Starting phenix.real_space_refine on Sat Mar 23 04:49:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1z_14453/03_2024/7z1z_14453.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1z_14453/03_2024/7z1z_14453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1z_14453/03_2024/7z1z_14453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1z_14453/03_2024/7z1z_14453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1z_14453/03_2024/7z1z_14453.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1z_14453/03_2024/7z1z_14453.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 138 5.49 5 S 132 5.16 5 C 22213 2.51 5 N 6243 2.21 5 O 6867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 248": "OD1" <-> "OD2" Residue "Q ASP 366": "OD1" <-> "OD2" Residue "J TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ASP 118": "OD1" <-> "OD2" Residue "J GLU 126": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 206": "OE1" <-> "OE2" Residue "K TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 248": "OD1" <-> "OD2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 248": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35605 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2235 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain: "B" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2130 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "D" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2051 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain breaks: 1 Chain: "E" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2116 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "F" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2115 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 247} Chain breaks: 1 Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1647 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 674 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 667 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "X" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "W" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "U" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "I" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2235 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain: "J" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "K" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2130 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "L" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2051 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain breaks: 1 Chain: "M" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2116 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "N" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2115 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 247} Chain breaks: 1 Chain: "O" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1647 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "P" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "Y" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Z" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "a" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 329 SG CYS A 40 52.555 98.275 57.044 1.00 82.30 S ATOM 350 SG CYS A 43 55.029 100.117 57.886 1.00 80.20 S ATOM 2550 SG CYS B 40 141.347 77.147 78.894 1.00234.54 S ATOM 2571 SG CYS B 43 140.373 75.690 76.304 1.00237.78 S ATOM 4203 SG CYS C 40 112.859 55.219 47.405 1.00165.74 S ATOM 4224 SG CYS C 43 115.169 57.021 48.375 1.00154.11 S ATOM 8384 SG CYS E 40 35.028 89.415 83.743 1.00201.72 S ATOM 8405 SG CYS E 43 36.217 86.876 85.415 1.00192.57 S ATOM 10469 SG CYS F 40 51.442 57.845 50.351 1.00254.89 S ATOM 10490 SG CYS F 43 49.499 55.856 51.548 1.00254.39 S ATOM 12615 SG CYS G 40 27.432 33.168 82.886 1.00236.12 S ATOM 12636 SG CYS G 43 28.446 35.251 80.527 1.00234.83 S ATOM 18796 SG CYS I 40 112.929 111.593 57.211 1.00 82.30 S ATOM 18817 SG CYS I 43 110.445 109.764 58.051 1.00 80.20 S ATOM 21017 SG CYS J 40 23.984 133.086 78.061 1.00234.54 S ATOM 21038 SG CYS J 43 24.983 134.515 75.464 1.00237.78 S ATOM 22670 SG CYS K 40 52.782 154.640 46.597 1.00165.74 S ATOM 22691 SG CYS K 43 50.461 152.852 47.564 1.00154.11 S ATOM 26851 SG CYS M 40 130.237 120.704 83.969 1.00201.72 S ATOM 26872 SG CYS M 43 129.036 123.262 85.604 1.00192.57 S ATOM 28936 SG CYS N 40 114.167 151.949 50.107 1.00254.89 S ATOM 28957 SG CYS N 43 116.103 153.948 51.301 1.00254.39 S ATOM 31082 SG CYS O 40 137.932 176.928 82.593 1.00236.12 S ATOM 31103 SG CYS O 43 136.935 174.822 80.247 1.00234.83 S Time building chain proxies: 18.49, per 1000 atoms: 0.52 Number of scatterers: 35605 At special positions: 0 Unit cell: (165.6, 211.14, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 132 16.00 P 138 15.00 O 6867 8.00 N 6243 7.00 C 22213 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 - 3.50 Amino acid : False - 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: 15.07 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 40 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 16 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 12 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 40 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 40 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 43 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 40 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 43 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 40 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 43 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 40 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" ND1 HIS N 16 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 12 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 40 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" ND1 HIS O 16 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS O 12 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 43 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 40 " Number of angles added : 23 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7538 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 54 sheets defined 51.6% alpha, 15.3% beta 62 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 