0) cc_final: 0.8562 (tt0) REVERT: R 135 MET cc_start: 0.9247 (mtm) cc_final: 0.8961 (mtm) REVERT: R 151 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8600 (mptt) REVERT: S 48 ASN cc_start: 0.8205 (t160) cc_final: 0.7760 (t160) REVERT: S 110 GLU cc_start: 0.9018 (tt0) cc_final: 0.8747 (tt0) REVERT: S 149 ASN cc_start: 0.9070 (t0) cc_final: 0.8724 (t0) REVERT: S 156 ASP cc_start: 0.9008 (m-30) cc_final: 0.8753 (m-30) REVERT: T 62 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8155 (mt-10) REVERT: T 116 GLU cc_start: 0.9188 (mp0) cc_final: 0.8640 (mp0) REVERT: U 18 ARG cc_start: 0.8670 (ptp-170) cc_final: 0.8300 (ptp-170) REVERT: U 40 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8720 (pt0) REVERT: U 62 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: U 110 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8373 (mm-30) REVERT: U 154 TYR cc_start: 0.8730 (m-80) cc_final: 0.8501 (m-80) REVERT: W 16 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8628 (mm-40) REVERT: W 62 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: X 18 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: Y 109 ASP cc_start: 0.8419 (m-30) cc_final: 0.7941 (m-30) REVERT: Z 16 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8214 (mtm-85) REVERT: Z 40 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8627 (m-30) outliers start: 112 outliers final: 16 residues processed: 627 average time/residue: 0.9340 time to fit residues: 673.3018 Evaluate side-chains 520 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 489 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 230 VAL Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain W residue 62 GLN Chi-restraints excluded: chain W residue 124 ASP Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 33 LYS Chi-restraints excluded: chain X residue 156 GLN Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 112 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 143 optimal weight: 0.4980 chunk 217 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 369 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 140 GLN ** 3 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 271 GLN B 16 GLN D 26 GLN F 69 GLN G 30 ASN G 119 GLN H 149 ASN J 149 ASN L 26 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN T 119 GLN U 48 ASN U 69 GLN Y 48 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.055406 restraints weight = 77034.449| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.02 r_work: 0.2619 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36474 Z= 0.149 Angle : 0.562 10.419 49626 Z= 0.270 Chirality : 0.036 0.148 5486 Planarity : 0.004 0.052 6460 Dihedral : 10.283 81.515 6592 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Rotamer: Outliers : 2.46 % Allowed : 19.43 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.12), residues: 4479 helix: 2.43 (0.08), residues: 3515 sheet: 0.77 (0.98), residues: 32 loop : 0.10 (0.22), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 18 TYR 0.015 0.001 TYR 1 105 PHE 0.012 0.001 PHE F 123 TRP 0.004 0.001 TRP 1 49 HIS 0.008 0.002 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00342 (36474) covalent geometry : angle 0.56187 (49626) hydrogen bonds : bond 0.04143 ( 2653) hydrogen bonds : angle 3.98537 ( 7851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 519 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9065 (ptpt) cc_final: 0.8654 (ptmt) REVERT: 1 147 ASP cc_start: 0.9145 (m-30) cc_final: 0.8923 (m-30) REVERT: 2 31 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: 2 49 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8260 (tp) REVERT: 2 271 GLN cc_start: 0.8143 (mt0) cc_final: 0.7848 (mt0) REVERT: 3 238 ARG cc_start: 0.8352 (tmt170) cc_final: 0.7670 (tmm160) REVERT: 3 253 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7964 (mtt-85) REVERT: 3 265 ARG cc_start: 0.7475 (mtm110) cc_final: 0.6975 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8181 (tptt) cc_final: 0.7950 (tptt) REVERT: B 8 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8025 (mt-10) REVERT: B 33 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8442 (mm-30) REVERT: C 88 GLU cc_start: 0.8990 (tt0) cc_final: 0.8508 (tt0) REVERT: C 167 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8566 (ttm170) REVERT: D 50 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8464 (tp40) REVERT: D 132 GLU cc_start: 0.8874 (tp30) cc_final: 0.8389 (tp30) REVERT: E 88 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: E 135 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8651 (mtm) REVERT: F 3 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8536 (tttt) REVERT: G 18 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: H 48 ASN cc_start: 0.8423 (m-40) cc_final: 0.8111 (m-40) REVERT: H 118 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: I 84 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (mt) REVERT: I 88 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: I 149 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8692 (pp) REVERT: I 151 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8749 (tppt) REVERT: J 132 GLU cc_start: 0.8866 (tp30) cc_final: 0.8431 (tp30) REVERT: K 18 GLU cc_start: 0.8507 (pm20) cc_final: 0.8042 (pm20) REVERT: L 24 GLU cc_start: 0.9045 (mp0) cc_final: 0.8821 (mp0) REVERT: L 54 ASP cc_start: 0.8701 (m-30) cc_final: 0.8397 (m-30) REVERT: L 156 ASP cc_start: 0.8989 (m-30) cc_final: 0.8783 (m-30) REVERT: M 7 THR cc_start: 0.9076 (m) cc_final: 0.8570 (p) REVERT: O 6 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8548 (mp) REVERT: O 109 ASP cc_start: 0.8864 (m-30) cc_final: 0.8502 (m-30) REVERT: P 133 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8034 (tp40) REVERT: P 151 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8788 (tptt) REVERT: Q 24 GLU cc_start: 0.9190 (mp0) cc_final: 0.8790 (mp0) REVERT: Q 110 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8735 (mm-30) REVERT: Q 140 ASN cc_start: 0.8862 (m110) cc_final: 0.8402 (m110) REVERT: R 18 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8049 (pt0) REVERT: R 135 MET cc_start: 0.9201 (mtm) cc_final: 0.8890 (mtm) REVERT: S 48 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7810 (t160) REVERT: S 110 GLU cc_start: 0.8986 (tt0) cc_final: 0.8784 (tt0) REVERT: S 149 ASN cc_start: 0.8982 (t0) cc_final: 0.8684 (t0) REVERT: T 62 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8208 (mt-10) REVERT: U 62 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: W 16 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8656 (mm-40) REVERT: W 62 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: W 110 GLU cc_start: 0.8733 (tp30) cc_final: 0.8120 (tp30) REVERT: Y 62 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: Y 109 ASP cc_start: 0.8556 (m-30) cc_final: 0.8054 (m-30) REVERT: Z 16 ARG cc_start: 0.8270 (mtp180) cc_final: 0.8030 (mtm-85) REVERT: Z 40 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8824 (m-30) outliers start: 87 outliers final: 20 residues processed: 572 average time/residue: 0.9981 time to fit residues: 652.5214 Evaluate side-chains 524 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 486 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 182 ASP Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 253 