Starting phenix.real_space_refine on Sat Feb 7 08:44:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k81_62157/02_2026/9k81_62157.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k81_62157/02_2026/9k81_62157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k81_62157/02_2026/9k81_62157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k81_62157/02_2026/9k81_62157.map" model { file = "/net/cci-nas-00/data/ceres_data/9k81_62157/02_2026/9k81_62157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k81_62157/02_2026/9k81_62157.cif" } resolution = 2.53 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= 0.015 sd= 0.208 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: 5 Type Number sf(0) Gaussians Zn 43 6.06 5 S 25 5.16 5 C 20125 2.51 5 N 5550 2.21 5 O 6050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31793 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "B" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "C" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "D" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "E" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "F" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "G" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "H" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "I" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "J" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "K" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "L" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "M" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "N" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "O" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "P" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "Q" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "R" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "S" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "T" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "U" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "V" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "W" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "X" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "Y" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1270 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.94, per 1000 atoms: 0.22 Number of scatterers: 31793 At special positions: 0 Unit cell: (117.426, 121.735, 184.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 43 29.99 S 25 16.00 O 6050 8.00 N 5550 7.00 C 20125 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: 2.94 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 25 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS B 125 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" NE2 HIS A 147 " pdb="ZN ZN A 202 " - pdb=" NE2 HIS L 79 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 25 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS D 125 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" NE2 HIS B 147 " pdb="ZN ZN B 202 " - pdb=" NE2 HIS N 79 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS C 25 " pdb="ZN ZN C 201 " - pdb=" NE2 HIS A 125 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS O 147 " pdb="ZN ZN C 202 " - pdb=" NE2 HIS C 79 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" NE2 HIS E 25 " pdb="ZN ZN C 203 " - pdb=" NE2 HIS C 125 " pdb=" ZN C 204 " pdb="ZN ZN C 204 " - pdb=" NE2 HIS C 147 " pdb="ZN ZN C 204 " - pdb=" NE2 HIS J 79 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS D 25 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS F 125 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" NE2 HIS D 147 " pdb="ZN ZN D 202 " - pdb=" NE2 HIS P 79 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" NE2 HIS E 125 " pdb="ZN ZN E 201 " - pdb=" NE2 HIS G 25 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" NE2 HIS E 147 " pdb="ZN ZN E 202 " - pdb=" NE2 HIS H 79 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" NE2 HIS G 147 " pdb="ZN ZN F 201 " - pdb=" NE2 HIS F 79 " pdb=" ZN F 202 " pdb="ZN ZN F 202 " - pdb=" NE2 HIS F 25 " pdb="ZN ZN F 202 " - pdb=" NE2 HIS H 125 " pdb=" ZN F 203 " pdb="ZN ZN F 203 " - pdb=" NE2 HIS F 147 " pdb="ZN ZN F 203 " - pdb=" NE2 HIS R 79 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS S 147 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" NE2 HIS H 25 " pdb="ZN ZN H 201 " - pdb=" NE2 HIS J 125 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 147 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS T 79 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 147 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 25 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS G 125 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" NE2 HIS K 25 " pdb="ZN ZN I 203 " - pdb=" NE2 HIS I 125 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" NE2 HIS J 25 " pdb="ZN ZN J 201 " - pdb=" NE2 HIS L 125 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" NE2 HIS J 147 " pdb="ZN ZN J 202 " - pdb=" NE2 HIS V 79 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" NE2 HIS K 147 " pdb="ZN ZN K 201 " - pdb=" NE2 HIS B 79 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS M 25 " pdb="ZN ZN K 202 " - pdb=" NE2 HIS K 125 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" NE2 HIS L 25 " pdb="ZN ZN L 201 " - pdb=" NE2 HIS N 125 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS L 147 " pdb="ZN ZN L 202 " - pdb=" NE2 HIS X 79 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" NE2 HIS M 147 " pdb="ZN ZN M 201 " - pdb=" NE2 HIS A 79 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" NE2 HIS N 25 " pdb="ZN ZN N 201 " - pdb=" NE2 HIS P 125 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 147 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS Y 79 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" NE2 HIS O 25 " pdb="ZN ZN O 201 " - pdb=" NE2 HIS M 125 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" NE2 HIS P 25 " pdb="ZN ZN P 201 " - pdb=" NE2 HIS R 125 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" NE2 HIS Q 147 " pdb="ZN ZN Q 201 " - pdb=" NE2 HIS E 79 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" NE2 HIS Q 25 " pdb="ZN ZN Q 202 " - pdb=" NE2 HIS O 125 " pdb=" ZN Q 203 " pdb="ZN ZN Q 203 " - pdb=" NE2 HIS Q 125 " pdb="ZN ZN Q 203 " - pdb=" NE2 HIS S 25 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 25 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS T 125 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" NE2 HIS U 25 " pdb="ZN ZN S 201 " - pdb=" NE2 HIS S 125 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 25 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS V 125 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" NE2 HIS U 147 " pdb="ZN ZN U 201 " - pdb=" NE2 HIS I 79 " pdb=" ZN U 202 " pdb="ZN ZN U 202 " - pdb=" NE2 HIS U 125 " pdb="ZN ZN U 202 " - pdb=" NE2 HIS W 25 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" NE2 HIS V 25 " pdb="ZN ZN V 201 " - pdb=" NE2 HIS X 125 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" NE2 HIS W 147 " pdb="ZN ZN W 201 " - pdb=" NE2 HIS K 79 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" NE2 HIS X 25 " pdb="ZN ZN X 201 " - pdb=" NE2 HIS Y 125 " 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 0 sheets defined 94.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 26 removed outlier: 3.637A pdb=" N ALA A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.509A pdb=" N LEU A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 Processing helix chain 'A' and resid 70 through 87 Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 112 through 129 Processing helix chain 'A' and resid 131 through 151 Processing helix chain 'A' and resid 154 through 172 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.962A pdb=" N VAL B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 68 Processing helix chain 'B' and resid 70 through 87 removed outlier: 3.580A pdb=" N ASP B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 109 Processing helix chain 'B' and resid 112 through 129 Processing helix chain 'B' and resid 131 through 152 Processing helix chain 'B' and resid 154 through 172 Processing helix chain 'C' and resid 5 through 26 Processing helix chain 'C' and resid 28 through 45 removed outlier: 3.532A pdb=" N LEU C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 68 Processing helix chain 'C' and resid 70 through 87 Processing helix chain 'C' and resid 89 through 110 Processing helix chain 'C' and resid 112 through 129 Processing helix chain 'C' and resid 131 through 151 Processing helix chain 'C' and resid 154 through 172 Processing helix chain 'D' and resid 5 through 26 Processing helix chain 'D' and resid 28 through 45 removed outlier: 3.978A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 68 Processing helix chain 'D' and resid 70 through 87 Processing helix chain 'D' and resid 89 through 110 Processing helix chain 'D' and resid 112 through 129 Processing helix chain 'D' and resid 131 through 152 Processing helix chain 'D' and resid 154 through 172 Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 28 through 45 removed outlier: 3.527A pdb=" N LEU E 32 " --> pdb=" O PRO E 28 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 68 Processing helix chain 'E' and resid 70 through 87 Processing helix chain 'E' and resid 89 through 110 Processing helix chain 'E' and resid 112 through 129 Processing helix chain 'E' and resid 131 through 151 Processing helix chain 'E' and resid 154 through 172 Processing helix chain 'F' and resid 5 through 26 Processing helix chain 'F' and resid 28 through 45 removed outlier: 3.927A pdb=" N VAL F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 68 Processing helix chain 'F' and resid 70 through 87 removed outlier: 3.512A pdb=" N ASP F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 110 Processing helix chain 'F' and resid 112 through 129 Processing helix chain 'F' and resid 131 through 152 Processing helix chain 'F' and resid 154 through 172 Processing helix chain 'G' and resid 5 through 26 Processing helix chain 'G' and resid 28 through 45 removed outlier: 3.563A pdb=" N LEU G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 68 Processing helix chain 'G' and resid 70 through 87 Processing helix chain 'G' and resid 89 through 109 Processing helix chain 'G' and resid 112 through 129 Processing helix chain 'G' and resid 131 through 151 Processing helix chain 'G' and resid 154 through 172 Processing helix chain 'H' and resid 5 through 26 Processing helix chain 'H' and resid 28 through 45 removed outlier: 4.006A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 68 Processing helix chain 'H' and resid 70 through 87 Processing helix chain 'H' and resid 89 through 110 Processing helix chain 'H' and resid 112 through 129 Processing helix chain 'H' and resid 131 through 152 Processing helix chain 'H' and resid 154 through 172 Processing helix chain 'I' and resid 5 through 26 Processing helix chain 'I' and resid 28 through 45 removed outlier: 3.517A pdb=" N LEU I 32 " --> pdb=" O PRO I 28 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 68 Processing helix chain 'I' and resid 70 through 87 Processing helix chain 'I' and resid 89 through 110 Processing helix chain 'I' and resid 112 through 129 Processing helix chain 'I' and resid 131 through 151 Processing helix chain 'I' and resid 154 through 172 Processing helix chain 'J' and resid 5 through 26 Processing helix chain 'J' and resid 28 through 45 removed outlier: 3.970A pdb=" N VAL J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 68 Processing helix chain 'J' and resid 70 through 88 Processing helix chain 'J' and resid 89 through 110 Processing helix chain 'J' and resid 112 through 129 Processing helix chain 'J' and resid 131 through 152 Processing helix chain 'J' and resid 154 through 172 Processing helix chain 'K' and resid 5 through 26 Processing helix chain 'K' and resid 28 through 45 removed outlier: 3.572A pdb=" N LEU K 32 " --> pdb=" O PRO K 28 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 Processing helix chain 'K' and resid 70 through 87 Processing helix chain 'K' and resid 89 through 110 Processing helix chain 'K' and resid 112 through 129 Processing helix chain 'K' and resid 131 through 151 Processing helix chain 'K' and resid 154 through 172 Processing helix chain 'L' and resid 5 through 26 Processing helix chain 'L' and resid 28 through 45 removed outlier: 3.878A pdb=" N VAL L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 68 Processing helix chain 'L' and resid 70 through 87 Processing helix chain 'L' and resid 89 through 110 Processing helix chain 'L' and resid 112 through 129 Processing helix chain 'L' and resid 131 through 152 Processing helix chain 'L' and resid 154 through 172 Processing helix chain 'M' and resid 5 through 26 Processing helix chain 'M' and resid 28 through 45 removed outlier: 3.567A pdb=" N LEU M 32 " --> pdb=" O PRO M 28 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 68 Processing helix chain 'M' and resid 70 through 87 Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 112 through 129 Processing helix chain 'M' and resid 131 through 151 Processing helix chain 'M' and resid 154 through 172 Processing helix chain 'N' and resid 5 through 26 Processing helix chain 'N' and resid 28 through 45 removed outlier: 3.930A pdb=" N VAL N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 68 Processing helix chain 'N' and resid 70 through 87 Processing helix chain 'N' and resid 89 through 109 Processing helix chain 'N' and resid 112 through 129 Processing helix chain 'N' and resid 131 through 152 Processing helix chain 'N' and resid 154 through 172 Processing helix chain 'O' and resid 5 through 26 Processing helix chain 'O' and resid 28 through 45 removed outlier: 3.524A pdb=" N LEU O 32 " --> pdb=" O PRO O 28 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 68 Processing helix chain 'O' and resid 70 through 87 Processing helix chain 'O' and resid 89 through 110 Processing helix chain 'O' and resid 112 through 129 Processing helix chain 'O' and resid 131 through 151 Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'P' and resid 5 through 26 Processing helix chain 'P' and resid 28 through 45 removed outlier: 3.863A pdb=" N VAL P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 68 Processing helix chain 'P' and resid 70 through 87 Processing helix chain 'P' and resid 89 through 110 Processing helix chain 'P' and resid 112 through 129 Processing helix chain 'P' and resid 131 through 152 Processing helix chain 'P' and resid 154 through 172 Processing helix chain 'Q' and resid 5 through 26 Processing helix chain 'Q' and resid 28 through 45 removed outlier: 3.901A pdb=" N VAL Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 68 Processing