11.27 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 29 through 39 removed outlier: 3.502A pdb=" N GLN A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.505A pdb=" N ASN A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.936A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.820A pdb=" N SER A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.556A pdb=" N ARG B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 101 " --> pdb=" O GLN B 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.784A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 removed outlier: 3.546A pdb=" N THR B 184 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 216 removed outlier: 3.685A pdb=" N ARG B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 146 through 168 removed outlier: 3.556A pdb=" N ARG C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 166 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 removed outlier: 3.602A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.715A pdb=" N ILE C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE C 201 " --> pdb=" O PRO C 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.516A pdb=" N LYS C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.666A pdb=" N LYS D 14 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.935A pdb=" N ASP D 35 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 removed outlier: 3.501A pdb=" N PHE D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.556A pdb=" N LEU D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 173 through 188 Processing helix chain 'D' and resid 196 through 220 removed outlier: 4.080A pdb=" N LYS D 215 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS D 217 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 95 through 110 removed outlier: 3.505A pdb=" N PHE E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 136 removed outlier: 3.607A pdb=" N LEU E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 168 removed outlier: 3.811A pdb=" N GLU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 187 removed outlier: 3.752A pdb=" N THR E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR E 184 " --> pdb=" O GLY E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 216 removed outlier: 3.946A pdb=" N GLN E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN E 212 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 18 through 27 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 40 through 46 removed outlier: 3.529A pdb=" N ASN F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 110 removed outlier: 3.558A pdb=" N VAL F 101 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE F 110 " --> pdb=" O TRP F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.712A pdb=" N LEU F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.987A pdb=" N ARG F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 188 removed outlier: 3.720A pdb=" N GLY F 180 " --> pdb=" O SER F 176 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE F 183 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 184 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 218 removed outlier: 3.731A pdb=" N GLN F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE F 210 " --> pdb=" O GLU F 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS F 215 " --> pdb=" O GLN F 211 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS F 217 " --> pdb=" O GLN F 213 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 40 through 46 removed outlier: 3.508A pdb=" N ASN G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 removed outlier: 3.795A pdb=" N MET G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET G 109 " --> pdb=" O LYS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 136 removed outlier: 4.366A pdb=" N TYR G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 168 removed outlier: 4.165A pdb=" N VAL G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU G 154 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS G 157 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS G 166 " --> pdb=" O ASN G 162 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 187 removed outlier: 3.561A pdb=" N ILE G 183 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR G 184 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 215 removed outlier: 3.880A pdb=" N GLN G 207 " --> pdb=" O PHE G 203 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 208 " --> pdb=" O ASN G 204 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN G 212 " --> pdb=" O GLN G 208 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN G 213 " --> pdb=" O ARG G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 removed outlier: 4.363A pdb=" N MET H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 136 Processing helix chain 'H' and resid 146 through 165 removed outlier: 3.810A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 189 removed outlier: 3.755A pdb=" N THR H 184 " --> pdb=" O GLY H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 207 Processing helix chain 'H' and resid 208 through 215 removed outlier: 6.246A pdb=" N GLN H 211 " --> pdb=" O GLN H 208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 215 " --> pdb=" O GLN H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'R' and resid 349 through 363 Processing helix chain 'R' and resid 369 through 383 removed outlier: 3.707A pdb=" N CYS R 373 " --> pdb=" O ASP R 369 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP R 378 " --> pdb=" O ILE R 374 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU R 383 " --> pdb=" O GLU R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 386 through 392 removed outlier: 3.542A pdb=" N ALA R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 404 removed outlier: 4.004A pdb=" N LYS R 402 " --> pdb=" O THR R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 409 through 429 removed outlier: 3.857A pdb=" N MET R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 363 Processing helix chain 'Q' and resid 369 through 383 removed outlier: 3.542A pdb=" N LEU Q 383 " --> pdb=" O GLU Q 379 " (cutoff:3.500A) Processing helix chain 'Q' and resid 386 through 392 Processing helix chain 'Q' and resid 394 through 