ARG Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain W residue 62 GLN Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 366 optimal weight: 0.0980 chunk 324 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 399 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 140 GLN 3 271 GLN B 16 GLN D 26 GLN D 62 GLN E 133 GLN F 22 ASN G 12 GLN G 119 GLN H 62 GLN H 149 ASN J 149 ASN L 26 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN Q 58 GLN R 133 GLN S 16 GLN T 119 GLN U 16 GLN X 12 GLN Y 48 ASN Y 69 GLN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.061667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.054223 restraints weight = 76957.096| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.01 r_work: 0.2590 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36474 Z= 0.172 Angle : 0.570 10.275 49626 Z= 0.273 Chirality : 0.037 0.141 5486 Planarity : 0.004 0.066 6460 Dihedral : 10.413 80.918 6591 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 2.83 % Allowed : 18.98 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.12), residues: 4479 helix: 2.46 (0.08), residues: 3513 sheet: 0.99 (0.96), residues: 32 loop : 0.10 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Y 18 TYR 0.017 0.001 TYR 3 263 PHE 0.010 0.001 PHE F 123 TRP 0.006 0.001 TRP 2 137 HIS 0.007 0.002 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00400 (36474) covalent geometry : angle 0.56954 (49626) hydrogen bonds : bond 0.03901 ( 2653) hydrogen bonds : angle 3.93759 ( 7851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 500 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9121 (ptpt) cc_final: 0.8866 (ptpt) REVERT: 1 147 ASP cc_start: 0.9118 (m-30) cc_final: 0.8881 (m-30) REVERT: 2 31 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: 2 41 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7920 (tmt170) REVERT: 2 49 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8362 (tp) REVERT: 2 89 ASN cc_start: 0.8389 (p0) cc_final: 0.8116 (p0) REVERT: 2 271 GLN cc_start: 0.8245 (mt0) cc_final: 0.7975 (mt0) REVERT: 3 228 ASN cc_start: 0.6929 (t0) cc_final: 0.6651 (t0) REVERT: 3 238 ARG cc_start: 0.8322 (tmt170) cc_final: 0.7642 (ttp-170) REVERT: 3 240 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7394 (tp30) REVERT: 3 253 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8031 (mtt-85) REVERT: 3 265 ARG cc_start: 0.7530 (mtm110) cc_final: 0.7014 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8294 (tptt) cc_final: 0.8088 (tptt) REVERT: B 8 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8124 (mt-10) REVERT: B 26 GLN cc_start: 0.9103 (mt0) cc_final: 0.8824 (mt0) REVERT: B 33 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8530 (mm-30) REVERT: C 88 GLU cc_start: 0.9023 (tt0) cc_final: 0.8557 (tt0) REVERT: D 24 GLU cc_start: 0.9353 (mp0) cc_final: 0.9120 (mp0) REVERT: D 132 GLU cc_start: 0.8915 (tp30) cc_final: 0.8449 (tp30) REVERT: E 34 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: E 88 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: E 135 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8673 (mtm) REVERT: F 3 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8532 (tttt) REVERT: F 110 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8315 (mm-30) REVERT: H 48 ASN cc_start: 0.8504 (m-40) cc_final: 0.8183 (m-40) REVERT: H 118 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: H 156 ASP cc_start: 0.9132 (m-30) cc_final: 0.8908 (m-30) REVERT: I 84 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8746 (mt) REVERT: I 88 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: I 149 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8655 (pp) REVERT: I 151 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8780 (tppt) REVERT: J 63 LYS cc_start: 0.9251 (tptt) cc_final: 0.9042 (tppp) REVERT: J 132 GLU cc_start: 0.8930 (tp30) cc_final: 0.8565 (tp30) REVERT: K 18 GLU cc_start: 0.8563 (pm20) cc_final: 0.8051 (pm20) REVERT: L 24 GLU cc_start: 0.9031 (mp0) cc_final: 0.8821 (mp0) REVERT: L 54 ASP cc_start: 0.8716 (m-30) cc_final: 0.8394 (m-30) REVERT: M 87 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8590 (mtp) REVERT: O 6 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8496 (mp) REVERT: O 109 ASP cc_start: 0.8895 (m-30) cc_final: 0.8553 (m-30) REVERT: P 133 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8133 (tp40) REVERT: P 151 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8470 (mmmm) REVERT: Q 24 GLU cc_start: 0.9204 (mp0) cc_final: 0.8829 (mp0) REVERT: Q 110 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8700 (mm-30) REVERT: R 18 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8042 (pt0) REVERT: R 40 ASP cc_start: 0.9223 (OUTLIER) cc_final: 0.8983 (m-30) REVERT: R 135 MET cc_start: 0.9193 (mtm) cc_final: 0.8914 (mtm) REVERT: S 48 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7697 (t160) REVERT: S 51 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8303 (ttp80) REVERT: S 110 GLU cc_start: 0.8983 (tt0) cc_final: 0.8773 (tt0) REVERT: S 118 GLU cc_start: 0.8606 (mp0) cc_final: 0.8272 (mp0) REVERT: S 149 ASN cc_start: 0.8987 (t0) cc_final: 0.8605 (t0) REVERT: T 62 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8245 (mt-10) REVERT: U 62 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: V 133 GLN cc_start: 0.8555 (mp10) cc_final: 0.8280 (mp-120) REVERT: W 16 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8845 (mm-40) REVERT: W 110 GLU cc_start: 0.8786 (tp30) cc_final: 0.8192 (tp30) REVERT: Y 62 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: Y 109 ASP cc_start: 0.8636 (m-30) cc_final: 0.8183 (m-30) REVERT: Y 118 GLU cc_start: 0.8138 (pm20) cc_final: 0.7828 (mp0) REVERT: Y 156 ASP cc_start: 0.9181 (m-30) cc_final: 0.8918 (m-30) REVERT: Z 40 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8853 (OUTLIER) REVERT: Z 87 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8915 (mtp) outliers start: 100 outliers final: 35 residues processed: 560 average time/residue: 0.9717 time to fit residues: 621.9766 Evaluate side-chains 533 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 478 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 157 ASP Chi-restraints excluded: chain 1 residue 182 ASP Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 253 ARG Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 149 ILE Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 87 MET Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 271 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 140 GLN 3 271 GLN B 16 GLN C 119 GLN D 26 GLN D 62 GLN E 112 ASN E 133 GLN F 22 ASN G 12 GLN H 62 GLN H 149 ASN J 149 ASN L 26 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN T 119 GLN ** W 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 48 ASN Y 50 GLN Y 69 GLN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.059539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.052170 restraints weight = 77980.347| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.00 r_work: 0.2534 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2444 r_free = 0.2444 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 36474 Z= 0.259 Angle : 0.629 9.815 49626 Z= 0.303 Chirality : 0.041 0.142 5486 Planarity : 0.004 0.070 6460 Dihedral : 10.426 80.203 6591 