helix chain 'Q' and resid 70 through 88 Processing helix chain 'Q' and resid 89 through 110 Processing helix chain 'Q' and resid 112 through 129 Processing helix chain 'Q' and resid 131 through 151 Processing helix chain 'Q' and resid 154 through 172 Processing helix chain 'R' and resid 5 through 26 Processing helix chain 'R' and resid 28 through 45 removed outlier: 3.507A pdb=" N LEU R 32 " --> pdb=" O PRO R 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 68 Processing helix chain 'R' and resid 70 through 88 Processing helix chain 'R' and resid 89 through 110 Processing helix chain 'R' and resid 112 through 129 Processing helix chain 'R' and resid 131 through 152 Processing helix chain 'R' and resid 154 through 172 Processing helix chain 'S' and resid 5 through 26 Processing helix chain 'S' and resid 28 through 45 removed outlier: 4.006A pdb=" N VAL S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 68 Processing helix chain 'S' and resid 70 through 87 Processing helix chain 'S' and resid 89 through 110 Processing helix chain 'S' and resid 112 through 129 Processing helix chain 'S' and resid 131 through 151 Processing helix chain 'S' and resid 154 through 172 Processing helix chain 'T' and resid 5 through 26 Processing helix chain 'T' and resid 28 through 45 removed outlier: 3.938A pdb=" N VAL T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 68 Processing helix chain 'T' and resid 70 through 88 Processing helix chain 'T' and resid 89 through 109 Processing helix chain 'T' and resid 112 through 129 Processing helix chain 'T' and resid 131 through 152 Processing helix chain 'T' and resid 154 through 172 Processing helix chain 'U' and resid 5 through 26 Processing helix chain 'U' and resid 28 through 45 removed outlier: 4.050A pdb=" N VAL U 45 " --> pdb=" O ALA U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 68 removed outlier: 3.669A pdb=" N VAL U 51 " --> pdb=" O ASP U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 87 Processing helix chain 'U' and resid 89 through 109 removed outlier: 3.555A pdb=" N VAL U 93 " --> pdb=" O ASP U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 129 Processing helix chain 'U' and resid 131 through 151 Processing helix chain 'U' and resid 154 through 172 Processing helix chain 'V' and resid 5 through 26 Processing helix chain 'V' and resid 28 through 45 removed outlier: 4.008A pdb=" N VAL V 45 " --> pdb=" O ALA V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 68 Processing helix chain 'V' and resid 70 through 88 Processing helix chain 'V' and resid 89 through 109 Processing helix chain 'V' and resid 112 through 129 Processing helix chain 'V' and resid 131 through 152 Processing helix chain 'V' and resid 154 through 172 Processing helix chain 'W' and resid 5 through 26 Processing helix chain 'W' and resid 28 through 45 removed outlier: 3.965A pdb=" N VAL W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 68 removed outlier: 3.708A pdb=" N VAL W 51 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 87 Processing helix chain 'W' and resid 89 through 109 Processing helix chain 'W' and resid 112 through 129 Processing helix chain 'W' and resid 131 through 151 Processing helix chain 'W' and resid 154 through 172 Processing helix chain 'X' and resid 5 through 26 Processing helix chain 'X' and resid 28 through 45 removed outlier: 3.986A pdb=" N VAL X 45 " --> pdb=" O ALA X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 68 Processing helix chain 'X' and resid 70 through 88 Processing helix chain 'X' and resid 89 through 109 Processing helix chain 'X' and resid 112 through 129 Processing helix chain 'X' and resid 131 through 152 Processing helix chain 'X' and resid 154 through 172 Processing helix chain 'Y' and resid 5 through 26 Processing helix chain 'Y' and resid 28 through 45 removed outlier: 3.527A pdb=" N LEU Y 32 " --> pdb=" O PRO Y 28 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL Y 45 " --> pdb=" O ALA Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 68 Processing helix chain 'Y' and resid 70 through 88 Processing helix chain 'Y' and resid 89 through 110 Processing helix chain 'Y' and resid 112 through 129 Processing helix chain 'Y' and resid 131 through 152 Processing helix chain 'Y' and resid 154 through 172 3171 hydrogen bonds defined for protein. 9513 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: 5.72 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11025 1.34 - 1.45: 1181 1.45 - 1.57: 19744 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 32000 Sorted by residual: bond pdb=" C ASN D 59 " pdb=" O ASN D 59 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.19e-02 7.06e+03 2.02e+00 bond pdb=" N ASN G 59 " pdb=" CA ASN G 59 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.23e-02 6.61e+03 1.93e+00 bond pdb=" C ASN L 59 " pdb=" O ASN L 59 " ideal model delta sigma weight residual 1.237 1.221 0.016 1.19e-02 7.06e+03 1.80e+00 bond pdb=" C ILE G 58 " pdb=" N ASN G 59 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.36e-02 5.41e+03 1.79e+00 bond pdb=" C ASN G 59 " pdb=" O ASN G 59 " ideal model delta sigma weight residual 1.237 1.222 0.015 1.19e-02 7.06e+03 1.58e+00 ... (remaining 31995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 42510 1.56 - 3.13: 751 3.13 - 4.69: 140 4.69 - 6.26: 40 6.26 - 7.82: 9 Bond angle restraints: 43450 Sorted by residual: angle pdb=" CA GLU Y 98 " pdb=" CB GLU Y 98 " pdb=" CG GLU Y 98 " ideal model delta sigma weight residual 114.10 121.19 -7.09 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CG ARG Y 168 " pdb=" CD ARG Y 168 " pdb=" NE ARG Y 168 " ideal model delta sigma weight residual 112.00 118.72 -6.72 2.20e+00 2.07e-01 9.33e+00 angle pdb=" CG ARG I 168 " pdb=" CD ARG I 168 " pdb=" NE ARG I 168 " ideal model delta sigma weight residual 112.00 118.12 -6.12 2.20e+00 2.07e-01 7.74e+00 angle pdb=" CG ARG R 168 " pdb=" CD ARG R 168 " pdb=" NE ARG R 168 " ideal model delta sigma weight residual 112.00 117.11 -5.11 2.20e+00 2.07e-01 5.39e+00 angle pdb=" N ASP G 34 " pdb=" CA ASP G 34 " pdb=" CB ASP G 34 " ideal model delta sigma weight residual 110.12 113.51 -3.39 1.47e+00 4.63e-01 5.31e+00 ... (remaining 43445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17007 17.93 - 35.87: 2070 35.87 - 53.80: 697 53.80 - 71.73: 134 71.73 - 89.66: 67 Dihedral angle restraints: 19975 sinusoidal: 7700 harmonic: 12275 Sorted by residual: dihedral pdb=" CA ASP T 87 " pdb=" C ASP T 87 " pdb=" N ARG T 88 " pdb=" CA ARG T 88 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP Y 87 " pdb=" C ASP Y 87 " pdb=" N ARG Y 88 " pdb=" CA ARG Y 88 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASP V 87 " pdb=" C ASP V 87 " pdb=" N ARG V 88 " pdb=" CA ARG V 88 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 19972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 5252 0.074 - 0.148: 254 0.148 - 0.221: 9 0.221 - 0.295: 7 0.295 - 0.369: 3 Chirality restraints: 5525 Sorted by residual: chirality pdb=" CG LEU P 52 " pdb=" CB LEU P 52 " pdb=" CD1 LEU P 52 " pdb=" CD2 LEU P 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CG LEU L 52 " pdb=" CB LEU L 52 " pdb=" CD1 LEU L 52 " pdb=" CD2 LEU L 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU N 52 " pdb=" CB LEU N 52 " pdb=" CD1 LEU N 52 " pdb=" CD2 LEU N 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5522 not shown) Planarity restraints: 5625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU Q 44 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" CD GLU Q 44 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU Q 44 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU Q 44 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 34 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" CG ASP A 34 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP A 34 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 34 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL O 153 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO O 154 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO O 154 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO O 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 5622 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 225 2.50 - 3.10: 22832 3.10 - 3.70: 50858 3.70 - 4.30: 69931 4.30 - 4.90: 118898 Nonbonded interactions: 262744 Sorted by model distance: nonbonded pdb=" OD2 ASP D 143 " pdb="ZN ZN D 202 " model vdw 1.897 2.230 nonbonded pdb=" OD2 ASP L 143 " pdb="ZN ZN L 202 " model vdw 1.900 2.230 nonbonded pdb=" OD2 ASP D 21 " pdb="ZN ZN D 201 " model vdw 1.915 2.230 nonbonded pdb=" OD2 ASP B 21 " pdb="ZN ZN B 201 " model vdw 1.927 2.230 nonbonded pdb=" OD2 ASP A 21 " pdb="ZN ZN A 201 " model vdw 1.928 2.230 ... (remaining 262739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 173) selection = (chain 'B' and resid 4 through 173) selection = (chain 'C' and resid 4 through 173) selection = (chain 'D' and resid 4 through 173) selection = (chain 'E' and resid 4 through 173) selection = (chain 'F' and resid 4 through 173) selection = (chain 'G' and resid 4 through 173) selection = (chain 'H' and resid 4 through 173) selection = (chain 'I' and resid 4 through 173) selection = (chain 'J' and resid 4 through 173) selection = (chain 'K' and resid 4 through 173) selection = (chain 'L' and resid 4 through 173) selection = (chain 'M' and resid 4 through 173) selection = (chain 'N' and resid 4 through 173) selection = (chain 'O' and resid 4 through 173) selection = (chain 'P' and resid 4 through 173) selection = (chain 'Q' and resid 4 through 173) selection = (chain 'R' and resid 4 through 173) selection = (chain 'S' and resid 4 through 173) selection = (chain 'T' and resid 4 through 173) selection = (chain 'U' and resid 4 through 173) selection = (chain 'V' and resid 4 through 173) selection = (chain 'W' and resid 4 through 173) selection = (chain 'X' and resid 4 through 173) selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 31.600 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.316 32086 Z= 0.353 Angle : 0.556 7.822 43450 Z= 0.292 Chirality : 0.042 0.369 5525 Planarity : 0.005 0.055 5625 Dihedral : 18.503 89.665 11975 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.80 % Allowed : 29.04 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.82 (0.12), residues: 4200 helix: 2.45 (0.07), residues: 3950 sheet: None (None), residues: 0 loop : 3.87 (0.51), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 168 TYR 0.020 0.003 TYR F 170 HIS 0.004 0.001 HIS T 125 Details of bonding type rmsd covalent geometry : bond 0.00506 (32000) covalent geometry : angle 0.55617 (43450) hydrogen bonds : bond 0.12755 ( 3171) hydrogen bonds : angle 4.25890 ( 9513) metal coordination : bond 0.16444 ( 86) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 771 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8548 (mtmt) REVERT: B 143 ASP cc_start: 0.8801 (t0) cc_final: 0.8525 (t70) REVERT: B 163 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (mtpp) REVERT: C 163 LYS cc_start: 0.8264 (ttmm) cc_final: 0.8063 (mtpp) REVERT: D 52 LEU cc_start: 0.8305 (mt) cc_final: 0.8096 (mm) REVERT: D 155 ASP cc_start: 0.8498 (m-30) cc_final: 0.8294 (m-30) REVERT: F 36 GLU cc_start: 0.8744 (tt0) cc_final: 0.8434 (tt0) REVERT: F 144 LYS cc_start: 0.8731 (tmtm) cc_final: 0.8419 (tptt) REVERT: F 167 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: G 23 LYS cc_start: 0.9091 (tppt) cc_final: 0.8765 (mttt) REVERT: G 24 LYS cc_start: 0.8517 (mttp) cc_final: 0.8249 (mttp) REVERT: G 140 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7804 (mt-10) REVERT: H 163 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7937 (mtpp) REVERT: I 24 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8525 (mtpt) REVERT: J 167 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: J 170 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6108 (m-10) REVERT: K 108 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8086 (mtmt) REVERT: K 163 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8022 (mtpp) REVERT: L 157 GLU cc_start: 0.7850 (mp0) cc_final: 0.7528 (mp0) REVERT: M 77 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8839 (mt) REVERT: M 98 GLU cc_start: 0.8507 (tp30) cc_final: 0.8131 (tp30) REVERT: M 140 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7762 (mt-10) REVERT: M 163 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8219 (mtpp) REVERT: N 56 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8465 (mtp180) REVERT: N 88 ARG cc_start: 0.8552 (mtt90) cc_final: 0.8281 (mtt180) REVERT: O 24 LYS cc_start: 0.8631 (tppt) cc_final: 0.8329 (mttp) REVERT: O 94 ASP cc_start: 0.7827 (m-30) cc_final: 0.7535 (m-30) REVERT: O 98 GLU cc_start: 0.8356 (tp30) cc_final: 0.8096 (tp30) REVERT: P 90 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7049 (mt-10) REVERT: P 94 ASP cc_start: 0.8068 (m-30) cc_final: 0.7501 (m-30) REVERT: P 170 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6334 (m-10) REVERT: Q 98 GLU cc_start: 0.8221 (tp30) cc_final: 0.7957 (tp30) REVERT: Q 140 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7658 (mt-10) REVERT: Q 157 GLU cc_start: 0.7969 (mp0) cc_final: 0.7638 (mp0) REVERT: R 170 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5411 (m-10) REVERT: S 24 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7974 (mttp) REVERT: S 90 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6565 (mm-30) REVERT: S 140 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7230 (mt-10) REVERT: S 164 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: T 44 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7477 (mt-10) REVERT: U 24 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7938 (mttp) REVERT: U 88 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7058 (mtm-85) REVERT: U 90 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6560 (mp0) REVERT: U 98 GLU cc_start: 0.8082 (tp30) cc_final: 0.7848 (tp30) REVERT: V 37 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7871 (tpt-90) REVERT: V 94 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: W 13 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7227 (mtm-85) REVERT: W 140 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7308 (mt-10) REVERT: X 163 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7904 (mtpp) REVERT: Y 52 LEU cc_start: 0.7880 (tp) cc_final: 0.7223 (mm) REVERT: Y 131 ASP cc_start: 0.8570 (t0) cc_final: 0.8014 (t0) REVERT: Y 144 LYS cc_start: 0.7856 (tptm) cc_final: 0.7531 (tptp) REVERT: Y 163 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7721 (mtpp) outliers start: 89 outliers final: 35 residues processed: 816 average time/residue: 0.9177 time to fit residues: 846.4210 Evaluate side-chains 704 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 660 