404 removed outlier: 3.635A pdb=" N LYS Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 428 Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 29 through 39 removed outlier: 3.503A pdb=" N GLN I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 46 removed outlier: 3.505A pdb=" N ASN I 46 " --> pdb=" O VAL I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 126 through 136 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 removed outlier: 3.937A pdb=" N GLN I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS I 166 " --> pdb=" O ASN I 162 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU I 167 " --> pdb=" O THR I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 187 Processing helix chain 'I' and resid 196 through 208 Processing helix chain 'I' and resid 210 through 216 removed outlier: 3.819A pdb=" N SER I 216 " --> pdb=" O GLN I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 95 through 110 removed outlier: 3.557A pdb=" N ARG J 100 " --> pdb=" O GLY J 96 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL J 101 " --> pdb=" O GLN J 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET J 109 " --> pdb=" O LYS J 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE J 110 " --> pdb=" O TRP J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 146 through 168 removed outlier: 3.783A pdb=" N GLU J 165 " --> pdb=" O LYS J 161 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS J 166 " --> pdb=" O ASN J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 187 removed outlier: 3.545A pdb=" N THR J 184 " --> pdb=" O GLY J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 removed outlier: 3.685A pdb=" N ARG J 209 " --> pdb=" O LYS J 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 210 " --> pdb=" O GLU J 206 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN J 211 " --> pdb=" O GLN J 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 40 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 95 through 107 Processing helix chain 'K' and resid 125 through 136 Processing helix chain 'K' and resid 146 through 168 removed outlier: 3.556A pdb=" N ARG K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS K 166 " --> pdb=" O ASN K 162 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU K 167 " --> pdb=" O THR K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 removed outlier: 3.603A pdb=" N LEU K 182 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 187 " --> pdb=" O ILE K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 211 removed outlier: 3.715A pdb=" N ILE K 200 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 201 " --> pdb=" O PRO K 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU K 206 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN K 207 " --> pdb=" O PHE K 203 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN K 211 " --> pdb=" O GLN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 219 removed outlier: 4.516A pdb=" N LYS K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.667A pdb=" N LYS L 14 " --> pdb=" O GLU L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 26 Processing helix chain 'L' and resid 29 through 35 removed outlier: 3.936A pdb=" N ASP L 35 " --> pdb=" O THR L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 110 removed outlier: 3.500A pdb=" N PHE L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 135 removed outlier: 3.555A pdb=" N LEU L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 168 Processing helix chain 'L' and resid 173 through 188 Processing helix chain 'L' and resid 196 through 220 removed outlier: 4.081A pdb=" N LYS L 215 " --> pdb=" O GLN L 211 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER L 216 " --> pdb=" O GLN L 212 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS L 217 " --> pdb=" O GLN L 213 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN L 218 " --> pdb=" O SER L 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 16 Processing helix chain 'M' and resid 18 through 27 Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 95 through 110 removed outlier: 3.505A pdb=" N PHE M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG M 100 " --> pdb=" O GLY M 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET M 104 " --> pdb=" O ARG M 100 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 136 removed outlier: 3.606A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS M 133 " --> pdb=" O GLN M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 168 removed outlier: 3.810A pdb=" N GLU M 165 " --> pdb=" O LYS M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 187 removed outlier: 3.751A pdb=" N THR M 181 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU M 182 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 183 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR M 184 " --> pdb=" O GLY M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 216 removed outlier: 3.946A pdb=" N GLN M 211 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN M 212 " --> pdb=" O GLN M 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN M 213 " --> pdb=" O ARG M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 16 Processing helix chain 'N' and resid 18 through 27 Processing helix chain 'N' and resid 29 through 40 Processing helix chain 'N' and resid 40 through 46 removed outlier: 3.528A pdb=" N ASN N 46 " --> pdb=" O VAL N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 110 removed outlier: 3.557A pdb=" N VAL N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE N 110 " --> pdb=" O TRP N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 135 removed outlier: 3.713A pdb=" N LEU N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 165 removed outlier: 3.986A pdb=" N ARG N 155 " --> pdb=" O ALA N 151 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU N 165 " --> pdb=" O LYS N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 173 through 188 removed outlier: 3.719A pdb=" N GLY N 180 " --> pdb=" O SER N 176 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR N 181 " --> pdb=" O ALA N 177 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR N 184 " --> pdb=" O GLY N 180 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN N 