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 2.89 % Allowed : 18.61 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.12), residues: 4479 helix: 2.32 (0.08), residues: 3513 sheet: 1.03 (0.96), residues: 32 loop : 0.08 (0.22), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Y 18 TYR 0.017 0.001 TYR 1 105 PHE 0.011 0.002 PHE K 61 TRP 0.006 0.001 TRP J 129 HIS 0.007 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00606 (36474) covalent geometry : angle 0.62909 (49626) hydrogen bonds : bond 0.04357 ( 2653) hydrogen bonds : angle 4.06225 ( 7851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 485 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9173 (ptpt) cc_final: 0.8948 (ptpt) REVERT: 1 147 ASP cc_start: 0.9098 (m-30) cc_final: 0.8840 (m-30) REVERT: 2 31 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: 2 41 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7932 (tmt170) REVERT: 2 49 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8533 (tp) REVERT: 2 89 ASN cc_start: 0.8569 (p0) cc_final: 0.8341 (p0) REVERT: 3 238 ARG cc_start: 0.8318 (tmt170) cc_final: 0.7815 (ttp-170) REVERT: 3 240 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7481 (tp30) REVERT: 3 265 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7093 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8286 (tptt) cc_final: 0.8039 (tptt) REVERT: B 8 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8254 (mm-30) REVERT: B 33 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8684 (mm-30) REVERT: C 88 GLU cc_start: 0.8994 (tt0) cc_final: 0.8522 (tt0) REVERT: D 132 GLU cc_start: 0.8906 (tp30) cc_final: 0.8456 (tp30) REVERT: E 78 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7416 (ttp80) REVERT: E 88 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: E 119 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: E 135 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8729 (mtm) REVERT: F 3 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8728 (ttpt) REVERT: F 110 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8248 (mm-30) REVERT: G 18 GLU cc_start: 0.8687 (pm20) cc_final: 0.8457 (pm20) REVERT: G 85 ARG cc_start: 0.8610 (tpp80) cc_final: 0.7957 (tpt90) REVERT: H 156 ASP cc_start: 0.9125 (m-30) cc_final: 0.8888 (m-30) REVERT: I 18 GLU cc_start: 0.8476 (pm20) cc_final: 0.8029 (pm20) REVERT: I 149 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8604 (pp) REVERT: I 151 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8773 (tppt) REVERT: J 63 LYS cc_start: 0.9249 (tptt) cc_final: 0.9048 (tppp) REVERT: J 132 GLU cc_start: 0.9081 (tp30) cc_final: 0.8682 (tp30) REVERT: K 18 GLU cc_start: 0.8564 (pm20) cc_final: 0.8017 (pm20) REVERT: K 63 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8626 (mt-10) REVERT: L 24 GLU cc_start: 0.8981 (mp0) cc_final: 0.8736 (mp0) REVERT: L 54 ASP cc_start: 0.8728 (m-30) cc_final: 0.8389 (m-30) REVERT: M 87 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8540 (mtp) REVERT: O 109 ASP cc_start: 0.8920 (m-30) cc_final: 0.8612 (m-30) REVERT: O 124 ASP cc_start: 0.8907 (t0) cc_final: 0.8550 (t0) REVERT: P 133 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8150 (tp40) REVERT: P 135 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9103 (mtm) REVERT: Q 3 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7997 (ttpp) REVERT: Q 24 GLU cc_start: 0.9155 (mp0) cc_final: 0.8777 (mp0) REVERT: Q 110 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8670 (mm-30) REVERT: R 18 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8077 (pt0) REVERT: R 40 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.9008 (m-30) REVERT: R 135 MET cc_start: 0.9192 (mtm) cc_final: 0.8903 (mtm) REVERT: R 151 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8790 (mmmm) REVERT: S 8 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8411 (mm-30) REVERT: S 48 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7528 (t160) REVERT: S 51 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8318 (ttp80) REVERT: S 110 GLU cc_start: 0.8952 (tt0) cc_final: 0.8750 (tt0) REVERT: S 150 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8804 (mm-30) REVERT: T 62 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8223 (mt-10) REVERT: T 133 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8369 (mm110) REVERT: U 62 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: V 133 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8281 (mp-120) REVERT: W 16 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8844 (mm-40) REVERT: W 110 GLU cc_start: 0.8811 (tp30) cc_final: 0.8291 (tp30) REVERT: Y 62 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: Y 109 ASP cc_start: 0.8631 (m-30) cc_final: 0.8170 (m-30) REVERT: Y 118 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: Z 40 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8906 (m-30) REVERT: Z 116 GLU cc_start: 0.8680 (mp0) cc_final: 0.8474 (mp0) REVERT: Z 137 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8237 (p0) outliers start: 102 outliers final: 39 residues processed: 550 average time/residue: 0.9661 time to fit residues: 606.5450 Evaluate side-chains 530 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 471 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 157 ASP Chi-restraints excluded: chain 1 residue 182 ASP Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 87 MET Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain P residue 135 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 3 LYS Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain S residue 62 GLN Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 133 GLN Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 118 GLU Chi-restraints excluded: chain Y residue 128 SER Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 87 MET Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 7 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 353 optimal weight: 2.9990 chunk 414 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 379 optimal weight: 0.5980 chunk 326 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 76 ASN 3 228 ASN B 16 GLN C 119 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN F 22 ASN G 12 GLN G 119 GLN H 62 GLN J 149 ASN K 119 GLN L 26 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 119 GLN U 16 GLN Y 48 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.054141 restraints weight = 76406.261| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.00 r_work: 0.2589 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 36474 Z= 0.154 Angle : 0.562 10.263 49626 Z= 0.270 Chirality : 0.037 0.126 5486 Planarity : 0.004 0.082 6460 Dihedral : 10.365 81.588 6591 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.81 % Favored : 98.15 % Rotamer: Outliers : 2.43 % Allowed : 19.32 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.12), residues: 4479 helix: 2.45 (0.08), residues: 3525 sheet: 1.15 (0.95), residues: 32 loop : 0.17 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Y 18 TYR 0.015 0.001 TYR 1 105 PHE 0.010 0.001 PHE S 123 TRP 0.007 0.001 TRP 2 137 HIS 0.007 0.002 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00358 (36474) covalent geometry : angle 0.56246 (49626) hydrogen bonds : bond 0.03825 ( 2653) hydrogen bonds : angle 3.90577 ( 