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 30 ASP Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 30 ASP Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 94 ASP Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 30 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN D 59 ASN G 59 ASN H 128 GLN L 59 ASN M 59 ASN N 59 ASN S 59 ASN S 128 GLN V 128 GLN X 128 GLN Y 128 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.116840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093860 restraints weight = 30755.527| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.66 r_work: 0.2945 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32086 Z= 0.128 Angle : 0.466 6.887 43450 Z= 0.246 Chirality : 0.038 0.355 5525 Planarity : 0.006 0.051 5625 Dihedral : 5.653 70.512 4674 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 5.73 % Allowed : 24.60 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.62 (0.12), residues: 4200 helix: 2.88 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.81 (0.61), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 130 TYR 0.008 0.001 TYR N 161 HIS 0.003 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00274 (32000) covalent geometry : angle 0.46565 (43450) hydrogen bonds : bond 0.05116 ( 3171) hydrogen bonds : angle 3.35199 ( 9513) metal coordination : bond 0.00267 ( 86) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 673 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7664 (p0) cc_final: 0.7333 (OUTLIER) REVERT: A 52 LEU cc_start: 0.7881 (mt) cc_final: 0.7645 (mm) REVERT: B 24 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8517 (mtpt) REVERT: B 52 LEU cc_start: 0.8016 (mt) cc_final: 0.7806 (mm) REVERT: B 90 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 94 ASP cc_start: 0.8271 (m-30) cc_final: 0.7727 (m-30) REVERT: B 163 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7835 (mtpp) REVERT: B 164 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: B 170 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5272 (m-10) REVERT: C 24 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8272 (mtpt) REVERT: C 108 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7883 (mtpt) REVERT: C 144 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8207 (tttp) REVERT: D 161 TYR cc_start: 0.8645 (t80) cc_final: 0.8429 (t80) REVERT: D 163 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7816 (mtpp) REVERT: E 90 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7323 (mm-30) REVERT: E 130 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7777 (mmt90) REVERT: F 36 GLU cc_start: 0.8682 (tt0) cc_final: 0.8382 (tt0) REVERT: F 163 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7800 (mtpp) REVERT: G 23 LYS cc_start: 0.9001 (tppt) cc_final: 0.8777 (mttt) REVERT: G 24 LYS cc_start: 0.8476 (mttp) cc_final: 0.8227 (mttp) REVERT: G 140 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7620 (mt-10) REVERT: G 170 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6405 (m-10) REVERT: H 90 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: H 163 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7676 (mtpp) REVERT: H 170 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.5333 (m-10) REVERT: I 24 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8436 (mtpt) REVERT: J 30 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7657 (p0) REVERT: J 170 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5668 (m-10) REVERT: K 87 ASP cc_start: 0.6986 (m-30) cc_final: 0.6749 (m-30) REVERT: K 108 LYS cc_start: 0.8301 (mtmt) cc_final: 0.8067 (mtmt) REVERT: K 148 MET cc_start: 0.8480 (mtp) cc_final: 0.8146 (mtp) REVERT: L 56 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8569 (mtp180) REVERT: L 90 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: L 157 GLU cc_start: 0.7969 (mp0) cc_final: 0.7675 (mp0) REVERT: L 168 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6853 (ttm110) REVERT: M 49 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: M 144 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7948 (tmtm) REVERT: M 163 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8109 (mtpp) REVERT: N 130 ARG cc_start: 0.8240 (mmt-90) cc_final: 0.8024 (mmt-90) REVERT: O 30 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7482 (p0) REVERT: O 48 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7533 (ttp80) REVERT: O 94 ASP cc_start: 0.7966 (m-30) cc_final: 0.7718 (m-30) REVERT: P 144 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7976 (tmtm) REVERT: P 170 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6332 (m-10) REVERT: Q 140 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7635 (mt-10) REVERT: Q 170 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.5122 (m-10) REVERT: R 24 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8111 (mtmm) REVERT: R 130 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7502 (mmt90) REVERT: R 170 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5395 (m-10) REVERT: S 24 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8329 (mttp) REVERT: S 77 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8957 (mt) REVERT: S 140 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7386 (mt-10) REVERT: S 164 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7193 (mp0) REVERT: T 44 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7540 (mt-10) REVERT: T 108 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8266 (mtmp) REVERT: T 157 GLU cc_start: 0.7732 (mp0) cc_final: 0.7513 (mp0) REVERT: T 170 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6313 (m-10) REVERT: U 24 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8438 (mttp) REVERT: U 113 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8093 (tttp) REVERT: U 157 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: V 30 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7429 (p0) REVERT: V 37 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7922 (tpt-90) REVERT: V 89 ASP cc_start: 0.8318 (t0) cc_final: 0.7995 (t70) REVERT: V 137 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7511 (mtt180) REVERT: W 49 GLU cc_start: 0.7558 (mp0) cc_final: 0.7180 (tt0) REVERT: W 71 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7535 (tptm) REVERT: W 88 ARG cc_start: 0.5844 (mtm-85) cc_final: 0.5325 (mtp180) REVERT: W 137 ARG cc_start: 0.8083 (mtm-85) cc_final: 0.7805 (mtm-85) REVERT: W 140 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7788 (mt-10) REVERT: X 144 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7224 (tmtm) REVERT: X 161 TYR cc_start: 0.8611 (t80) cc_final: 0.8359 (t80) REVERT: X 163 LYS cc_start: 0.8336 (mtpt) cc_final: 0.8116 (mtpp) REVERT: Y 24 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8493 (mtpp) REVERT: Y 52 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7828 (mm) REVERT: Y 98 GLU cc_start: 0.8253 (tp30) cc_final: 0.7823 (tp30) REVERT: Y 137 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7564 (mtt180) REVERT: Y 144 LYS cc_start: 0.8642 (tptm) cc_final: 0.8396 (tmtm) REVERT: Y 170 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5252 (m-10) outliers start: 182 outliers final: 33 residues processed: 776 average time/residue: 0.8995 time to fit residues: 789.5514 Evaluate side-chains 691 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 627 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain O residue 30 ASP Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 131 ASP Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 137 ARG Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 144 LYS Chi-restraints excluded: chain X residue 167 GLU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 90 GLU Chi-restraints excluded: chain Y residue 137 ARG Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 88 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 415 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 406 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 128 GLN M 59 ASN Q 128 GLN R 59 ASN S 59 ASN S 128 GLN T 59 ASN V 128 GLN X 128 GLN Y 128 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093532 restraints weight = 30527.831| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.66 r_work: 0.2944 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32086 Z= 0.129 Angle : 0.459 7.013 43450 Z= 0.241 Chirality : 0.038 0.351 5525 Planarity : 0.006 0.071 5625 Dihedral : 4.375 46.190 4603 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 6.14 % Allowed : 24.16 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.89 (0.12), residues: 4200 helix: 3.06 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.76 (0.61), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 130 TYR 0.008 0.001 TYR N 161 HIS 0.002 0.000 HIS K 125 Details of bonding type rmsd covalent geometry : bond 0.00276 (32000) covalent geometry : angle 0.45935 (43450) hydrogen bonds : bond 0.05236 ( 3171) hydrogen bonds : angle 3.23198 ( 9513) metal coordination : bond 0.00205 ( 86) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 665 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7279 (p0) REVERT: A 102 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8404 (mmt-90) REVERT: A 131 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: A 161 TYR cc_start: 0.8577 (t80) cc_final: 0.8336 (t80) REVERT: A 170 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.5262 (m-10) REVERT: B 24 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8649 (mtpt) REVERT: B 90 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7294 (mm-30) REVERT: B 94 ASP cc_start: 0.8267 (m-30) cc_final: 0.7812 (m-30) REVERT: B 163 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7746 (mtpp) REVERT: B 170 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.5238 (m-10) REVERT: C 108 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7907 (mtpt) REVERT: C 144 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8193 (tttp) REVERT: C 170 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.5875 (m-10) REVERT: D 102 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8377 (mmt180) REVERT: E 44 GLU cc_start: 0.8524 (tt0) cc_final: 0.8117 (mt-10) REVERT: E 48 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6960 (ttp-110) REVERT: E 90 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7278 (mm-30) REVERT: E 130 ARG cc_start: 0.8051 (mpt-90) cc_final: 0.7664 (mmt90) REVERT: E 157 GLU cc_start: 0.8323 (mp0) cc_final: 0.7975 (mt-10) REVERT: F 36 GLU cc_start: 0.8678 (tt0) cc_final: 0.8364 (tt0) REVERT: G 23 LYS cc_start: 0.9035 (tppt) cc_final: 0.8834 (mttt) REVERT: G 102 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8434 (mtt-85) REVERT: G 140 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7628 (mt-10) REVERT: G 170 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6471 (m-10) REVERT: H 90 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: H 167 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7440 (pt0) REVERT: H 170 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5290 (m-10) REVERT: I 24 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8533 (mtpt) REVERT: I 144 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7292 (tttm) REVERT: I 170 TYR cc_start: 0.6704 (OUTLIER) cc_final: 0.6110 (m-10) REVERT: J 170 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.5716 (m-10) REVERT: K 108 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8076 (mtmt) REVERT: K 170 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.5978 (m-10) REVERT: L 56 ARG cc_start: 0.8821 (mtm180) cc_final: 0.8550 (mtp180) REVERT: L 90 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7196 (mm-30) REVERT: L 144 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7929 (tmtm) REVERT: L 157 GLU cc_start: 0.8060 (mp0) cc_final: 0.7695 (mp0) REVERT: L 168 ARG cc_start: 0.7019 (ttm-80) cc_final: 0.6788 (ttm110) REVERT: M 49 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: M 144 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8013 (tmtm) REVERT: M 163 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8117 (mtpp) REVERT: M 170 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6133 (m-10) REVERT: N 144 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7298 (tmtm) REVERT: N 170 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.5584 (m-10) REVERT: O 48 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7263 (ttp-110) REVERT: O 49 GLU cc_start: 0.7511 (mp0) cc_final: 0.7254 (tt0) REVERT: O 52 LEU cc_start: 0.8446 (tt) cc_final: 0.7877 (mt) REVERT: O 94 ASP cc_start: 0.7899 (m-30) cc_final: 0.7695 (m-30) REVERT: O 157 GLU cc_start: 0.8330 (mp0) cc_final: 0.8110 (mp0) REVERT: O 170 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.5768 (m-10) REVERT: P 94 ASP cc_start: 0.8193 (m-30) cc_final: 0.7806 (m-30) REVERT: P 144 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7580 (tmtm) REVERT: P 170 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.6114 (m-10) REVERT: Q 87 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: Q 140 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7619 (mt-10) REVERT: Q 157 GLU cc_start: 0.8184 (mp0) cc_final: 0.7861 (mp0) REVERT: Q 170 TYR cc_start: 0.6704 (OUTLIER) cc_final: 0.4960 (m-10) REVERT: R 130 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7519 (mmt90) REVERT: R 170 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.5486 (m-10) REVERT: S 77 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8934 (mt) REVERT: S 140 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7405 (mt-10) REVERT: S 164 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7183 (mp0) REVERT: T 44 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7541 (mt-10) REVERT: T 108 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8255 (mtmp) REVERT: T 140 GLU cc_start: 0.8246 (tp30) cc_final: 0.7614 (mt-10) REVERT: T 157 GLU cc_start: 0.7871 (mp0) cc_final: 0.7515 (mp0) REVERT: T 170 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6297 (m-10) REVERT: U 24 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8279 (mttp) REVERT: U 34 ASP cc_start: 0.7420 (m-30) cc_final: 0.7111 (m-30) REVERT: U 144 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8059 (tmtm) REVERT: U 157 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: U 170 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.4926 (m-10) REVERT: V 13 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.8148 (mtp-110) REVERT: V 37 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7765 (tpt-90) REVERT: V 98 GLU cc_start: 0.8632 (tp30) cc_final: 0.8420 (tp30) REVERT: V 140 GLU cc_start: 0.8194 (tp30) cc_final: 0.7444 (mm-30) REVERT: V 170 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: W 49 GLU cc_start: 0.7543 (mp0) cc_final: 0.7245 (tt0) REVERT: W 71 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7337 (tptp) REVERT: W 88 ARG cc_start: 0.6017 (mtm-85) cc_final: 0.5647 (mtp180) REVERT: W 90 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6707 (mt-10) REVERT: W 137 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: W 140 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7791 (mt-10) REVERT: W 164 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: W 170 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.5793 (m-10) REVERT: X 30 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7421 (p0) REVERT: Y 24 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8501 (mtpp) REVERT: Y 108 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (mttp) REVERT: Y 144 LYS cc_start: 0.8702 (tptm) cc_final: 0.8395 (tmtm) REVERT: Y 170 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5342 (m-10) outliers start: 195 outliers final: 42 residues processed: 780 average time/residue: 0.8567 time to fit residues: 756.7490 Evaluate side-chains 711 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 623 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 48 ARG Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 170 TYR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 170 TYR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 144 LYS Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 131 ASP Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 128 GLN Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 30 ASP Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 108 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 170 TYR Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 30 ASP Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 108 LYS Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 240 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 365 optimal weight: 9.9990 chunk 377 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN E 128 GLN Q 128 GLN V 128 GLN W 128 GLN X 128 GLN Y 128 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096910 restraints weight = 30877.712| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.68 r_work: 0.2997 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32086 Z= 0.108 Angle : 0.445 7.359 43450 Z= 0.231 Chirality : 0.038 0.428 5525 Planarity : 0.006 0.085 5625 Dihedral : 4.153 43.100 4597 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 4.85 % Allowed : 25.51 % Favored : 69.64 % 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: 5.18 (0.12), residues: 4200 helix: 3.25 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.74 (0.60), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 130 TYR 0.007 0.001 TYR N 161 HIS 0.001 0.000 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00215 (32000) covalent geometry : angle 0.44488 (43450) hydrogen bonds : bond 0.04254 ( 3171) hydrogen bonds : angle 3.05860 ( 9513) metal coordination : bond 0.00123 ( 86) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 637 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: A 170 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5175 (m-10) REVERT: B 90 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 94 ASP cc_start: 0.8232 (m-30) cc_final: 0.7776 (m-30) REVERT: B 163 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7835 (mtpp) REVERT: B 170 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5349 (m-10) REVERT: C 108 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7861 (mtpt) REVERT: C 144 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8120 (tttp) REVERT: C 164 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7488 (mp0) REVERT: C 170 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5681 (m-10) REVERT: D 102 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8399 (mmt180) REVERT: D 163 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7754 (mtpp) REVERT: E 44 GLU cc_start: 0.8423 (tt0) cc_final: 0.8002 (mt-10) REVERT: E 90 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7318 (mm-30) REVERT: E 130 ARG cc_start: 0.7776 (mpt-90) cc_final: 0.7521 (mmt90) REVERT: E 157 GLU cc_start: 0.8327 (mp0) cc_final: 0.7629 (mp0) REVERT: F 36 GLU cc_start: 0.8611 (tt0) cc_final: 0.8267 (tt0) REVERT: F 163 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7774 (mtpp) REVERT: G 23 LYS cc_start: 0.8955 (tppt) cc_final: 0.8738 (mttt) REVERT: G 102 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8407 (mtt-85) REVERT: G 140 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7606 (mt-10) REVERT: H 23 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8605 (ttmt) REVERT: H 170 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.5387 (m-10) REVERT: I 24 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8471 (mtpt) REVERT: I 144 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7288 (tttm) REVERT: J 30 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7360 (p0) REVERT: J 144 LYS cc_start: 0.8686 (tmtm) cc_final: 0.8423 (tptp) REVERT: J 170 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.5755 (m-10) REVERT: K 30 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.6941 (p0) REVERT: K 108 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8066 (mtmt) REVERT: K 144 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7963 (tttp) REVERT: L 144 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7894 (tmtm) REVERT: L 157 GLU cc_start: 0.8168 (mp0) cc_final: 0.7802 (mp0) REVERT: M 49 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: M 144 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7848 (tmtm) REVERT: M 157 GLU cc_start: 0.8386 (mp0) cc_final: 0.7747 (mp0) REVERT: M 163 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8220 (mtpp) REVERT: M 170 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.6227 (m-10) REVERT: N 113 LYS cc_start: 0.8279 (tttp) cc_final: 0.8068 (tttp) REVERT: N 170 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.5541 (m-10) REVERT: O 48 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6741 (ttp-110) REVERT: O 52 LEU cc_start: 0.8404 (tt) cc_final: 0.7904 (mt) REVERT: O 94 ASP cc_start: 0.7890 (m-30) cc_final: 0.7678 (m-30) REVERT: O 157 GLU cc_start: 0.8381 (mp0) cc_final: 0.8161 (mp0) REVERT: O 170 TYR cc_start: 0.6704 (OUTLIER) cc_final: 0.5662 (m-10) REVERT: P 94 ASP cc_start: 0.8158 (m-30) cc_final: 0.7831 (m-30) REVERT: P 144 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7591 (tmtm) REVERT: P 161 TYR cc_start: 0.8542 (t80) cc_final: 0.8301 (t80) REVERT: P 170 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.5993 (m-10) REVERT: Q 30 ASP cc_start: 0.7844 (p0) cc_final: 0.7129 (p0) REVERT: Q 34 ASP cc_start: 0.6840 (m-30) cc_final: 0.6243 (m-30) REVERT: Q 87 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6594 (m-30) REVERT: Q 157 GLU cc_start: 0.8133 (mp0) cc_final: 0.7748 (mp0) REVERT: Q 170 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.4970 (m-10) REVERT: R 24 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8166 (mtmm) REVERT: R 36 GLU cc_start: 0.8573 (tt0) cc_final: 0.8368 (tt0) REVERT: R 130 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7386 (mmt90) REVERT: R 170 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.5498 (m-10) REVERT: S 24 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8154 (mttp) REVERT: S 34 ASP cc_start: 0.7011 (m-30) cc_final: 0.6782 (m-30) REVERT: S 77 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (mt) REVERT: S 140 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7402 (mt-10) REVERT: S 164 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7230 (mp0) REVERT: S 170 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5055 (m-10) REVERT: T 44 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7536 (mt-10) REVERT: T 102 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8378 (mtt180) REVERT: T 108 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8082 (mttp) REVERT: T 130 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7548 (mmt90) REVERT: T 140 GLU cc_start: 0.8215 (tp30) cc_final: 0.7642 (mt-10) REVERT: T 157 GLU cc_start: 0.7976 (mp0) cc_final: 0.7595 (mp0) REVERT: T 164 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7164 (mp0) REVERT: T 170 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.6346 (m-10) REVERT: U 24 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8298 (mttp) REVERT: U 34 ASP cc_start: 0.7199 (m-30) cc_final: 0.6790 (m-30) REVERT: U 144 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7980 (tmtm) REVERT: U 157 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: U 170 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.4806 (m-10) REVERT: V 37 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7737 (tpt-90) REVERT: V 98 GLU cc_start: 0.8694 (tp30) cc_final: 0.8428 (tp30) REVERT: V 140 GLU cc_start: 0.8200 (tp30) cc_final: 0.7434 (mm-30) REVERT: V 144 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7121 (tttm) REVERT: V 170 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: W 30 ASP cc_start: 0.7744 (p0) cc_final: 0.7509 (p0) REVERT: W 49 GLU cc_start: 0.7525 (mp0) cc_final: 0.7208 (tt0) REVERT: W 71 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7384 (tptm) REVERT: W 88 ARG cc_start: 0.5911 (mtm-85) cc_final: 0.5643 (mtp180) REVERT: W 137 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7794 (mtm-85) REVERT: W 140 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7830 (mt-10) REVERT: W 164 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: W 170 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6058 (m-10) REVERT: X 140 GLU cc_start: 0.8085 (tp30) cc_final: 0.7641 (mt-10) REVERT: X 170 TYR cc_start: 0.6395 (OUTLIER) cc_final: 0.5543 (m-10) REVERT: Y 98 GLU cc_start: 0.8257 (tp30) cc_final: 0.7531 (tp30) REVERT: Y 131 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: Y 144 LYS cc_start: 0.8663 (tptm) cc_final: 0.8340 (tmtm) REVERT: Y 170 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.5323 (m-10) outliers start: 154 outliers final: 30 residues processed: 732 average time/residue: 0.9447 time to fit residues: 780.9735 Evaluate side-chains 649 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 577 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 144 LYS Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 128 GLN Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain S residue 170 TYR Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 131 ASP Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 170 TYR Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 170 TYR Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 291 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 413 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN N 128 GLN Q 128 GLN V 128 GLN W 128 GLN Y 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091253 restraints weight = 31367.729| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.71 r_work: 0.2909 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32086 Z= 0.147 Angle : 0.492 9.404 43450 Z= 0.255 Chirality : 0.040 0.492 5525 Planarity : 0.006 0.060 5625 Dihedral : 3.972 42.532 4593 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 5.80 % Allowed : 24.79 % Favored : 69.42 % 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: 5.06 (0.12), residues: 4200 helix: 3.17 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.67 (0.60), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 130 TYR 0.008 0.001 TYR F 170 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00335 (32000) covalent geometry : angle 0.49239 (43450) hydrogen bonds : bond 0.05712 ( 3171) hydrogen bonds : angle 3.22347 ( 9513) metal coordination : bond 0.00231 ( 86) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 641 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7476 (p0) REVERT: A 170 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.5400 (m-10) REVERT: B 90 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7300 (mm-30) REVERT: B 94 ASP cc_start: 0.8267 (m-30) cc_final: 0.7774 (m-30) REVERT: B 108 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8146 (mtmt) REVERT: B 163 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7778 (mtpp) REVERT: B 170 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.5312 (m-10) REVERT: C 102 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8400 (mmt-90) REVERT: C 108 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7929 (mtpt) REVERT: C 144 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8167 (tttp) REVERT: C 170 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6003 (m-10) REVERT: D 102 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8356 (mmt180) REVERT: D 170 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.5106 (m-10) REVERT: E 44 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: E 49 GLU cc_start: 0.7659 (mp0) cc_final: 0.7328 (tt0) REVERT: E 157 GLU cc_start: 0.8341 (mp0) cc_final: 0.7638 (mp0) REVERT: E 170 TYR cc_start: 0.6686 (OUTLIER) cc_final: 0.6242 (m-10) REVERT: F 36 GLU cc_start: 0.8692 (tt0) cc_final: 0.8405 (tt0) REVERT: F 94 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: G 23 LYS cc_start: 0.9001 (tppt) cc_final: 0.8790 (mttt) REVERT: G 102 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8502 (mtt-85) REVERT: G 131 ASP cc_start: 0.8309 (m-30) cc_final: 0.8009 (m-30) REVERT: G 140 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7635 (mt-10) REVERT: H 167 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7450 (pt0) REVERT: H 170 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.5110 (m-10) REVERT: I 24 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8532 (mtpt) REVERT: I 144 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7311 (tttm) REVERT: J 24 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8410 (mtpt) REVERT: J 144 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8433 (tptp) REVERT: J 167 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: J 170 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.5724 (m-10) REVERT: K 108 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8068 (mtmt) REVERT: K 144 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8178 (tttp) REVERT: L 90 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: L 98 GLU cc_start: 0.8523 (tp30) cc_final: 0.8262 (tp30) REVERT: L 144 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7999 (tmtm) REVERT: L 157 GLU cc_start: 0.8302 (mp0) cc_final: 0.7904 (mp0) REVERT: M 49 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: M 144 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8042 (tmtm) REVERT: M 157 GLU cc_start: 0.8368 (mp0) cc_final: 0.7678 (mp0) REVERT: M 163 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8076 (mtpp) REVERT: M 167 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: M 170 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6156 (m-10) REVERT: N 113 LYS cc_start: 0.8382 (tttp) cc_final: 0.8149 (tttp) REVERT: N 170 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.5630 (m-10) REVERT: O 48 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7495 (ttp-110) REVERT: O 108 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8173 (mtmt) REVERT: O 170 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.5748 (m-10) REVERT: P 94 ASP cc_start: 0.8413 (m-30) cc_final: 0.8018 (m-30) REVERT: P 131 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: P 144 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7531 (tmtm) REVERT: P 161 TYR cc_start: 0.8531 (t80) cc_final: 0.8323 (t80) REVERT: P 170 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5893 (m-10) REVERT: Q 87 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: Q 157 GLU cc_start: 0.8152 (mp0) cc_final: 0.7752 (mp0) REVERT: Q 170 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.5043 (m-10) REVERT: R 24 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8287 (mtmm) REVERT: R 130 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7490 (mmt90) REVERT: R 140 GLU cc_start: 0.8113 (tp30) cc_final: 0.7682 (mt-10) REVERT: R 144 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8041 (tmtm) REVERT: R 170 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.5627 (m-10) REVERT: S 24 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8160 (mttp) REVERT: S 77 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8921 (mt) REVERT: S 140 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7421 (mt-10) REVERT: S 164 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7226 (mp0) REVERT: S 170 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.5055 (m-10) REVERT: T 102 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8490 (mtt-85) REVERT: T 108 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8270 (mttp) REVERT: T 130 ARG cc_start: 0.8105 (tpp80) cc_final: 0.7541 (mmt90) REVERT: T 131 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8107 (t0) REVERT: T 140 GLU cc_start: 0.8226 (tp30) cc_final: 0.7620 (mt-10) REVERT: T 164 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7106 (mp0) REVERT: T 170 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6302 (m-10) REVERT: U 24 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8428 (mttp) REVERT: U 34 ASP cc_start: 0.7473 (m-30) cc_final: 0.7199 (m-30) REVERT: U 37 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8063 (mmt180) REVERT: U 144 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8085 (tmtm) REVERT: U 157 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: U 170 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.4909 (m-10) REVERT: V 37 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7733 (tpt-90) REVERT: V 98 GLU cc_start: 0.8710 (tp30) cc_final: 0.8468 (tp30) REVERT: V 137 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7993 (mtt-85) REVERT: V 140 GLU cc_start: 0.8219 (tp30) cc_final: 0.7473 (mm-30) REVERT: V 144 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7321 (tttm) REVERT: V 170 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6522 (m-10) REVERT: W 49 GLU cc_start: 0.7632 (mp0) cc_final: 0.7355 (tt0) REVERT: W 71 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7571 (tptm) REVERT: W 88 ARG cc_start: 0.6071 (mtm-85) cc_final: 0.5737 (mtp180) REVERT: W 90 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6788 (mm-30) REVERT: W 137 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7787 (mtm-85) REVERT: W 140 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7856 (mt-10) REVERT: W 157 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7965 (mp0) REVERT: W 167 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: W 170 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6149 (m-10) REVERT: X 24 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8563 (mtpp) REVERT: X 131 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: X 170 TYR cc_start: 0.6504 (OUTLIER) cc_final: 0.5628 (m-10) REVERT: Y 24 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8542 (mtpp) REVERT: Y 98 GLU cc_start: 0.8241 (tp30) cc_final: 0.7526 (tp30) REVERT: Y 144 LYS cc_start: 0.8740 (tptm) cc_final: 0.8391 (tmtm) REVERT: Y 170 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.5526 (m-10) outliers start: 184 outliers final: 49 residues processed: 744 average time/residue: 0.8577 time to fit residues: 723.8052 Evaluate side-chains 722 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 616 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 170 TYR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 167 GLU Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 144 LYS Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 108 LYS Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 131 ASP Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 131 ASP Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 170 TYR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 108 LYS Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 131 ASP Chi-restraints excluded: chain V residue 137 ARG Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain V residue 170 TYR Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 170 TYR Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 30 ASP Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 130 ARG Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 247 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 361 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 345 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 341 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 GLN N 59 ASN N 128 GLN V 128 GLN Y 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.115190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092115 restraints weight = 31207.055| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.69 r_work: 0.2916 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32086 Z= 0.144 Angle : 0.498 9.333 43450 Z= 0.256 Chirality : 0.039 0.482 5525 Planarity : 0.006 0.051 5625 Dihedral : 3.913 42.629 4587 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 5.80 % Allowed : 24.76 % Favored : 69.45 % 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: 5.04 (0.12), residues: 4200 helix: 3.16 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.62 (0.59), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 168 TYR 0.008 0.001 TYR K 170 HIS 0.002 0.001 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00329 (32000) covalent geometry : angle 0.49802 (43450) hydrogen bonds : bond 0.05545 ( 3171) hydrogen bonds : angle 3.19904 ( 9513) metal coordination : bond 0.00234 ( 86) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 624 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7454 (p0) REVERT: A 52 LEU cc_start: 0.7861 (mt) cc_final: 0.7613 (mm) REVERT: A 108 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7960 (mtpt) REVERT: A 131 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: A 161 TYR cc_start: 0.8623 (t80) cc_final: 0.8396 (t80) REVERT: A 170 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.5419 (m-10) REVERT: B 90 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 94 ASP cc_start: 0.8315 (m-30) cc_final: 0.7818 (m-30) REVERT: B 108 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8200 (mtmt) REVERT: B 163 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7775 (mtpp) REVERT: B 170 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5348 (m-10) REVERT: C 102 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8387 (mmt-90) REVERT: C 108 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7941 (mtpt) REVERT: C 144 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8165 (tttp) REVERT: C 164 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7520 (mp0) REVERT: C 170 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6037 (m-10) REVERT: D 102 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8374 (mmt180) REVERT: D 163 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7881 (mtpp) REVERT: D 170 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5133 (m-10) REVERT: E 44 GLU cc_start: 0.8445 (tt0) cc_final: 0.8067 (mt-10) REVERT: E 108 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7961 (mttp) REVERT: E 157 GLU cc_start: 0.8361 (mp0) cc_final: 0.7624 (mp0) REVERT: E 163 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7874 (mtpp) REVERT: E 170 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.6309 (m-10) REVERT: F 36 GLU cc_start: 0.8695 (tt0) cc_final: 0.8394 (tt0) REVERT: F 94 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: G 23 LYS cc_start: 0.8989 (tppt) cc_final: 0.8765 (mttt) REVERT: G 102 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8509 (mtt-85) REVERT: G 140 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7678 (mt-10) REVERT: H 170 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.5060 (m-10) REVERT: I 24 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8548 (mtpt) REVERT: J 24 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8350 (mtpt) REVERT: J 144 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8463 (tptp) REVERT: J 170 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.5877 (m-10) REVERT: K 30 ASP cc_start: 0.7906 (p0) cc_final: 0.7410 (p0) REVERT: K 102 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8593 (mmt180) REVERT: K 108 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8071 (mtmt) REVERT: K 144 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8191 (tttp) REVERT: L 90 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: L 94 ASP cc_start: 0.8132 (m-30) cc_final: 0.7866 (m-30) REVERT: L 98 GLU cc_start: 0.8471 (tp30) cc_final: 0.8195 (tp30) REVERT: L 144 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8139 (tmtm) REVERT: L 157 GLU cc_start: 0.8313 (mp0) cc_final: 0.7911 (mp0) REVERT: M 49 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: M 144 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7976 (tmtm) REVERT: M 157 GLU cc_start: 0.8372 (mp0) cc_final: 0.7687 (mp0) REVERT: M 163 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8090 (mtpp) REVERT: M 167 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: M 170 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6049 (m-10) REVERT: N 113 LYS cc_start: 0.8325 (tttp) cc_final: 0.8103 (tttp) REVERT: N 137 ARG cc_start: 0.8248 (mtt90) cc_final: 0.8019 (mtt-85) REVERT: N 170 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.5593 (m-10) REVERT: O 48 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7487 (ttp-110) REVERT: O 52 LEU cc_start: 0.8626 (tt) cc_final: 0.7983 (mt) REVERT: O 108 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8298 (mtmt) REVERT: O 170 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.5746 (m-10) REVERT: P 24 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8300 (mtpt) REVERT: P 94 ASP cc_start: 0.8389 (m-30) cc_final: 0.7996 (m-30) REVERT: P 144 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7540 (tmtm) REVERT: P 161 TYR cc_start: 0.8547 (t80) cc_final: 0.8327 (t80) REVERT: Q 87 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: Q 157 GLU cc_start: 0.8088 (mp0) cc_final: 0.7686 (mp0) REVERT: Q 164 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: Q 170 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.5227 (m-10) REVERT: R 24 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8295 (mtmm) REVERT: R 90 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7209 (mm-30) REVERT: R 130 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7511 (mmt90) REVERT: R 140 GLU cc_start: 0.8128 (tp30) cc_final: 0.7710 (mt-10) REVERT: R 144 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8010 (tmtm) REVERT: R 170 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.5797 (m-10) REVERT: S 24 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8129 (mttp) REVERT: S 77 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8911 (mt) REVERT: S 140 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7448 (mt-10) REVERT: S 164 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7241 (mp0) REVERT: S 170 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5205 (m-10) REVERT: T 102 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8482 (mtt-85) REVERT: T 108 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8257 (mttp) REVERT: T 131 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8099 (t0) REVERT: T 140 GLU cc_start: 0.8255 (tp30) cc_final: 0.7671 (mt-10) REVERT: T 164 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7117 (mp0) REVERT: T 170 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.6285 (m-10) REVERT: U 24 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8409 (mttp) REVERT: U 30 ASP cc_start: 0.7996 (p0) cc_final: 0.7669 (p0) REVERT: U 34 ASP cc_start: 0.7466 (m-30) cc_final: 0.7150 (m-30) REVERT: U 37 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8057 (mmt180) REVERT: U 144 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8072 (tmtm) REVERT: U 157 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: U 170 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.4952 (m-10) REVERT: V 37 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7710 (tpt-90) REVERT: V 90 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: V 98 GLU cc_start: 0.8680 (tp30) cc_final: 0.8349 (tp30) REVERT: V 137 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7988 (mtt-85) REVERT: V 140 GLU cc_start: 0.8225 (tp30) cc_final: 0.7475 (mm-30) REVERT: V 144 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7332 (tttm) REVERT: W 49 GLU cc_start: 0.7642 (mp0) cc_final: 0.7354 (tt0) REVERT: W 71 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7368 (tptp) REVERT: W 88 ARG cc_start: 0.6019 (mtm-85) cc_final: 0.5704 (mtp180) REVERT: W 90 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6819 (mm-30) REVERT: W 137 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7773 (mtm-85) REVERT: W 140 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7851 (mt-10) REVERT: W 157 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8158 (mp0) REVERT: W 167 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: W 170 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6194 (m-10) REVERT: X 87 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: X 90 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7671 (mm-30) REVERT: X 140 GLU cc_start: 0.8102 (tp30) cc_final: 0.7679 (mt-10) REVERT: X 170 TYR cc_start: 0.6575 (OUTLIER) cc_final: 0.5729 (m-10) REVERT: Y 24 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8569 (mtpp) REVERT: Y 98 GLU cc_start: 0.8283 (tp30) cc_final: 0.7548 (tp30) REVERT: Y 144 LYS cc_start: 0.8744 (tptm) cc_final: 0.8384 (tmtm) REVERT: Y 170 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.5807 (m-10) outliers start: 184 outliers final: 56 residues processed: 732 average time/residue: 0.8967 time to fit residues: 746.0789 Evaluate side-chains 720 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 607 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 170 TYR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain K residue 144 LYS Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 108 LYS Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 170 TYR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 30 ASP Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 108 LYS Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 131 ASP Chi-restraints excluded: chain V residue 137 ARG Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 131 ASP Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 87 ASP Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 170 TYR Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 30 ASP Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 130 ARG Chi-restraints excluded: chain Y residue 167 GLU Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 275 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 379 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 GLN F 128 GLN N 59 ASN N 128 GLN O 128 GLN S 59 ASN V 128 GLN Y 128 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.090560 restraints weight = 31120.137| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.68 r_work: 0.2892 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32086 Z= 0.169 Angle : 0.525 9.949 43450 Z= 0.271 Chirality : 0.041 0.508 5525 Planarity : 0.006 0.084 5625 Dihedral : 3.967 43.380 4587 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 5.76 % Allowed : 25.07 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.91 (0.11), residues: 4200 helix: 3.08 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.60 (0.59), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 130 TYR 0.011 0.001 TYR I 170 HIS 0.003 0.001 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00401 (32000) covalent geometry : angle 0.52455 (43450) hydrogen bonds : bond 0.06184 ( 3171) hydrogen bonds : angle 3.28939 ( 9513) metal coordination : bond 0.00285 ( 86) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 638 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7827 (mt) cc_final: 0.7605 (mm) REVERT: A 108 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8051 (mtpt) REVERT: A 131 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: A 170 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.5625 (m-10) REVERT: B 17 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8721 (t) REVERT: B 90 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 94 ASP cc_start: 0.8333 (m-30) cc_final: 0.7829 (m-30) REVERT: B 108 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8216 (mtmt) REVERT: B 163 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7720 (mtpp) REVERT: B 170 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.5406 (m-10) REVERT: C 102 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8373 (mmt-90) REVERT: C 108 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8044 (mtpt) REVERT: C 144 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8168 (tttp) REVERT: C 170 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6169 (m-10) REVERT: D 102 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8442 (mmt180) REVERT: D 170 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.5196 (m-10) REVERT: E 44 GLU cc_start: 0.8469 (tt0) cc_final: 0.8101 (mt-10) REVERT: E 49 GLU cc_start: 0.7652 (mp0) cc_final: 0.7364 (tt0) REVERT: E 108 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7994 (mttp) REVERT: E 157 GLU cc_start: 0.8342 (mp0) cc_final: 0.7644 (mp0) REVERT: F 36 GLU cc_start: 0.8668 (tt0) cc_final: 0.8380 (tt0) REVERT: F 94 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: F 157 GLU cc_start: 0.8435 (mp0) cc_final: 0.8188 (mp0) REVERT: F 170 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.4884 (m-10) REVERT: G 23 LYS cc_start: 0.9010 (tppt) cc_final: 0.8776 (mttt) REVERT: G 102 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8506 (mtt-85) REVERT: G 140 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7666 (mt-10) REVERT: H 108 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8183 (mtpt) REVERT: H 167 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7457 (pt0) REVERT: H 170 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.4935 (m-10) REVERT: I 24 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8542 (mtpt) REVERT: I 49 GLU cc_start: 0.7716 (mp0) cc_final: 0.7480 (tt0) REVERT: I 94 ASP cc_start: 0.8086 (m-30) cc_final: 0.7876 (m-30) REVERT: J 24 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8374 (mtpt) REVERT: J 131 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (t0) REVERT: J 170 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.5644 (m-10) REVERT: K 102 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8623 (mmt180) REVERT: K 108 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8055 (mtmt) REVERT: L 90 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: L 94 ASP cc_start: 0.8156 (m-30) cc_final: 0.7874 (m-30) REVERT: L 98 GLU cc_start: 0.8527 (tp30) cc_final: 0.8268 (tp30) REVERT: L 130 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7624 (mmt90) REVERT: L 144 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8083 (tmtm) REVERT: L 157 GLU cc_start: 0.8356 (mp0) cc_final: 0.8075 (mp0) REVERT: M 49 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: M 144 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7972 (tmtm) REVERT: M 157 GLU cc_start: 0.8358 (mp0) cc_final: 0.7667 (mp0) REVERT: M 163 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8102 (mtpp) REVERT: M 167 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: M 170 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.5990 (m-10) REVERT: N 113 LYS cc_start: 0.8349 (tttp) cc_final: 0.8119 (tttp) REVERT: N 130 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.8122 (mmt-90) REVERT: N 170 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.5612 (m-10) REVERT: O 48 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7584 (ttp-110) REVERT: O 108 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8250 (mtmt) REVERT: O 170 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5807 (m-10) REVERT: P 24 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8320 (mtpt) REVERT: P 94 ASP cc_start: 0.8433 (m-30) cc_final: 0.8031 (m-30) REVERT: P 144 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7527 (tmtm) REVERT: P 161 TYR cc_start: 0.8555 (t80) cc_final: 0.8313 (t80) REVERT: P 164 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7310 (mp0) REVERT: P 167 GLU cc_start: 0.8076 (pt0) cc_final: 0.7825 (tm-30) REVERT: P 170 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.5914 (m-10) REVERT: Q 87 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: Q 157 GLU cc_start: 0.8102 (mp0) cc_final: 0.7687 (mp0) REVERT: Q 164 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: Q 170 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5225 (m-10) REVERT: R 24 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8305 (mtmm) REVERT: R 90 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7158 (mm-30) REVERT: R 130 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7518 (mmt90) REVERT: R 144 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8043 (tmtm) REVERT: R 170 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.5690 (m-10) REVERT: S 24 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8120 (mttp) REVERT: S 77 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8915 (mt) REVERT: S 131 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8091 (t0) REVERT: S 140 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7467 (mt-10) REVERT: S 144 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7689 (tmtm) REVERT: S 164 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7208 (mp0) REVERT: S 170 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.5199 (m-10) REVERT: T 102 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (mtt-85) REVERT: T 108 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8268 (mttp) REVERT: T 130 ARG cc_start: 0.8127 (mpp80) cc_final: 0.7566 (mmt90) REVERT: T 131 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8061 (t0) REVERT: T 140 GLU cc_start: 0.8155 (tp30) cc_final: 0.7540 (mt-10) REVERT: T 164 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7115 (mp0) REVERT: T 170 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6167 (m-10) REVERT: U 24 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8489 (mttp) REVERT: U 34 ASP cc_start: 0.7528 (m-30) cc_final: 0.7255 (m-30) REVERT: U 37 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8103 (mmt180) REVERT: U 144 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8062 (tmtm) REVERT: U 157 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: U 170 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.4871 (m-10) REVERT: V 37 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7706 (tpt-90) REVERT: V 90 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: V 137 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8007 (mtt-85) REVERT: V 140 GLU cc_start: 0.8210 (tp30) cc_final: 0.7449 (mm-30) REVERT: V 144 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7269 (tttm) REVERT: W 49 GLU cc_start: 0.7646 (mp0) cc_final: 0.7400 (tt0) REVERT: W 71 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7572 (tptm) REVERT: W 88 ARG cc_start: 0.6141 (mtm-85) cc_final: 0.5790 (mtp180) REVERT: W 137 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: W 140 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7858 (mt-10) REVERT: W 157 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8174 (mp0) REVERT: W 167 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: W 170 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: X 87 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7341 (m-30) REVERT: X 90 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7658 (mm-30) REVERT: X 170 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.5788 (m-10) REVERT: Y 98 GLU cc_start: 0.8282 (tp30) cc_final: 0.7545 (tp30) REVERT: Y 144 LYS cc_start: 0.8660 (tptm) cc_final: 0.8374 (tmtm) REVERT: Y 170 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6112 (m-10) outliers start: 183 outliers final: 60 residues processed: 740 average time/residue: 0.8618 time to fit residues: 726.3767 Evaluate side-chains 746 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 625 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 170 TYR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 102 ARG Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 108 LYS Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 30 ASP Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 131 ASP Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 170 TYR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 30 ASP Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 131 ASP Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 108 LYS Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 151 LEU Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 137 ARG Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 167 GLU Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 87 ASP Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 170 TYR Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 30 ASP Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 90 GLU Chi-restraints excluded: chain Y residue 130 ARG Chi-restraints excluded: chain Y residue 167 GLU Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 335 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 378 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 375 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 GLN F 128 GLN N 128 GLN V 128 GLN Y 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094400 restraints weight = 30788.881| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.68 r_work: 0.2961 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32086 Z= 0.125 Angle : 0.494 9.901 43450 Z= 0.255 Chirality : 0.039 0.469 5525 Planarity : 0.006 0.048 5625 Dihedral : 3.879 41.852 4587 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.41 % Allowed : 26.27 % Favored : 69.32 % 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: 5.18 (0.12), residues: 4200 helix: 3.25 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.65 (0.59), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 130 TYR 0.010 0.001 TYR I 170 HIS 0.002 0.000 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00271 (32000) covalent geometry : angle 0.49401 (43450) hydrogen bonds : bond 0.04798 ( 3171) hydrogen bonds : angle 3.11566 ( 9513) metal coordination : bond 0.00172 ( 86) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 611 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7917 (mt) cc_final: 0.7664 (mm) REVERT: A 108 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7915 (mtpt) REVERT: A 131 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: A 163 LYS cc_start: 0.8294 (ttmm) cc_final: 0.8092 (mtpp) REVERT: A 170 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.5596 (m-10) REVERT: B 90 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 94 ASP cc_start: 0.8274 (m-30) cc_final: 0.7806 (m-30) REVERT: B 108 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8029 (mtmp) REVERT: B 163 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7801 (mtpp) REVERT: B 170 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.5402 (m-10) REVERT: C 102 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8386 (mmt-90) REVERT: C 108 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7931 (mtpt) REVERT: C 144 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8175 (tttp) REVERT: C 164 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7541 (mp0) REVERT: C 170 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: D 102 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8342 (mmt180) REVERT: D 163 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7909 (mtpp) REVERT: D 170 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.5201 (m-10) REVERT: E 44 GLU cc_start: 0.8393 (tt0) cc_final: 0.8011 (mt-10) REVERT: E 157 GLU cc_start: 0.8408 (mp0) cc_final: 0.7710 (mp0) REVERT: E 163 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7889 (mtpp) REVERT: E 170 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6421 (m-10) REVERT: F 36 GLU cc_start: 0.8682 (tt0) cc_final: 0.8354 (tt0) REVERT: F 94 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: F 157 GLU cc_start: 0.8460 (mp0) cc_final: 0.8206 (mp0) REVERT: F 163 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7743 (mtpp) REVERT: F 170 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.4841 (m-10) REVERT: G 23 LYS cc_start: 0.9002 (tppt) cc_final: 0.8772 (mttt) REVERT: G 102 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8466 (mtt-85) REVERT: G 140 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7606 (mt-10) REVERT: H 167 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7524 (pt0) REVERT: H 170 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.4890 (m-10) REVERT: I 24 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8526 (mtpt) REVERT: I 94 ASP cc_start: 0.7995 (m-30) cc_final: 0.7751 (m-30) REVERT: J 144 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8452 (tptp) REVERT: J 170 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.5747 (m-10) REVERT: K 108 LYS cc_start: 0.8270 (mtmt) cc_final: 0.8012 (mtmt) REVERT: K 144 LYS cc_start: 0.8406 (tttp) cc_final: 0.8189 (tttp) REVERT: L 90 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: L 98 GLU cc_start: 0.8441 (tp30) cc_final: 0.8140 (tp30) REVERT: L 144 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8088 (tmtm) REVERT: M 49 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: M 144 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7966 (tmtm) REVERT: M 157 GLU cc_start: 0.8392 (mp0) cc_final: 0.7711 (mp0) REVERT: M 163 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8108 (mtpp) REVERT: M 167 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: M 170 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6152 (m-10) REVERT: N 13 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8342 (mtm110) REVERT: N 113 LYS cc_start: 0.8259 (tttp) cc_final: 0.8048 (tttp) REVERT: N 137 ARG cc_start: 0.8261 (mtt90) cc_final: 0.8036 (mtt-85) REVERT: N 167 GLU cc_start: 0.8238 (tt0) cc_final: 0.8019 (tm-30) REVERT: N 170 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.5552 (m-10) REVERT: O 48 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7507 (ttp-110) REVERT: O 52 LEU cc_start: 0.8443 (tt) cc_final: 0.7857 (mt) REVERT: O 108 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (mtmt) REVERT: O 170 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.5750 (m-10) REVERT: P 24 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8153 (mtpt) REVERT: P 94 ASP cc_start: 0.8341 (m-30) cc_final: 0.7935 (m-30) REVERT: P 144 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7538 (tmtm) REVERT: P 161 TYR cc_start: 0.8609 (t80) cc_final: 0.8345 (t80) REVERT: P 167 GLU cc_start: 0.8127 (pt0) cc_final: 0.7867 (tm-30) REVERT: P 170 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.6021 (m-10) REVERT: Q 87 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: Q 157 GLU cc_start: 0.8144 (mp0) cc_final: 0.7711 (mp0) REVERT: Q 170 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.5245 (m-10) REVERT: R 24 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8235 (mtmm) REVERT: R 90 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7070 (mm-30) REVERT: R 130 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7467 (mmt90) REVERT: R 140 GLU cc_start: 0.8033 (tp30) cc_final: 0.7671 (mt-10) REVERT: R 144 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7997 (tmtm) REVERT: R 157 GLU cc_start: 0.8245 (mp0) cc_final: 0.7873 (mm-30) REVERT: R 170 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.5555 (m-10) REVERT: S 77 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8907 (mt) REVERT: S 140 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7394 (mt-10) REVERT: S 164 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7219 (mp0) REVERT: S 170 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.5147 (m-10) REVERT: T 102 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8436 (mtt-85) REVERT: T 108 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8222 (mtmp) REVERT: T 130 ARG cc_start: 0.8137 (mpp80) cc_final: 0.7587 (mmt90) REVERT: T 140 GLU cc_start: 0.8222 (tp30) cc_final: 0.7639 (mt-10) REVERT: T 164 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7142 (mp0) REVERT: T 170 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6105 (m-10) REVERT: U 24 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8381 (mttp) REVERT: U 34 ASP cc_start: 0.7363 (m-30) cc_final: 0.7104 (m-30) REVERT: U 37 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8030 (mmt180) REVERT: U 144 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8008 (tmtm) REVERT: U 157 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: U 170 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.4910 (m-10) REVERT: V 37 ARG cc_start: 0.7971 (mmm160) cc_final: 0.7687 (tpt-90) REVERT: V 90 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: V 140 GLU cc_start: 0.8183 (tp30) cc_final: 0.7430 (mm-30) REVERT: V 144 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7143 (tttm) REVERT: W 34 ASP cc_start: 0.7375 (m-30) cc_final: 0.7124 (m-30) REVERT: W 49 GLU cc_start: 0.7593 (mp0) cc_final: 0.7285 (tt0) REVERT: W 71 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7290 (tptp) REVERT: W 88 ARG cc_start: 0.5956 (mtm-85) cc_final: 0.5649 (mtp180) REVERT: W 137 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7778 (mtm-85) REVERT: W 140 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7822 (mt-10) REVERT: W 157 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8155 (mp0) REVERT: W 170 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6221 (m-10) REVERT: X 87 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: X 90 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7655 (mm-30) REVERT: X 91 GLU cc_start: 0.8268 (tp30) cc_final: 0.7995 (tt0) REVERT: X 140 GLU cc_start: 0.8135 (tp30) cc_final: 0.7731 (mt-10) REVERT: X 170 TYR cc_start: 0.6565 (OUTLIER) cc_final: 0.5748 (m-10) REVERT: Y 98 GLU cc_start: 0.8207 (tp30) cc_final: 0.7438 (tp30) REVERT: Y 144 LYS cc_start: 0.8718 (tptm) cc_final: 0.8384 (tmtm) REVERT: Y 170 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6054 (m-10) outliers start: 140 outliers final: 48 residues processed: 693 average time/residue: 0.8661 time to fit residues: 683.9932 Evaluate side-chains 688 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 590 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain E residue 170 TYR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 170 TYR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 108 LYS Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain S residue 170 TYR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 30 ASP Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 151 LEU Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 87 ASP Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 151 LEU Chi-restraints excluded: chain X residue 170 TYR Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 90 GLU Chi-restraints excluded: chain Y residue 130 ARG Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 38 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 GLN Y 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.090027 restraints weight = 30790.903| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.67 r_work: 0.2885 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32086 Z= 0.185 Angle : 0.564 9.804 43450 Z= 0.289 Chirality : 0.042 0.506 5525 Planarity : 0.007 0.110 5625 Dihedral : 3.991 43.400 4587 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.54 % Allowed : 26.30 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.05 (0.11), residues: 4200 helix: 3.15 (0.07), residues: 3975 sheet: None (None), residues: 0 loop : 6.32 (0.52), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 130 TYR 0.012 0.001 TYR K 170 HIS 0.003 0.001 HIS Q 25 Details of bonding type rmsd covalent geometry : bond 0.00448 (32000) covalent geometry : angle 0.56354 (43450) hydrogen bonds : bond 0.06436 ( 3171) hydrogen bonds : angle 3.32526 ( 9513) metal coordination : bond 0.00298 ( 86) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 628 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7782 (mt) cc_final: 0.7552 (mm) REVERT: A 108 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8035 (mtpt) REVERT: A 131 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: A 170 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.5583 (m-10) REVERT: B 17 SER cc_start: 0.8933 (m) cc_final: 0.8702 (t) REVERT: B 90 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7327 (mm-30) REVERT: B 94 ASP cc_start: 0.8300 (m-30) cc_final: 0.7796 (m-30) REVERT: B 108 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8236 (mtmt) REVERT: B 163 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7732 (mtpp) REVERT: B 170 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5442 (m-10) REVERT: C 102 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8361 (mmt-90) REVERT: C 108 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8037 (mtpt) REVERT: C 144 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8113 (tttp) REVERT: C 170 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6234 (m-10) REVERT: D 102 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8415 (mmt180) REVERT: D 170 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5332 (m-10) REVERT: E 44 GLU cc_start: 0.8461 (tt0) cc_final: 0.8096 (mt-10) REVERT: E 49 GLU cc_start: 0.7699 (mp0) cc_final: 0.7409 (tt0) REVERT: E 108 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7962 (mttp) REVERT: E 157 GLU cc_start: 0.8374 (mp0) cc_final: 0.7686 (mp0) REVERT: E 163 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7858 (mtpp) REVERT: E 170 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6529 (m-10) REVERT: F 36 GLU cc_start: 0.8696 (tt0) cc_final: 0.8409 (tt0) REVERT: F 94 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: F 157 GLU cc_start: 0.8449 (mp0) cc_final: 0.8188 (mp0) REVERT: F 170 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.4934 (m-10) REVERT: G 23 LYS cc_start: 0.9008 (tppt) cc_final: 0.8775 (mttt) REVERT: G 102 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8526 (mtt-85) REVERT: G 140 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7616 (mt-10) REVERT: H 167 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7494 (pt0) REVERT: H 170 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.4891 (m-10) REVERT: I 24 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8552 (mtpt) REVERT: I 94 ASP cc_start: 0.7994 (m-30) cc_final: 0.7752 (m-30) REVERT: J 170 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.5651 (m-10) REVERT: K 108 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8059 (mtmt) REVERT: L 90 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: L 98 GLU cc_start: 0.8511 (tp30) cc_final: 0.8267 (tp30) REVERT: L 144 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8097 (tmtm) REVERT: L 157 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8123 (mp0) REVERT: M 49 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: M 144 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8009 (tmtm) REVERT: M 157 GLU cc_start: 0.8383 (mp0) cc_final: 0.7704 (mp0) REVERT: M 163 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8080 (mtpp) REVERT: M 167 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: M 170 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6010 (m-10) REVERT: N 113 LYS cc_start: 0.8378 (tttp) cc_final: 0.8152 (tttp) REVERT: N 137 ARG cc_start: 0.8258 (mtt90) cc_final: 0.8029 (mtt-85) REVERT: N 167 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: N 170 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.5579 (m-10) REVERT: O 48 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7548 (ttp-110) REVERT: O 108 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8293 (mtmt) REVERT: O 170 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.5857 (m-10) REVERT: P 24 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8302 (mtpt) REVERT: P 94 ASP cc_start: 0.8397 (m-30) cc_final: 0.7992 (m-30) REVERT: P 144 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7605 (tmtm) REVERT: P 167 GLU cc_start: 0.8095 (pt0) cc_final: 0.7809 (tm-30) REVERT: P 170 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5818 (m-10) REVERT: Q 87 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: Q 157 GLU cc_start: 0.8149 (mp0) cc_final: 0.7712 (mp0) REVERT: Q 164 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: Q 170 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.5260 (m-10) REVERT: R 24 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8318 (mtmm) REVERT: R 90 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7145 (mm-30) REVERT: R 130 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7572 (mmt90) REVERT: R 140 GLU cc_start: 0.8159 (tp30) cc_final: 0.7731 (mt-10) REVERT: R 144 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8055 (tmtm) REVERT: R 170 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.5699 (m-10) REVERT: S 24 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8139 (mttp) REVERT: S 77 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8850 (mt) REVERT: S 131 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8082 (t0) REVERT: S 140 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7424 (mt-10) REVERT: S 144 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7682 (tmtm) REVERT: S 164 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7175 (mp0) REVERT: S 170 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.5119 (m-10) REVERT: T 108 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8281 (mttp) REVERT: T 130 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7559 (mmt90) REVERT: T 131 ASP cc_start: 0.8385 (m-30) cc_final: 0.8093 (t0) REVERT: T 140 GLU cc_start: 0.8150 (tp30) cc_final: 0.7552 (mt-10) REVERT: T 164 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7112 (mp0) REVERT: T 170 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.6150 (m-10) REVERT: U 24 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8472 (mttp) REVERT: U 37 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8137 (mmt180) REVERT: U 63 VAL cc_start: 0.8770 (t) cc_final: 0.8529 (t) REVERT: U 90 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7021 (mt-10) REVERT: U 144 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8067 (tmtm) REVERT: U 157 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: U 170 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.4975 (m-10) REVERT: V 37 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7747 (tpt-90) REVERT: V 98 GLU cc_start: 0.8638 (tp30) cc_final: 0.8280 (tp30) REVERT: V 137 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8017 (mtt-85) REVERT: V 140 GLU cc_start: 0.8239 (tp30) cc_final: 0.7458 (mm-30) REVERT: V 144 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7344 (tttm) REVERT: W 49 GLU cc_start: 0.7646 (mp0) cc_final: 0.7368 (tt0) REVERT: W 71 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7572 (tptm) REVERT: W 88 ARG cc_start: 0.6135 (mtm-85) cc_final: 0.5779 (mtp180) REVERT: W 137 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7884 (mtm-85) REVERT: W 140 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7848 (mt-10) REVERT: W 157 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8160 (mp0) REVERT: W 170 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6106 (m-10) REVERT: X 87 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: X 90 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7627 (mm-30) REVERT: X 170 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6106 (m-10) REVERT: Y 24 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8631 (mtpp) REVERT: Y 98 GLU cc_start: 0.8307 (tp30) cc_final: 0.7560 (tp30) REVERT: Y 144 LYS cc_start: 0.8681 (tptm) cc_final: 0.8393 (tmtm) REVERT: Y 170 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6231 (m-10) outliers start: 144 outliers final: 54 residues processed: 705 average time/residue: 0.8764 time to fit residues: 703.2328 Evaluate side-chains 719 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 611 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 170 TYR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 170 TYR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 108 LYS Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 131 ASP Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 170 TYR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 30 ASP Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 130 ARG Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 151 LEU Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 137 ARG Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 87 ASP Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain X residue 170 TYR Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 30 ASP Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 90 GLU Chi-restraints excluded: chain Y residue 130 ARG Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 157 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 GLN G 128 GLN H 128 GLN I 128 GLN Y 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095480 restraints weight = 30686.192| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.68 r_work: 0.2979 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32086 Z= 0.122 Angle : 0.508 10.059 43450 Z= 0.263 Chirality : 0.039 0.464 5525 Planarity : 0.006 0.051 5625 Dihedral : 3.873 41.401 4587 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.78 % Allowed : 27.43 % Favored : 68.79 % 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: 5.42 (0.11), residues: 4200 helix: 3.39 (0.07), residues: 3975 sheet: None (None), residues: 0 loop : 6.40 (0.52), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 130 TYR 0.009 0.001 TYR I 170 HIS 0.001 0.000 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00259 (32000) covalent geometry : angle 0.50770 (43450) hydrogen bonds : bond 0.04542 ( 3171) hydrogen bonds : angle 3.10905 ( 9513) metal coordination : bond 0.00144 ( 86) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 594 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7890 (mt) cc_final: 0.7641 (mm) REVERT: A 108 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7928 (mtpt) REVERT: A 131 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: A 157 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: A 170 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5655 (m-10) REVERT: B 90 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 94 ASP cc_start: 0.8251 (m-30) cc_final: 0.7788 (m-30) REVERT: B 108 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8028 (mtmp) REVERT: B 170 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.5394 (m-10) REVERT: C 102 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8379 (mmt-90) REVERT: C 108 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7917 (mtpt) REVERT: C 144 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8165 (tttp) REVERT: C 164 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7529 (mp0) REVERT: C 170 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6057 (m-10) REVERT: D 102 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (mmt180) REVERT: D 163 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7843 (mtpp) REVERT: D 170 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5321 (m-10) REVERT: E 44 GLU cc_start: 0.8370 (tt0) cc_final: 0.7993 (mt-10) REVERT: E 108 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7937 (mttp) REVERT: E 157 GLU cc_start: 0.8352 (mp0) cc_final: 0.7680 (mp0) REVERT: E 163 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7903 (mtpp) REVERT: E 170 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6518 (m-10) REVERT: F 36 GLU cc_start: 0.8618 (tt0) cc_final: 0.8273 (tt0) REVERT: F 94 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: F 157 GLU cc_start: 0.8502 (mp0) cc_final: 0.8256 (mp0) REVERT: F 163 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7772 (mtpp) REVERT: F 170 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.4797 (m-10) REVERT: G 23 LYS cc_start: 0.8995 (tppt) cc_final: 0.8762 (mttt) REVERT: G 102 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8491 (mtt-85) REVERT: G 140 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7607 (mt-10) REVERT: H 90 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: H 167 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7494 (pt0) REVERT: H 170 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.4880 (m-10) REVERT: I 24 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8525 (mtpt) REVERT: I 94 ASP cc_start: 0.7844 (m-30) cc_final: 0.7612 (m-30) REVERT: I 128 GLN cc_start: 0.8352 (tt0) cc_final: 0.8102 (tt0) REVERT: I 144 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7256 (tttm) REVERT: J 144 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8434 (tptt) REVERT: J 170 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.5779 (m-10) REVERT: K 108 LYS cc_start: 0.8292 (mtmt) cc_final: 0.8044 (mtmt) REVERT: L 90 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: L 98 GLU cc_start: 0.8426 (tp30) cc_final: 0.8118 (tp30) REVERT: L 144 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8109 (tmtm) REVERT: L 157 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8161 (mp0) REVERT: L 170 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5899 (m-10) REVERT: M 49 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: M 144 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7965 (tmtm) REVERT: M 157 GLU cc_start: 0.8387 (mp0) cc_final: 0.7712 (mp0) REVERT: M 163 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8079 (mtpp) REVERT: M 167 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: M 170 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6033 (m-10) REVERT: N 13 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8331 (mtm110) REVERT: N 113 LYS cc_start: 0.8233 (tttp) cc_final: 0.8025 (tttp) REVERT: N 137 ARG cc_start: 0.8257 (mtt90) cc_final: 0.8034 (mtt90) REVERT: N 167 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: N 170 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.5376 (m-10) REVERT: O 48 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7476 (ttp-110) REVERT: O 52 LEU cc_start: 0.8478 (tt) cc_final: 0.7872 (mt) REVERT: O 108 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8167 (mtmt) REVERT: O 170 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.5783 (m-10) REVERT: P 24 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8117 (mtpt) REVERT: P 144 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7536 (tmtm) REVERT: P 161 TYR cc_start: 0.8583 (t80) cc_final: 0.8295 (t80) REVERT: P 164 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7312 (mp0) REVERT: P 167 GLU cc_start: 0.8120 (pt0) cc_final: 0.7874 (tm-30) REVERT: P 170 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.6034 (m-10) REVERT: Q 87 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6772 (m-30) REVERT: Q 157 GLU cc_start: 0.8181 (mp0) cc_final: 0.7743 (mp0) REVERT: Q 161 TYR cc_start: 0.8572 (t80) cc_final: 0.8363 (t80) REVERT: Q 170 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.5172 (m-10) REVERT: R 24 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8235 (mtmm) REVERT: R 90 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7050 (mm-30) REVERT: R 130 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7469 (mmt90) REVERT: R 140 GLU cc_start: 0.8127 (tp30) cc_final: 0.7698 (mt-10) REVERT: R 144 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7931 (tmtm) REVERT: R 157 GLU cc_start: 0.8237 (mp0) cc_final: 0.7864 (mm-30) REVERT: R 170 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.5553 (m-10) REVERT: S 77 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8912 (mt) REVERT: S 140 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7389 (mt-10) REVERT: S 144 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7541 (tmtm) REVERT: S 164 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7213 (mp0) REVERT: S 170 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5087 (m-10) REVERT: T 90 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: T 98 GLU cc_start: 0.8474 (tp30) cc_final: 0.8149 (tp30) REVERT: T 108 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8130 (mttp) REVERT: T 130 ARG cc_start: 0.8080 (mpp80) cc_final: 0.7533 (mmt90) REVERT: T 140 GLU cc_start: 0.8305 (tp30) cc_final: 0.7777 (mt-10) REVERT: T 164 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7145 (mp0) REVERT: T 170 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6048 (m-10) REVERT: U 30 ASP cc_start: 0.7866 (p0) cc_final: 0.7618 (p0) REVERT: U 37 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8008 (mmt180) REVERT: U 90 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7036 (mt-10) REVERT: U 144 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8005 (tmtm) REVERT: U 157 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: U 170 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.4983 (m-10) REVERT: V 37 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7741 (tpt-90) REVERT: V 98 GLU cc_start: 0.8592 (tp30) cc_final: 0.8265 (tp30) REVERT: V 140 GLU cc_start: 0.8177 (tp30) cc_final: 0.7423 (mm-30) REVERT: V 144 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7170 (tttm) REVERT: W 49 GLU cc_start: 0.7574 (mp0) cc_final: 0.7285 (tt0) REVERT: W 71 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7329 (tptp) REVERT: W 88 ARG cc_start: 0.5942 (mtm-85) cc_final: 0.5640 (mtp180) REVERT: W 137 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7767 (mtm-85) REVERT: W 140 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7799 (mt-10) REVERT: W 157 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8145 (mp0) REVERT: W 170 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6222 (m-10) REVERT: X 87 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: X 90 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7668 (mm-30) REVERT: X 91 GLU cc_start: 0.8271 (tp30) cc_final: 0.8004 (tt0) REVERT: Y 24 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8599 (mtpp) REVERT: Y 98 GLU cc_start: 0.8202 (tp30) cc_final: 0.7426 (tp30) REVERT: Y 144 LYS cc_start: 0.8699 (tptm) cc_final: 0.8351 (tmtm) REVERT: Y 170 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6144 (m-10) outliers start: 120 outliers final: 37 residues processed: 659 average time/residue: 0.9177 time to fit residues: 686.7035 Evaluate side-chains 654 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 562 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 170 TYR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 170 TYR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 170 TYR Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 170 TYR Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 170 TYR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 144 LYS Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 167 GLU Chi-restraints excluded: chain M residue 170 TYR Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 170 TYR Chi-restraints excluded: chain O residue 48 ARG Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 108 LYS Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain O residue 170 TYR Chi-restraints excluded: chain P residue 144 LYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain Q residue 87 ASP Chi-restraints excluded: chain Q residue 108 LYS Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain Q residue 170 TYR Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 108 LYS Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 170 TYR Chi-restraints excluded: chain S residue 77 ILE Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 170 TYR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 90 GLU Chi-restraints excluded: chain T residue 108 LYS Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 113 LYS Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 151 LEU Chi-restraints excluded: chain U residue 157 GLU Chi-restraints excluded: chain U residue 170 TYR Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain V residue 130 ARG Chi-restraints excluded: chain V residue 144 LYS Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain W residue 170 TYR Chi-restraints excluded: chain X residue 87 ASP Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 170 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 103 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 226 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 346 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 GLN H 128 GLN N 128 GLN Y 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092249 restraints weight = 31167.494| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.71 r_work: 0.2927 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32086 Z= 0.142 Angle : 0.533 10.103 43450 Z= 0.274 Chirality : 0.040 0.490 5525 Planarity : 0.006 0.055 5625 Dihedral : 3.813 42.013 4585 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.56 % Allowed : 27.59 % Favored : 68.85 % 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: 5.19 (0.11), residues: 4200 helix: 3.26 (0.07), residues: 4025 sheet: None (None), residues: 0 loop : 6.64 (0.59), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 130 TYR 0.010 0.001 TYR I 170 HIS 0.002 0.000 HIS H 147 Details of bonding type rmsd covalent geometry : bond 0.00322 (32000) covalent geometry : angle 0.53266 (43450) hydrogen bonds : bond 0.05340 ( 3171) hydrogen bonds : angle 3.18449 ( 9513) metal coordination : bond 0.00210 ( 86) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14080.22 seconds wall clock time: 239 minutes 2.87 seconds (14342.87 seconds total)