186 " --> pdb=" O LEU N 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS N 188 " --> pdb=" O THR N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 218 removed outlier: 3.731A pdb=" N GLN N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG N 209 " --> pdb=" O LYS N 205 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE N 210 " --> pdb=" O GLU N 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS N 215 " --> pdb=" O GLN N 211 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER N 216 " --> pdb=" O GLN N 212 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS N 217 " --> pdb=" O GLN N 213 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN N 218 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 18 through 27 Processing helix chain 'O' and resid 29 through 40 Processing helix chain 'O' and resid 40 through 46 removed outlier: 3.509A pdb=" N ASN O 46 " --> pdb=" O VAL O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 110 removed outlier: 3.794A pdb=" N MET O 104 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET O 109 " --> pdb=" O LYS O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 136 removed outlier: 4.366A pdb=" N TYR O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 168 removed outlier: 4.165A pdb=" N VAL O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU O 154 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS O 157 " --> pdb=" O VAL O 153 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN O 158 " --> pdb=" O GLU O 154 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS O 166 " --> pdb=" O ASN O 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU O 167 " --> pdb=" O THR O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 187 removed outlier: 3.561A pdb=" N ILE O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR O 184 " --> pdb=" O GLY O 180 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU O 185 " --> pdb=" O THR O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 215 removed outlier: 3.881A pdb=" N GLN O 207 " --> pdb=" O PHE O 203 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN O 212 " --> pdb=" O GLN O 208 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN O 213 " --> pdb=" O ARG O 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 removed outlier: 4.362A pdb=" N MET P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 136 Processing helix chain 'P' and resid 146 through 165 removed outlier: 3.809A pdb=" N GLU P 165 " --> pdb=" O LYS P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 189 removed outlier: 3.754A pdb=" N THR P 184 " --> pdb=" O GLY P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 207 Processing helix chain 'P' and resid 208 through 215 removed outlier: 6.245A pdb=" N GLN P 211 " --> pdb=" O GLN P 208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS P 215 " --> pdb=" O GLN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 267 through 269 No H-bonds generated for 'chain 'P' and resid 267 through 269' Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 6.390A pdb=" N LEU A 115 " --> pdb=" O THR A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.895A pdb=" N TRP A 245 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.566A pdb=" N TRP B 63 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 115 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 91 removed outlier: 3.690A pdb=" N GLU C 89 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 74 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE C 75 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 68 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP C 63 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C 115 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.005A pdb=" N CYS C 224 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.966A pdb=" N TRP C 245 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 252 " --> pdb=" O TRP C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.887A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 86 through 87 removed outlier: 5.875A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 117 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 242 removed outlier: 5.507A pdb=" N GLY D 239 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR D 226 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 241 " --> pdb=" O CYS D 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 245 through 246 removed outlier: 3.556A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 86 through 91 removed outlier: 3.743A pdb=" N GLU E 89 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 76 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 74 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 77 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER E 117 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 233 through 241 removed outlier: 6.278A pdb=" N GLY E 235 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS E 230 " --> pdb=" O GLY E 235 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP E 237 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR E 228 " --> pdb=" O TRP E 237 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY E 239 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR E 226 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 245 through 246 removed outlier: 3.615A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 264 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 63 through 69 removed outlier: 3.694A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 89 " --> pdb=" O LEU F 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 114 through 117 removed outlier: 6.867A pdb=" N LEU F 115 " --> pdb=" O THR F 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 238 through 242 removed outlier: 6.575A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AC3, first strand: chain 'F' and resid 250 through 254 Processing sheet with id=AC4, first strand: chain 'G' and resid 86 through 87 removed outlier: 4.267A pdb=" N ILE G 74 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.627A pdb=" N ILE G 75 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 79 " --> pdb=" O GLN G 64 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP G 63 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR G 140 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER G 117 " --> pdb=" O THR G 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 86 through 91 removed outlier: 4.104A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU H 115 " --> pdb=" O THR H 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 223 through 224 Processing sheet with id=AC8, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AC9, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.811A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 63 through 69 Processing sheet with id=AD2, first strand: chain 'I' and resid 114 through 117 removed outlier: 6.390A pdb=" N LEU I 115 " --> pdb=" O THR I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 240 through 242 Processing sheet with id=AD4, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=AD5, first strand: chain 'I' and resid 245 through 246 removed outlier: 3.896A pdb=" N TRP I 245 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.567A pdb=" N TRP J 63 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU J 115 " --> pdb=" O THR J 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 86 through 91 removed outlier: 3.689A pdb=" N GLU K 89 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE K 74 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE K 75 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR K 68 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP K 63 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU K 115 " --> pdb=" O THR K 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 238 through 242 removed outlier: 6.005A pdb=" N CYS K 224 " --> pdb=" O PRO K 240 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 245 through 246 removed outlier: 3.966A pdb=" N TRP K 245 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL K 252 " --> pdb=" O TRP K 245 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.887A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 86 through 87 removed outlier: 5.874A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER L 117 " --> pdb=" O THR L 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 238 through 242 removed outlier: 5.507A pdb=" N GLY L 239 " --> pdb=" O TYR L 226 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR L 226 " --> pdb=" O GLY L 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR L 241 " --> pdb=" O CYS L 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 245 through 246 removed outlier: 3.556A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 86 through 91 removed outlier: 3.744A pdb=" N GLU M 89 " --> pdb=" O LEU M 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU M 76 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE M 74 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL M 77 " --> pdb=" O ASP M 66 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER M 117 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 233 through 241 removed outlier: 6.277A pdb=" N GLY M 235 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS M 230 " --> pdb=" O GLY M 235 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP M 237 " --> pdb=" O THR M 228 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR M 228 " --> pdb=" O TRP M 237 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY M 239 " --> pdb=" O TYR M 226 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR M 226 " --> pdb=" O GLY M 239 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 245 through 246 removed outlier: 3.616A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE M 264 " --> pdb=" O ILE M 251 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 63 through 69 removed outlier: 3.694A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU N 89 " --> pdb=" O LEU N 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 114 through 117 removed outlier: 6.866A pdb=" N LEU N 115 " --> pdb=" O THR N 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'N' and resid 238 through 242 removed outlier: 6.576A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AF3, first strand: chain 'N' and resid 250 through 254 Processing sheet with id=AF4, first strand: chain 'O' and resid 86 through 87 removed outlier: 4.266A pdb=" N ILE O 74 " --> pdb=" O VAL O 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.627A pdb=" N ILE O 75 " --> pdb=" O THR O 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL O 79 " --> pdb=" O GLN O 64 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP O 63 " --> pdb=" O GLN O 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR O 140 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER O 117 " --> pdb=" O THR O 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 86 through 91 removed outlier: 4.104A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU P 115 " --> pdb=" O THR P 140 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 223 through 224 Processing sheet with id=AF8, first strand: chain 'P' and resid 229 through 230 Processing sheet with id=AF9, first strand: chain 'P' and resid 245 through 246 removed outlier: 3.810A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) 1552 hydrogen bonds defined for protein. 4542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 300 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 13.45 Time building geometry restraints manager: 16.31 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: 10707 1.34 - 1.46: 6374 1.46 - 1.57: 19126 1.57 - 1.69: 272 1.69 - 1.81: 226 Bond restraints: 36705 Sorted by residual: bond pdb=" C ILE H 168 " pdb=" N PRO H 169 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.66e+00 bond pdb=" C ILE P 168 " pdb=" N PRO P 169 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C ILE E 168 " pdb=" N PRO E 169 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 9.50e-01 bond pdb=" CB GLN A 211 " pdb=" CG GLN A 211 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.36e-01 bond pdb=" CB GLN I 211 " pdb=" CG GLN I 211 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.18e-01 ... (remaining 36700 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.98: 1522 105.98 - 112.99: 19625 112.99 - 120.01: 12731 120.01 - 127.03: 15534 127.03 - 134.04: 836 Bond angle restraints: 50248 Sorted by residual: angle pdb=" CA GLY L 247 " pdb=" C GLY L 247 " pdb=" N ASP L 248 " ideal model delta sigma weight residual 114.65 117.17 -2.52 9.20e-01 1.18e+00 7.49e+00 angle pdb=" CA GLY D 247 " pdb=" C GLY D 247 " pdb=" N ASP D 248 " ideal model delta sigma weight residual 114.65 117.14 -2.49 9.20e-01 1.18e+00 7.35e+00 angle pdb=" N ILE D 168 " pdb=" CA ILE D 168 " pdb=" C ILE D 168 " ideal model delta sigma weight residual 108.88 114.48 -5.60 2.16e+00 2.14e-01 6.73e+00 angle pdb=" N ILE L 168 " pdb=" CA ILE L 168 " pdb=" C ILE L 168 " ideal model delta sigma weight residual 108.88 114.47 -5.59 2.16e+00 2.14e-01 6.70e+00 angle pdb=" CA GLN I 211 " pdb=" CB GLN I 211 " pdb=" CG GLN I 211 " ideal model delta sigma weight residual 114.10 119.21 -5.11 2.00e+00 2.50e-01 6.52e+00 ... (remaining 50243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 20355 27.60 - 55.20: 1066 55.20 - 82.79: 117 82.79 - 110.39: 12 110.39 - 137.99: 2 Dihedral angle restraints: 21552 sinusoidal: 9895 harmonic: 11657 Sorted by residual: dihedral pdb=" C4' DG W 20 " pdb=" C3' DG W 20 " pdb=" O3' DG W 20 " pdb=" P DT W 21 " ideal model delta sinusoidal sigma weight residual 220.00 82.01 137.99 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DG Z 20 " pdb=" C3' DG Z 20 " pdb=" O3' DG Z 20 " pdb=" P DT Z 21 " ideal model delta sinusoidal sigma weight residual 220.00 82.02 137.98 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLU H 219 " pdb=" C GLU H 219 " pdb=" N LYS H 220 " pdb=" CA LYS H 220 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 21549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3805 0.034 - 0.069: 1108 0.069 - 0.103: 368 0.103 - 0.137: 139 0.137 - 0.172: 12 Chirality restraints: 5432 Sorted by residual: chirality pdb=" CA VAL H 79 " pdb=" N VAL H 79 " pdb=" C VAL H 79 " pdb=" CB VAL H 79 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA VAL P 79 " pdb=" N VAL P 79 " pdb=" C VAL P 79 " pdb=" CB VAL P 79 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA GLN D 218 " pdb=" N GLN D 218 " pdb=" C GLN D 218 " pdb=" CB GLN D 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 5429 not shown) Planarity restraints: 5969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 273 " -0.064 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO I 274 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO I 274 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO I 274 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 273 " -0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A 274 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 272 " 0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO A 273 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " 0.046 5.00e-02 4.00e+02 ... (remaining 5966 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5048 2.76 - 3.29: 34919 3.29 - 3.83: 59506 3.83 - 4.36: 67800 4.36 - 4.90: 111512 Nonbonded interactions: 278785 Sorted by model distance: nonbonded pdb=" OG1 THR M 95 " pdb=" OE1 GLU M 98 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR E 95 " pdb=" OE1 GLU E 98 " model vdw 2.225 2.440 nonbonded pdb=" O ASP L 61 " pdb=" OG SER L 114 " model vdw 2.225 2.440 nonbonded pdb=" O ASP D 61 " pdb=" OG SER D 114 " model vdw 2.226 2.440 nonbonded pdb=" O ASP C 18 " pdb=" OG SER C 21 " model vdw 2.227 2.440 ... (remaining 278780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'C' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'D' and resid 4 through 272) selection = (chain 'E' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'F' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'I' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'K' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'L' and resid 4 through 272) selection = (chain 'M' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'N' and (resid 4 through 36 or resid 61 through 272)) } ncs_group { reference = (chain 'B' and (resid 2 through 215 or resid 301)) selection = (chain 'G' and (resid 2 through 215 or resid 301)) selection = (chain 'J' and (resid 2 through 215 or resid 301)) selection = (chain 'O' and (resid 2 through 215 or resid 301)) } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 348 through 428) } ncs_group { reference = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'X' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 8.710 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 104.160 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.240 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 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 : 0.002 0.043 36705 Z= 0.139 Angle : 0.510 6.930 50248 Z= 0.274 Chirality : 0.040 0.172 5432 Planarity : 0.004 0.097 5969 Dihedral : 15.201 137.992 14014 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3971 helix: 1.14 (0.12), residues: 1808 sheet: 0.22 (0.21), residues: 694 loop : -1.02 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 245 HIS 0.004 0.001 HIS K 69 PHE 0.020 0.001 PHE N 203 TYR 0.014 0.001 TYR M 225 ARG 0.009 0.001 ARG J 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 929 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6596 (mm-30) REVERT: A 35 ASP cc_start: 0.7200 (t70) cc_final: 0.6947 (t0) REVERT: A 57 LYS cc_start: 0.7254 (tttm) cc_final: 0.7035 (ttmm) REVERT: A 76 LEU cc_start: 0.7704 (tp) cc_final: 0.7502 (tp) REVERT: A 98 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6776 (mm-30) REVERT: A 118 ASP cc_start: 0.7437 (p0) cc_final: 0.7225 (p0) REVERT: A 162 ASN cc_start: 0.8250 (t0) cc_final: 0.7718 (t0) REVERT: A 165 GLU cc_start: 0.7374 (tp30) cc_final: 0.7154 (tp30) REVERT: A 199 ASP cc_start: 0.6741 (t0) cc_final: 0.6433 (t0) REVERT: A 255 ASP cc_start: 0.5707 (t0) cc_final: 0.5411 (t0) REVERT: A 262 LEU cc_start: 0.6868 (mm) cc_final: 0.6650 (mt) REVERT: B 89 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6116 (mt-10) REVERT: B 97 GLN cc_start: 0.7627 (tp40) cc_final: 0.7247 (tp40) REVERT: B 124 VAL cc_start: 0.7406 (t) cc_final: 0.7200 (p) REVERT: B 129 GLN cc_start: 0.7735 (tt0) cc_final: 0.7365 (mt0) REVERT: B 140 THR cc_start: 0.8113 (m) cc_final: 0.7818 (t) REVERT: B 190 LYS