7851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 503 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9181 (ptpt) cc_final: 0.8729 (pttt) REVERT: 1 147 ASP cc_start: 0.9077 (m-30) cc_final: 0.8856 (m-30) REVERT: 2 31 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: 2 41 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7953 (tmt170) REVERT: 2 49 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8499 (tp) REVERT: 2 89 ASN cc_start: 0.8482 (p0) cc_final: 0.8246 (p0) REVERT: 3 238 ARG cc_start: 0.8288 (tmt170) cc_final: 0.7929 (ttp-170) REVERT: 3 265 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7026 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8299 (tptt) cc_final: 0.8070 (tptt) REVERT: B 8 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8354 (mm-30) REVERT: B 26 GLN cc_start: 0.9149 (mt0) cc_final: 0.8871 (mt0) REVERT: B 33 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8560 (mm-30) REVERT: C 88 GLU cc_start: 0.9014 (tt0) cc_final: 0.8550 (tt0) REVERT: D 132 GLU cc_start: 0.8867 (tp30) cc_final: 0.8339 (tp30) REVERT: E 88 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: E 119 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: E 135 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8690 (mtm) REVERT: F 3 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8366 (tttt) REVERT: F 110 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8175 (mm-30) REVERT: F 157 TYR cc_start: 0.9121 (t80) cc_final: 0.8895 (t80) REVERT: G 18 GLU cc_start: 0.8594 (pm20) cc_final: 0.8328 (pm20) REVERT: G 85 ARG cc_start: 0.8615 (tpp80) cc_final: 0.7936 (tpt90) REVERT: H 156 ASP cc_start: 0.9082 (m-30) cc_final: 0.8802 (m-30) REVERT: I 18 GLU cc_start: 0.8495 (pm20) cc_final: 0.8022 (pm20) REVERT: I 149 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8640 (pp) REVERT: I 151 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8799 (tppt) REVERT: J 50 GLN cc_start: 0.8628 (tp40) cc_final: 0.8215 (tp-100) REVERT: J 54 ASP cc_start: 0.8482 (m-30) cc_final: 0.8227 (m-30) REVERT: J 63 LYS cc_start: 0.9248 (tptt) cc_final: 0.9045 (tppp) REVERT: J 132 GLU cc_start: 0.9002 (tp30) cc_final: 0.8624 (tp30) REVERT: K 18 GLU cc_start: 0.8524 (pm20) cc_final: 0.7978 (pm20) REVERT: K 63 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8616 (mt-10) REVERT: L 24 GLU cc_start: 0.9029 (mp0) cc_final: 0.8681 (mp0) REVERT: L 54 ASP cc_start: 0.8656 (m-30) cc_final: 0.8320 (m-30) REVERT: M 87 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8554 (mtp) REVERT: O 3 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8154 (tttt) REVERT: O 6 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8446 (mp) REVERT: O 109 ASP cc_start: 0.8908 (m-30) cc_final: 0.8490 (m-30) REVERT: O 124 ASP cc_start: 0.8887 (t0) cc_final: 0.8554 (t0) REVERT: O 157 TYR cc_start: 0.9273 (t80) cc_final: 0.9070 (t80) REVERT: P 18 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: P 133 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8159 (tp40) REVERT: P 135 MET cc_start: 0.9277 (mtp) cc_final: 0.9010 (mtm) REVERT: Q 24 GLU cc_start: 0.9126 (mp0) cc_final: 0.8772 (mp0) REVERT: Q 110 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8671 (mm-30) REVERT: R 18 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8055 (pt0) REVERT: R 40 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8978 (m-30) REVERT: R 135 MET cc_start: 0.9179 (mtm) cc_final: 0.8897 (mtm) REVERT: R 151 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8848 (mmmm) REVERT: S 8 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8403 (mt-10) REVERT: S 48 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7816 (t160) REVERT: S 110 GLU cc_start: 0.8982 (tt0) cc_final: 0.8781 (tt0) REVERT: S 118 GLU cc_start: 0.8593 (mp0) cc_final: 0.8266 (mp0) REVERT: T 62 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8240 (mt-10) REVERT: T 116 GLU cc_start: 0.9090 (mp0) cc_final: 0.8610 (mp0) REVERT: U 62 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: U 140 ASN cc_start: 0.9003 (m110) cc_final: 0.8777 (m-40) REVERT: V 33 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8657 (ttmm) REVERT: V 133 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8287 (mp-120) REVERT: W 16 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8826 (mm-40) REVERT: W 110 GLU cc_start: 0.8800 (tp30) cc_final: 0.8307 (tp30) REVERT: X 119 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8748 (mt0) REVERT: Y 62 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: Y 109 ASP cc_start: 0.8655 (m-30) cc_final: 0.8180 (m-30) REVERT: Y 118 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: Z 40 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8878 (OUTLIER) REVERT: Z 116 GLU cc_start: 0.8700 (mp0) cc_final: 0.8444 (mp0) outliers start: 86 outliers final: 33 residues processed: 551 average time/residue: 0.9711 time to fit residues: 611.1059 Evaluate side-chains 531 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 480 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 182 ASP Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 160 GLU Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 135 MET Chi-restraints excluded: chain T residue 156 GLN Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 133 GLN Chi-restraints excluded: chain X residue 119 GLN Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 118 GLU Chi-restraints excluded: chain Y residue 128 SER Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 183 optimal weight: 0.6980 chunk 423 optimal weight: 0.9990 chunk 420 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 293 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 361 optimal weight: 0.9990 chunk 434 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 140 GLN ** 3 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN C 119 GLN E 133 GLN F 22 ASN G 12 GLN G 119 GLN H 62 GLN H 149 ASN L 26 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN T 119 GLN U 16 GLN V 156 GLN X 12 GLN Y 48 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.061972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.054614 restraints weight = 76539.943| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.01 r_work: 0.2603 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36474 Z= 0.145 Angle : 0.555 10.235 49626 Z= 0.268 Chirality : 0.036 0.126 5486 Planarity : 0.004 0.093 6460 Dihedral : 10.345 81.457 6591 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.90 % Favored : 98.06 % Rotamer: Outliers : 2.49 % Allowed : 19.63 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.12), residues: 4479 helix: 2.53 (0.08), residues: 3523 sheet: 1.12 (0.94), residues: 32 loop : 0.18 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG Y 18 TYR 0.015 0.001 TYR S 92 PHE 0.009 0.001 PHE S 123 TRP 0.006 0.001 TRP 1 49 HIS 0.007 0.002 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00337 (36474) covalent geometry : angle 0.55535 (49626) hydrogen bonds : bond 0.03738 ( 2653) hydrogen bonds : angle 3.85530 ( 7851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 499 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9179 (ptpt) cc_final: 0.8732 (pttt) REVERT: 1 147 ASP cc_start: 0.9083 (m-30) cc_final: 0.8830 (m-30) REVERT: 2 31 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: 2 41 