cc_start: 0.8676 (mttp) cc_final: 0.8471 (mttm) REVERT: C 9 GLU cc_start: 0.7588 (tp30) cc_final: 0.7107 (tp30) REVERT: C 24 LEU cc_start: 0.7872 (mm) cc_final: 0.7517 (mp) REVERT: C 105 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7361 (ttpp) REVERT: C 186 ASN cc_start: 0.7990 (m-40) cc_final: 0.7616 (t0) REVERT: C 203 PHE cc_start: 0.7336 (t80) cc_final: 0.7006 (t80) REVERT: C 204 ASN cc_start: 0.8471 (m-40) cc_final: 0.8162 (m110) REVERT: C 208 GLN cc_start: 0.7119 (tt0) cc_final: 0.6382 (tp40) REVERT: C 238 GLN cc_start: 0.6901 (mt0) cc_final: 0.6698 (mt0) REVERT: C 245 TRP cc_start: 0.7866 (m-90) cc_final: 0.7525 (m-90) REVERT: C 254 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7568 (ttmm) REVERT: D 70 TYR cc_start: 0.6979 (t80) cc_final: 0.6313 (t80) REVERT: D 103 THR cc_start: 0.6824 (t) cc_final: 0.6274 (p) REVERT: D 104 MET cc_start: 0.6727 (mmp) cc_final: 0.5872 (mmp) REVERT: D 167 LEU cc_start: 0.8632 (tt) cc_final: 0.8344 (tt) REVERT: D 236 GLU cc_start: 0.7259 (mp0) cc_final: 0.6759 (mp0) REVERT: D 238 GLN cc_start: 0.8824 (mt0) cc_final: 0.8402 (mt0) REVERT: D 268 ASP cc_start: 0.7323 (p0) cc_final: 0.6545 (p0) REVERT: E 38 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7790 (mm-40) REVERT: E 61 ASP cc_start: 0.7859 (t70) cc_final: 0.7028 (t0) REVERT: E 80 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 99 PHE cc_start: 0.7883 (m-80) cc_final: 0.6989 (m-80) REVERT: E 103 THR cc_start: 0.8484 (t) cc_final: 0.8186 (p) REVERT: E 131 LEU cc_start: 0.8968 (mt) cc_final: 0.8465 (mt) REVERT: E 153 VAL cc_start: 0.8851 (t) cc_final: 0.8012 (p) REVERT: E 155 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7174 (mtt180) REVERT: E 157 HIS cc_start: 0.8442 (m90) cc_final: 0.8036 (m-70) REVERT: E 158 GLN cc_start: 0.8066 (pt0) cc_final: 0.7852 (pt0) REVERT: E 163 THR cc_start: 0.8088 (p) cc_final: 0.7736 (p) REVERT: E 181 THR cc_start: 0.8499 (p) cc_final: 0.8169 (p) REVERT: E 202 ILE cc_start: 0.7675 (tp) cc_final: 0.7439 (tp) REVERT: E 211 GLN cc_start: 0.8042 (pm20) cc_final: 0.7408 (pp30) REVERT: E 224 CYS cc_start: 0.7782 (t) cc_final: 0.7402 (p) REVERT: E 271 PHE cc_start: 0.7705 (m-80) cc_final: 0.6859 (m-80) REVERT: F 62 HIS cc_start: 0.7415 (m170) cc_final: 0.6815 (m170) REVERT: F 77 VAL cc_start: 0.8537 (t) cc_final: 0.8193 (m) REVERT: F 103 THR cc_start: 0.7745 (t) cc_final: 0.7501 (p) REVERT: F 113 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7020 (mmtm) REVERT: F 157 HIS cc_start: 0.8966 (m90) cc_final: 0.8751 (m90) REVERT: F 160 LEU cc_start: 0.8968 (tp) cc_final: 0.8557 (tp) REVERT: F 176 SER cc_start: 0.7907 (m) cc_final: 0.7664 (p) REVERT: F 210 ILE cc_start: 0.8151 (mm) cc_final: 0.7861 (mm) REVERT: F 267 LYS cc_start: 0.8281 (pttp) cc_final: 0.8063 (pttm) REVERT: G 63 TRP cc_start: 0.6040 (t-100) cc_final: 0.5805 (m100) REVERT: G 110 PHE cc_start: 0.7599 (m-80) cc_final: 0.7223 (m-80) REVERT: G 150 GLN cc_start: 0.7687 (mm110) cc_final: 0.7334 (mm110) REVERT: G 157 HIS cc_start: 0.8536 (m90) cc_final: 0.8329 (m90) REVERT: G 186 ASN cc_start: 0.6861 (m-40) cc_final: 0.6525 (m110) REVERT: H 85 LEU cc_start: 0.7810 (tp) cc_final: 0.7489 (tp) REVERT: H 87 TYR cc_start: 0.7624 (t80) cc_final: 0.7396 (t80) REVERT: H 104 MET cc_start: 0.8590 (mpp) cc_final: 0.8301 (mpp) REVERT: H 132 MET cc_start: 0.7736 (tpt) cc_final: 0.7154 (tpt) REVERT: H 161 LYS cc_start: 0.8471 (mttt) cc_final: 0.7970 (ptpp) REVERT: H 164 LEU cc_start: 0.8159 (mt) cc_final: 0.7889 (tp) REVERT: H 184 THR cc_start: 0.8248 (m) cc_final: 0.7967 (p) REVERT: H 186 ASN cc_start: 0.8157 (m-40) cc_final: 0.7898 (p0) REVERT: H 198 MET cc_start: 0.8118 (mpp) cc_final: 0.7862 (mpp) REVERT: H 201 PHE cc_start: 0.8356 (t80) cc_final: 0.7947 (t80) REVERT: H 205 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8202 (mmmm) REVERT: H 210 ILE cc_start: 0.7840 (mm) cc_final: 0.7625 (tp) REVERT: R 367 ASN cc_start: 0.6514 (t0) cc_final: 0.6120 (t0) REVERT: R 413 MET cc_start: 0.6828 (mmm) cc_final: 0.6517 (mmm) REVERT: R 418 MET cc_start: 0.7396 (ppp) cc_final: 0.6946 (ppp) REVERT: Q 360 LYS cc_start: 0.5100 (ptpp) cc_final: 0.4809 (ptpp) REVERT: Q 387 MET cc_start: 0.7417 (tpp) cc_final: 0.6993 (mmm) REVERT: Q 418 MET cc_start: 0.7470 (ppp) cc_final: 0.7012 (ppp) REVERT: I 72 ASP cc_start: 0.7317 (t70) cc_final: 0.7110 (t70) REVERT: I 92 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7771 (mtpp) REVERT: I 95 THR cc_start: 0.8312 (p) cc_final: 0.8102 (t) REVERT: I 98 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6629 (mm-30) REVERT: I 162 ASN cc_start: 0.7896 (t0) cc_final: 0.7574 (t0) REVERT: I 238 GLN cc_start: 0.6839 (tm-30) cc_final: 0.6560 (tm-30) REVERT: I 254 LYS cc_start: 0.7525 (tptp) cc_final: 0.7283 (tptp) REVERT: J 92 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7717 (mtpp) REVERT: J 129 GLN cc_start: 0.7665 (tt0) cc_final: 0.7170 (mt0) REVERT: J 206 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7202 (tp30) REVERT: K 26 PHE cc_start: 0.6774 (m-80) cc_final: 0.6510 (m-80) REVERT: K 170 MET cc_start: 0.4922 (tmm) cc_final: 0.2986 (pmm) REVERT: K 222 ARG cc_start: 0.6460 (mtm110) cc_final: 0.5822 (ptp90) REVERT: L 104 MET cc_start: 0.5615 (mmp) cc_final: 0.5201 (mmp) REVERT: L 248 ASP cc_start: 0.6931 (p0) cc_final: 0.6631 (p0) REVERT: L 260 ARG cc_start: 0.6791 (mmm-85) cc_final: 0.6314 (mmm-85) REVERT: L 268 ASP cc_start: 0.7177 (p0) cc_final: 0.6925 (p0) REVERT: M 17 GLN cc_start: 0.6100 (mp-120) cc_final: 0.5863 (mp10) REVERT: M 35 ASP cc_start: 0.6469 (m-30) cc_final: 0.6125 (m-30) REVERT: M 61 ASP cc_start: 0.7561 (t70) cc_final: 0.6286 (t0) REVERT: M 62 HIS cc_start: 0.6465 (t70) cc_final: 0.5174 (t70) REVERT: M 99 PHE cc_start: 0.8074 (m-80) cc_final: 0.7118 (m-80) REVERT: M 101 VAL cc_start: 0.8568 (t) cc_final: 0.8171 (t) REVERT: M 155 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7522 (mtt180) REVERT: M 161 LYS cc_start: 0.8641 (mttt) cc_final: 0.8006 (mttt) REVERT: M 164 LEU cc_start: 0.8355 (mt) cc_final: 0.7522 (pp) REVERT: M 165 GLU cc_start: 0.7734 (mp0) cc_final: 0.7533 (mp0) REVERT: M 205 LYS cc_start: 0.7638 (tptt) cc_final: 0.7393 (tptt) REVERT: M 224 CYS cc_start: 0.7312 (t) cc_final: 0.6950 (t) REVERT: N 61 ASP cc_start: 0.5695 (t70) cc_final: 