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7920 (tmt170) REVERT: 2 49 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8476 (tp) REVERT: 2 89 ASN cc_start: 0.8473 (p0) cc_final: 0.8213 (p0) REVERT: 3 228 ASN cc_start: 0.7020 (t0) cc_final: 0.6797 (t0) REVERT: 3 238 ARG cc_start: 0.8263 (tmt170) cc_final: 0.8021 (ttp-170) REVERT: 3 265 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7007 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8308 (tptt) cc_final: 0.8086 (tptt) REVERT: B 26 GLN cc_start: 0.9152 (mt0) cc_final: 0.8872 (mt0) REVERT: B 33 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8635 (mm-30) REVERT: C 88 GLU cc_start: 0.9006 (tt0) cc_final: 0.8537 (tt0) REVERT: D 132 GLU cc_start: 0.8839 (tp30) cc_final: 0.8260 (tp30) REVERT: E 88 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: E 119 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8448 (mt0) REVERT: E 135 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8707 (mtm) REVERT: F 3 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8288 (tttt) REVERT: F 110 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8235 (mm-30) REVERT: F 157 TYR cc_start: 0.9124 (t80) cc_final: 0.8897 (t80) REVERT: G 18 GLU cc_start: 0.8576 (pm20) cc_final: 0.8147 (pm20) REVERT: G 85 ARG cc_start: 0.8622 (tpp80) cc_final: 0.7936 (tpt90) REVERT: H 156 ASP cc_start: 0.9033 (m-30) cc_final: 0.8754 (m-30) REVERT: I 18 GLU cc_start: 0.8511 (pm20) cc_final: 0.7969 (pm20) REVERT: I 149 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8664 (pp) REVERT: I 151 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8788 (tppt) REVERT: J 50 GLN cc_start: 0.8649 (tp40) cc_final: 0.8216 (tp-100) REVERT: J 54 ASP cc_start: 0.8487 (m-30) cc_final: 0.8217 (m-30) REVERT: J 132 GLU cc_start: 0.8969 (tp30) cc_final: 0.8605 (tp30) REVERT: J 150 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8616 (mm-30) REVERT: K 18 GLU cc_start: 0.8510 (pm20) cc_final: 0.7972 (pm20) REVERT: K 40 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8809 (m-30) REVERT: K 63 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8570 (mt-10) REVERT: L 24 GLU cc_start: 0.9059 (mp0) cc_final: 0.8707 (mp0) REVERT: L 54 ASP cc_start: 0.8666 (m-30) cc_final: 0.8330 (m-30) REVERT: M 87 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: O 3 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8116 (tttt) REVERT: O 6 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8442 (mp) REVERT: O 109 ASP cc_start: 0.8943 (m-30) cc_final: 0.8575 (m-30) REVERT: O 124 ASP cc_start: 0.8889 (t0) cc_final: 0.8566 (t0) REVERT: P 18 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: P 133 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8117 (tp40) REVERT: P 135 MET cc_start: 0.9270 (mtp) cc_final: 0.9007 (mtm) REVERT: Q 24 GLU cc_start: 0.9117 (mp0) cc_final: 0.8779 (mp0) REVERT: Q 110 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8642 (mm-30) REVERT: R 18 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7978 (pt0) REVERT: R 40 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.8997 (m-30) REVERT: R 135 MET cc_start: 0.9152 (mtm) cc_final: 0.8878 (mtm) REVERT: R 151 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8710 (tptt) REVERT: S 48 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7575 (t160) REVERT: S 51 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8393 (ttp80) REVERT: S 110 GLU cc_start: 0.8978 (tt0) cc_final: 0.8756 (tt0) REVERT: S 118 GLU cc_start: 0.8600 (mp0) cc_final: 0.8257 (mp0) REVERT: T 62 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8217 (mt-10) REVERT: T 116 GLU cc_start: 0.9089 (mp0) cc_final: 0.8620 (mp0) REVERT: U 140 ASN cc_start: 0.9009 (m110) cc_final: 0.8800 (m-40) REVERT: V 33 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8666 (ttmm) REVERT: V 133 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8323 (mp-120) REVERT: V 167 ARG cc_start: 0.8935 (ttm-80) cc_final: 0.8727 (ttm-80) REVERT: W 16 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8812 (mm-40) REVERT: W 110 GLU cc_start: 0.8772 (tp30) cc_final: 0.8271 (tp30) REVERT: X 119 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8776 (mt0) REVERT: Y 62 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: Y 109 ASP cc_start: 0.8668 (m-30) cc_final: 0.8183 (m-30) REVERT: Y 118 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: Z 40 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (OUTLIER) REVERT: Z 116 GLU cc_start: 0.8704 (mp0) cc_final: 0.8387 (mp0) REVERT: Z 137 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8164 (p0) outliers start: 88 outliers final: 35 residues processed: 550 average time/residue: 0.9582 time to fit residues: 602.4089 Evaluate side-chains 534 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 480 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 160 GLU Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 135 MET Chi-restraints excluded: chain T residue 156 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 133 GLN Chi-restraints excluded: chain X residue 33 LYS Chi-restraints excluded: chain X residue 119 GLN Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 118 GLU Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 87 MET Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 303 optimal weight: 0.6980 chunk 290 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 chunk 310 optimal weight: 1.9990 chunk 444 optimal weight: 0.7980 chunk 400 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 140 GLN 3 228 ASN B 16 GLN C 119 GLN D 62 GLN F 22 ASN G 12 GLN G 119 GLN H 62 GLN H 149 ASN L 26 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN T 119 GLN U 16 GLN X 12 GLN Y 48 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.053826 restraints weight = 76750.578| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.02 r_work: 0.2575 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36474 Z= 0.174 Angle : 0.577 10.129 49626 Z= 0.278 Chirality : 0.037 0.143 5486 Planarity : 0.004 0.105 6460 Dihedral : 10.343 80.655 6591 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Rotamer: Outliers : 2.40 % Allowed : 19.80 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.12), residues: 4479 helix: 2.52 (0.08), residues: 3514 sheet: 1.14 (0.92), residues: 32 loop : 0.12 (0.22), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG Y 18 TYR 0.018 0.001 TYR S 92 PHE 0.010 0.001 PHE V 61 TRP 0.006 0.001 TRP 1 49 HIS 0.007 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00408 (36474) covalent geometry : angle 0.57694 (49626) hydrogen bonds : bond 0.03869 ( 2653) hydrogen bonds : angle 3.89333 ( 7851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 491 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9210 (ptpt) cc_final: 0.8767 (pttt) REVERT: 1 147 ASP cc_start: 0.9051 (m-30) cc_final: 0.8813 (m-30) REVERT: 2 31 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: 2 41 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7907 (tmt170) REVERT: 2 49 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8488 (tp) REVERT: 2 89 ASN cc_start: 0.8508 (p0) cc_final: 0.8244 (p0) REVERT: 3 238 ARG cc_start: 0.8230 (tmt170) cc_final: 0.7963 (ttp-170) REVERT: 3 265 ARG cc_start: 0.7547 (mtm110) cc_final: 0.7007 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8290 (tptt) cc_final: 0.8068 (tptt) REVERT: B 26 GLN cc_start: 0.9144 (mt0) cc_final: 0.8856 (mt0) REVERT: B 33 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8636 (mm-30) REVERT: C 88 GLU cc_start: 0.9010 (tt0) cc_final: 0.8540 (tt0) REVERT: D 132 GLU cc_start: 0.8865 (tp30) cc_final: 0.8341 (tp30) REVERT: E 78 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7333 (ttp80) REVERT: E 88 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: E 119 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8457 (mt0) REVERT: E 135 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8688 (mtm) REVERT: F 3 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8355 (tttt) REVERT: F 110 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8160 (mm-30) REVERT: F 157 TYR cc_start: 0.9135 (t80) cc_final: 0.8922 (t80) REVERT: G 18 GLU cc_start: 0.8534 (pm20) cc_final: 0.8329 (pm20) REVERT: G 85 ARG cc_start: 0.8621 (tpp80) cc_final: 0.7941 (tpt90) REVERT: H 156 ASP cc_start: 0.9036 (m-30) cc_final: 0.8761 (m-30) REVERT: I 18 GLU cc_start: 0.8511 (pm20) cc_final: 0.7813 (pm20) REVERT: I 149 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8627 (pp) REVERT: I 151 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8792 (tppt) REVERT: J 50 GLN cc_start: 0.8631 (tp40) cc_final: 0.8183 (tp-100) REVERT: J 54 ASP cc_start: 0.8500 (m-30) cc_final: 0.8218 (m-30) REVERT: J 132 GLU cc_start: 0.8984 (tp30) cc_final: 0.8614 (tp30) REVERT: J 150 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8600 (mm-30) REVERT: K 18 GLU cc_start: 0.8520 (pm20) cc_final: 0.7946 (pm20) REVERT: K 40 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8800 (m-30) REVERT: K 63 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8568 (mt-10) REVERT: L 24 GLU cc_start: 0.9050 (mp0) cc_final: 0.8731 (mp0) REVERT: L 54 ASP cc_start: 0.8670 (m-30) cc_final: 0.8353 (m-30) REVERT: M 87 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8565 (mtp) REVERT: O 3 LYS cc_start: 0.8490 (mmmt) cc_final: 0.8181 (tttt) REVERT: O 6 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8464 (mp) REVERT: O 109 ASP cc_start: 0.8941 (m-30) cc_final: 0.8600 (m-30) REVERT: O 124 ASP cc_start: 0.8898 (t0) cc_final: 0.8551 (t0) REVERT: P 133 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8115 (tp40) REVERT: P 135 MET cc_start: 0.9280 (mtp) cc_final: 0.9069 (mtm) REVERT: Q 3 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8092 (mtpp) REVERT: Q 24 GLU cc_start: 0.9124 (mp0) cc_final: 0.8782 (mp0) REVERT: Q 110 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8654 (mm-30) REVERT: R 18 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7984 (pt0) REVERT: R 40 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8989 (m-30) REVERT: R 135 MET cc_start: 0.9114 (mtm) cc_final: 0.8906 (mtm) REVERT: R 151 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8706 (tptt) REVERT: S 48 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7580 (t160) REVERT: S 51 ARG cc_start: 0.8848 (ttp80) cc_final: 0.8384 (ttp80) REVERT: S 69 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8524 (mt0) REVERT: S 118 GLU cc_start: 0.8602 (mp0) cc_final: 0.8258 (mp0) REVERT: T 62 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8231 (mt-10) REVERT: T 116 GLU cc_start: 0.9122 (mp0) cc_final: 0.8636 (mp0) REVERT: U 62 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: U 140 ASN cc_start: 0.9027 (m110) cc_final: 0.8824 (m-40) REVERT: V 133 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8320 (mp-120) REVERT: W 16 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8825 (mm-40) REVERT: W 110 GLU cc_start: 0.8782 (tp30) cc_final: 0.8271 (tp30) REVERT: X 119 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8758 (mt0) REVERT: Y 62 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: Y 109 ASP cc_start: 0.8655 (m-30) cc_final: 0.8167 (m-30) REVERT: Y 118 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: Z 40 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8867 (OUTLIER) REVERT: Z 116 GLU cc_start: 0.8693 (mp0) cc_final: 0.8330 (mp0) REVERT: Z 137 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8144 (p0) outliers start: 85 outliers final: 38 residues processed: 542 average time/residue: 0.9754 time to fit residues: 602.9125 Evaluate side-chains 539 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 479 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 157 ASP Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 228 ASN Chi-restraints excluded: chain 3 residue 234 ASP Chi-restraints excluded: chain 3 residue 236 VAL Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain Q residue 3 LYS Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 160 GLU Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 135 MET Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 133 GLN Chi-restraints excluded: chain X residue 33 LYS Chi-restraints excluded: chain X residue 119 GLN Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 118 GLU Chi-restraints excluded: chain Y residue 128 SER Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 87 MET Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 7 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 420 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 76 ASN 2 140 GLN 3 228 ASN B 16 GLN C 119 GLN D 62 GLN F 22 ASN G 12 GLN G 119 GLN H 62 GLN J 149 ASN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN T 119 GLN T 133 GLN U 16 GLN X 12 GLN Y 48 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.061364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.053997 restraints weight = 76569.931| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.01 r_work: 0.2581 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36474 Z= 0.170 Angle : 0.580 10.146 49626 Z= 0.281 Chirality : 0.037 0.159 5486 Planarity : 0.004 0.113 6460 Dihedral : 10.341 80.761 6591 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 2.32 % Allowed : 19.97 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.12), residues: 4479 helix: 2.53 (0.08), residues: 3516 sheet: 1.16 (0.93), residues: 32 loop : 0.13 (0.22), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG Y 18 TYR 0.021 0.001 TYR S 92 PHE 0.012 0.001 PHE V 61 TRP 0.006 0.001 TRP 1 49 HIS 0.007 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00398 (36474) covalent geometry : angle 0.58044 (49626) hydrogen bonds : bond 0.03849 ( 2653) hydrogen bonds : angle 3.88791 ( 7851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 487 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9210 (ptpt) cc_final: 0.8772 (pttt) REVERT: 1 147 ASP cc_start: 0.9058 (m-30) cc_final: 0.8823 (m-30) REVERT: 2 31 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: 2 41 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7936 (tmt170) REVERT: 2 49 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8489 (tp) REVERT: 2 89 ASN cc_start: 0.8511 (p0) cc_final: 0.8245 (p0) REVERT: 3 238 ARG cc_start: 0.8226 (tmt170) cc_final: 0.7858 (ttp-170) REVERT: 3 265 ARG cc_start: 0.7575 (mtm110) cc_final: 0.7037 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8307 (tptt) cc_final: 0.8086 (tptt) REVERT: B 26 GLN cc_start: 0.9143 (mt0) cc_final: 0.8863 (mt0) REVERT: B 33 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8628 (mm-30) REVERT: C 88 GLU cc_start: 0.9009 (tt0) cc_final: 0.8539 (tt0) REVERT: D 132 GLU cc_start: 0.8875 (tp30) cc_final: 0.8345 (tp30) REVERT: E 78 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7333 (ttp80) REVERT: E 88 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: E 119 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8440 (mt0) REVERT: E 135 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8716 (mtm) REVERT: F 110 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8161 (mm-30) REVERT: F 157 TYR cc_start: 0.9143 (t80) cc_final: 0.8927 (t80) REVERT: G 18 GLU cc_start: 0.8568 (pm20) cc_final: 0.8363 (pm20) REVERT: G 85 ARG cc_start: 0.8620 (tpp80) cc_final: 0.7948 (tpt90) REVERT: H 156 ASP cc_start: 0.9046 (m-30) cc_final: 0.8768 (m-30) REVERT: I 18 GLU cc_start: 0.8519 (pm20) cc_final: 0.7817 (pm20) REVERT: I 149 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8657 (pp) REVERT: I 151 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8640 (mmtp) REVERT: J 50 GLN cc_start: 0.8643 (tp40) cc_final: 0.8281 (tp40) REVERT: J 54 ASP cc_start: 0.8512 (m-30) cc_final: 0.8268 (m-30) REVERT: J 132 GLU cc_start: 0.9002 (tp30) cc_final: 0.8627 (tp30) REVERT: J 150 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8545 (mm-30) REVERT: K 18 GLU cc_start: 0.8522 (pm20) cc_final: 0.7961 (pm20) REVERT: K 40 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8833 (m-30) REVERT: K 63 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8614 (mt-10) REVERT: L 54 ASP cc_start: 0.8682 (m-30) cc_final: 0.8342 (m-30) REVERT: M 87 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8575 (mtp) REVERT: O 3 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8196 (tttt) REVERT: O 6 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8473 (mp) REVERT: O 109 ASP cc_start: 0.8963 (m-30) cc_final: 0.8563 (m-30) REVERT: O 124 ASP cc_start: 0.8897 (t0) cc_final: 0.8568 (t0) REVERT: O 157 TYR cc_start: 0.9263 (t80) cc_final: 0.9056 (t80) REVERT: P 133 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: P 135 MET cc_start: 0.9291 (mtp) cc_final: 0.9077 (mtm) REVERT: Q 3 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: Q 24 GLU cc_start: 0.9120 (mp0) cc_final: 0.8779 (mp0) REVERT: Q 110 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8648 (mm-30) REVERT: R 18 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8004 (pt0) REVERT: R 40 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.8993 (m-30) REVERT: R 135 MET cc_start: 0.9127 (mtm) cc_final: 0.8905 (mtm) REVERT: R 151 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8705 (tptt) REVERT: S 48 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7566 (t160) REVERT: S 51 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8393 (ttp80) REVERT: S 69 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8524 (mt0) REVERT: S 118 GLU cc_start: 0.8596 (mp0) cc_final: 0.8251 (mp0) REVERT: T 62 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8234 (mt-10) REVERT: T 116 GLU cc_start: 0.9125 (mp0) cc_final: 0.8566 (mp0) REVERT: U 62 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: U 140 ASN cc_start: 0.9031 (m110) cc_final: 0.8830 (m-40) REVERT: V 33 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8686 (ttmm) REVERT: V 133 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8330 (mp-120) REVERT: W 110 GLU cc_start: 0.8783 (tp30) cc_final: 0.8290 (tp30) REVERT: X 119 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8770 (mt0) REVERT: Y 62 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: Y 109 ASP cc_start: 0.8658 (m-30) cc_final: 0.8172 (m-30) REVERT: Y 118 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: Z 40 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8871 (OUTLIER) REVERT: Z 116 GLU cc_start: 0.8721 (mp0) cc_final: 0.8344 (mp0) REVERT: Z 137 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8145 (p0) outliers start: 82 outliers final: 40 residues processed: 533 average time/residue: 0.9816 time to fit residues: 597.5014 Evaluate side-chains 542 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 480 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 157 ASP Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 228 ASN Chi-restraints excluded: chain 3 residue 234 ASP Chi-restraints excluded: chain 3 residue 236 VAL Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain Q residue 3 LYS Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 160 GLU Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 135 MET Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 133 GLN Chi-restraints excluded: chain X residue 33 LYS Chi-restraints excluded: chain X residue 119 GLN Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 118 GLU Chi-restraints excluded: chain Y residue 128 SER Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 87 MET Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 315 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 324 optimal weight: 0.9980 chunk 325 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 140 GLN 3 228 ASN B 16 GLN C 119 GLN D 62 GLN F 22 ASN G 12 GLN G 119 GLN H 62 GLN J 149 ASN K 119 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN T 119 GLN T 133 GLN T 156 GLN U 16 GLN X 12 GLN Y 48 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.061764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.054369 restraints weight = 76943.438| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.02 r_work: 0.2587 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2459 r_free = 0.2459 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36474 Z= 0.158 Angle : 0.576 10.171 49626 Z= 0.279 Chirality : 0.037 0.162 5486 Planarity : 0.004 0.120 6460 Dihedral : 10.351 81.072 6591 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Rotamer: Outliers : 2.12 % Allowed : 20.25 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.12), residues: 4479 helix: 2.56 (0.08), residues: 3516 sheet: 1.12 (0.93), residues: 32 loop : 0.13 (0.22), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG Y 18 TYR 0.022 0.001 TYR S 92 PHE 0.012 0.001 PHE V 61 TRP 0.006 0.001 TRP 2 137 HIS 0.007 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00370 (36474) covalent geometry : angle 0.57625 (49626) hydrogen bonds : bond 0.03791 ( 2653) hydrogen bonds : angle 3.86832 ( 7851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8958 Ramachandran restraints generated. 4479 Oldfield, 0 Emsley, 4479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 487 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 9 LYS cc_start: 0.9210 (ptpt) cc_final: 0.8779 (pttt) REVERT: 1 147 ASP cc_start: 0.9089 (m-30) cc_final: 0.8862 (m-30) REVERT: 2 31 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: 2 41 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7940 (tmt170) REVERT: 2 49 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8494 (tp) REVERT: 2 89 ASN cc_start: 0.8499 (p0) cc_final: 0.8218 (p0) REVERT: 3 238 ARG cc_start: 0.8221 (tmt170) cc_final: 0.7959 (ttp-170) REVERT: 3 265 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7024 (mtp-110) REVERT: 3 269 LYS cc_start: 0.8299 (tptt) cc_final: 0.8050 (tptt) REVERT: B 26 GLN cc_start: 0.9141 (mt0) cc_final: 0.8864 (mt0) REVERT: B 33 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8627 (mm-30) REVERT: C 88 GLU cc_start: 0.9018 (tt0) cc_final: 0.8550 (tt0) REVERT: D 132 GLU cc_start: 0.8884 (tp30) cc_final: 0.8291 (tp30) REVERT: E 78 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.7332 (ttp80) REVERT: E 88 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: E 119 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8441 (mt0) REVERT: E 135 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8719 (mtm) REVERT: F 3 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8489 (tttt) REVERT: F 6 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8949 (mt) REVERT: F 110 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8170 (mm-30) REVERT: F 157 TYR cc_start: 0.9143 (t80) cc_final: 0.8932 (t80) REVERT: G 18 GLU cc_start: 0.8559 (pm20) cc_final: 0.8352 (pm20) REVERT: H 62 GLN cc_start: 0.8785 (mt0) cc_final: 0.8453 (mm-40) REVERT: H 150 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8760 (mm-30) REVERT: H 156 ASP cc_start: 0.9064 (m-30) cc_final: 0.8793 (m-30) REVERT: I 18 GLU cc_start: 0.8467 (pm20) cc_final: 0.7779 (pm20) REVERT: I 149 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8641 (pp) REVERT: I 151 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8641 (mmtp) REVERT: J 50 GLN cc_start: 0.8658 (tp40) cc_final: 0.8299 (tp40) REVERT: J 54 ASP cc_start: 0.8509 (m-30) cc_final: 0.8263 (m-30) REVERT: J 132 GLU cc_start: 0.8981 (tp30) cc_final: 0.8618 (tp30) REVERT: J 150 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8535 (mm-30) REVERT: K 18 GLU cc_start: 0.8523 (pm20) cc_final: 0.7963 (pm20) REVERT: K 40 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8818 (m-30) REVERT: K 63 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8614 (mt-10) REVERT: L 54 ASP cc_start: 0.8677 (m-30) cc_final: 0.8333 (m-30) REVERT: M 87 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: O 3 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8206 (tttt) REVERT: O 6 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8473 (mp) REVERT: O 109 ASP cc_start: 0.8969 (m-30) cc_final: 0.8614 (m-30) REVERT: O 124 ASP cc_start: 0.8893 (t0) cc_final: 0.8504 (t0) REVERT: P 133 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8110 (tp40) REVERT: P 135 MET cc_start: 0.9292 (mtp) cc_final: 0.9079 (mtm) REVERT: Q 3 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8086 (mtpp) REVERT: Q 24 GLU cc_start: 0.9126 (mp0) cc_final: 0.8765 (mp0) REVERT: Q 110 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8652 (mm-30) REVERT: R 18 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8000 (pt0) REVERT: R 40 ASP cc_start: 0.9242 (OUTLIER) cc_final: 0.8997 (m-30) REVERT: R 135 MET cc_start: 0.9135 (mtm) cc_final: 0.8926 (mtm) REVERT: R 151 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8706 (tptt) REVERT: S 48 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7518 (t160) REVERT: S 51 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8437 (ttp80) REVERT: S 69 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: S 118 GLU cc_start: 0.8528 (mp0) cc_final: 0.8208 (mp0) REVERT: T 62 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8215 (mt-10) REVERT: T 116 GLU cc_start: 0.9124 (mp0) cc_final: 0.8572 (mp0) REVERT: T 156 GLN cc_start: 0.8288 (mt0) cc_final: 0.8010 (mp10) REVERT: U 62 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: V 33 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8688 (ttmm) REVERT: V 133 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8326 (mp-120) REVERT: W 110 GLU cc_start: 0.8788 (tp30) cc_final: 0.8299 (tp30) REVERT: W 124 ASP cc_start: 0.9106 (t0) cc_final: 0.8835 (t70) REVERT: X 119 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8750 (mt0) REVERT: Y 62 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: Y 109 ASP cc_start: 0.8659 (m-30) cc_final: 0.8176 (m-30) REVERT: Y 118 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: Z 40 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8874 (OUTLIER) REVERT: Z 116 GLU cc_start: 0.8721 (mp0) cc_final: 0.8314 (mp0) REVERT: Z 137 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8153 (p0) outliers start: 75 outliers final: 42 residues processed: 530 average time/residue: 1.0120 time to fit residues: 611.2864 Evaluate side-chains 540 residues out of total 3535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 475 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 25 VAL Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 157 ASP Chi-restraints excluded: chain 2 residue 31 GLU Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 246 SER Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 281 VAL Chi-restraints excluded: chain 2 residue 283 VAL Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 3 residue 225 ASN Chi-restraints excluded: chain 3 residue 228 ASN Chi-restraints excluded: chain 3 residue 234 ASP Chi-restraints excluded: chain 3 residue 236 VAL Chi-restraints excluded: chain 3 residue 244 ILE Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 284 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 78 ARG Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain Q residue 3 LYS Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 160 GLU Chi-restraints excluded: chain S residue 48 ASN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 135 MET Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 133 GLN Chi-restraints excluded: chain X residue 119 GLN Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 62 GLN Chi-restraints excluded: chain Y residue 118 GLU Chi-restraints excluded: chain Y residue 128 SER Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 87 MET Chi-restraints excluded: chain Z residue 137 ASP Chi-restraints excluded: chain Z residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 337 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 440 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 236 optimal weight: 0.7980 chunk 335 optimal weight: 0.6980 chunk 340 optimal weight: 2.9990 chunk 164 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 140 GLN 3 228 ASN B 16 GLN C 119 GLN D 62 GLN F 22 ASN G 12 GLN G 119 GLN J 149 ASN K 119 GLN ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 133 GLN S 16 GLN T 119 GLN T 133 GLN U 16 GLN V 133 GLN Y 48 ASN ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.062218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.054836 restraints weight = 76084.249| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.01 r_work: 0.2602 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36474 Z= 0.145 Angle : 0.566 10.228 49626 Z= 0.274 Chirality : 0.037 0.166 5486 Planarity : 0.004 0.124 6460 Dihedral : 10.353 81.333 6591 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 2.07 % Allowed : 20.25 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.12), residues: 4479 helix: 2.57 (0.08), residues: 3525 sheet: 1.12 (0.93), residues: 32 loop : 0.18 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG Y 18 TYR 0.024 0.001 TYR S 92 PHE 0.013 0.001 PHE V 61 TRP 0.006 0.001 TRP 2 137 HIS 0.007 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00339 (36474) covalent geometry : angle 0.56596 (49626) hydrogen bonds : bond 0.03721 ( 2653) hydrogen bonds : angle 3.84715 ( 7851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13604.34 seconds wall clock time: 232 minutes 20.53 seconds (13940.53 seconds total)