0.5437 (t70) REVERT: N 113 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7418 (mmtm) REVERT: N 157 HIS cc_start: 0.8721 (m90) cc_final: 0.8470 (m90) REVERT: N 176 SER cc_start: 0.7092 (m) cc_final: 0.6824 (p) REVERT: N 200 ILE cc_start: 0.7107 (mm) cc_final: 0.6884 (pt) REVERT: N 243 VAL cc_start: 0.8273 (t) cc_final: 0.7742 (m) REVERT: N 260 ARG cc_start: 0.6850 (mtm-85) cc_final: 0.6412 (mtm-85) REVERT: O 11 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8168 (mm-30) REVERT: O 104 MET cc_start: 0.7202 (mmp) cc_final: 0.6306 (mmp) REVERT: O 132 MET cc_start: 0.8071 (mpp) cc_final: 0.7825 (mpp) REVERT: O 155 ARG cc_start: 0.8687 (pmt170) cc_final: 0.8078 (tpt170) REVERT: O 201 PHE cc_start: 0.8538 (t80) cc_final: 0.7885 (t80) REVERT: O 205 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7931 (mttp) REVERT: O 208 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7462 (tm-30) REVERT: P 63 TRP cc_start: 0.6884 (m100) cc_final: 0.5748 (m100) REVERT: P 85 LEU cc_start: 0.6607 (tp) cc_final: 0.6083 (tp) REVERT: P 104 MET cc_start: 0.8189 (mpp) cc_final: 0.7697 (mpp) REVERT: P 132 MET cc_start: 0.7973 (tpt) cc_final: 0.7337 (tpt) REVERT: P 187 ILE cc_start: 0.8874 (mt) cc_final: 0.8571 (mt) REVERT: P 198 MET cc_start: 0.8087 (mpp) cc_final: 0.7877 (pmm) REVERT: P 201 PHE cc_start: 0.8450 (t80) cc_final: 0.7478 (t80) REVERT: P 202 ILE cc_start: 0.8811 (pt) cc_final: 0.8599 (pt) REVERT: P 205 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7397 (mmmm) REVERT: P 261 TYR cc_start: 0.7091 (m-80) cc_final: 0.6767 (m-80) outliers start: 0 outliers final: 0 residues processed: 929 average time/residue: 0.4837 time to fit residues: 706.6760 Evaluate side-chains 833 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 833 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 0.7980 chunk 310 optimal weight: 0.1980 chunk 172 optimal weight: 0.0050 chunk 106 optimal weight: 0.0170 chunk 209 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 195 optimal weight: 0.0980 chunk 239 optimal weight: 0.9980 chunk 372 optimal weight: 10.0000 overall best weight: 0.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN B 13 ASN C 39 GLN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 82 ASN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN H 129 GLN H 162 ASN H 266 ASN I 4 ASN I 17 GLN I 38 GLN ** I 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN M 139 HIS M 157 HIS M 204 ASN ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 36705 Z= 0.192 Angle : 0.622 10.656 50248 Z= 0.331 Chirality : 0.044 0.157 5432 Planarity : 0.004 0.072 5969 Dihedral : 16.178 140.921 5791 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.19 % Allowed : 9.13 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 3971 helix: 1.28 (0.12), residues: 1872 sheet: 0.16 (0.19), residues: 786 loop : -1.13 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP P 245 HIS 0.024 0.002 HIS K 16 PHE 0.022 0.001 PHE E 203 TYR 0.020 0.001 TYR N 134 ARG 0.005 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 868 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6644 (tt0) cc_final: 0.6442 (tt0) REVERT: A 34 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5680 (tp30) REVERT: A 57 LYS cc_start: 0.7178 (tttm) cc_final: 0.6917 (ttmm) REVERT: A 76 LEU cc_start: 0.7715 (tp) cc_final: 0.7465 (tp) REVERT: A 98 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 162 ASN cc_start: 0.8149 (t0) cc_final: 0.7695 (t0) REVERT: A 165 GLU cc_start: 0.7363 (tp30) cc_final: 0.7130 (tp30) REVERT: A 199 ASP cc_start: 0.6671 (t0) cc_final: 0.6415 (t0) REVERT: A 206 GLU cc_start: 0.6919 (tp30) cc_final: 0.6423 (tm-30) REVERT: A 223 PHE cc_start: 0.8137 (m-80) cc_final: 0.7590 (m-80) REVERT: A 238 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 262 LEU cc_start: 0.6879 (mm) cc_final: 0.6642 (mt) REVERT: B 140 THR cc_start: 0.8105 (m) cc_final: 0.7856 (t) REVERT: B 185 LEU cc_start: 0.7395 (mt) cc_final: 0.6895 (mp) REVERT: B 206 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6820 (tp30) REVERT: B 208 GLN cc_start: 0.7356 (tt0) cc_final: 0.6991 (tt0) REVERT: C 9 GLU cc_start: 0.7777 (tp30) cc_final: 0.7389 (tp30) REVERT: C 24 LEU cc_start: 0.7948 (mm) cc_final: 0.7594 (mp) REVERT: C 25 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 105 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7438 (ttpp) REVERT: C 186 ASN cc_start: 0.8057 (m-40) cc_final: 0.7773 (t0) REVERT: C 203 PHE cc_start: 0.7071 (t80) cc_final: 0.6808 (t80) REVERT: C 205 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8174 (mmmt) REVERT: C 222 ARG cc_start: 0.4664 (ptm160) cc_final: 0.4017 (ptm160) REVERT: C 245 TRP cc_start: 0.7853 (m-90) cc_final: 0.7388 (m-90) REVERT: C 267 LYS cc_start: 0.8270 (pttp) cc_final: 0.7960 (pttp) REVERT: D 70 TYR cc_start: 0.6912 (t80) cc_final: 0.6571 (t80) REVERT: D 103 THR cc_start: 0.6991 (t) cc_final: 0.6289 (p) REVERT: D 104 MET cc_start: 0.6766 (mmp) cc_final: 0.5886 (mmp) REVERT: D 205 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7525 (tppt) REVERT: D 212 GLN cc_start: 0.7182 (tm-30) cc_final: 0.6956 (tm-30) REVERT: D 238 GLN cc_start: 0.8818 (mt0) cc_final: 0.8380 (mt0) REVERT: D 254 LYS cc_start: 0.6935 (tppp) cc_final: 0.6710 (tppt) REVERT: D 268 ASP cc_start: 0.7388 (p0) cc_final: 0.6664 (p0) REVERT: E 61 ASP cc_start: 0.7626 (t70) cc_final: 0.7207 (t0) REVERT: E 99 PHE cc_start: 0.8096 (m-80) cc_final: 0.7180 (m-80) REVERT: E 103 THR cc_start: 0.8620 (t) cc_final: 0.8397 (p) REVERT: E 129 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7728 (mm-40) REVERT: E 153 VAL cc_start: 0.8849 (t) cc_final: 0.8018 (p) REVERT: E 157 HIS cc_start: 0.8302 (m90) cc_final: 0.7991 (m-70) REVERT: E 162 ASN cc_start: 0.8494 (m110) cc_final: 0.8277 (p0) REVERT: E 163 THR cc_start: 0.8033 (p) cc_final: 0.7701 (p) REVERT: E 178 LEU cc_start: 0.8114 (tp) cc_final: 0.7794 (pp) REVERT: E 181 THR cc_start: 0.8377 (p) cc_final: 0.8051 (t) REVERT: E 185 LEU cc_start: 0.7857 (mm) cc_final: 0.7630 (mm) REVERT: E 202 ILE cc_start: 0.7468 (tp) cc_final: 0.7235 (tp) REVERT: E 219 GLU cc_start: 0.8459 (mp0) cc_final: 0.8233 (pm20) REVERT: E 225 TYR cc_start: 0.5534 (t80) cc_final: 0.4881 (t80) REVERT: E 270 LYS cc_start: 0.6840 (mtpt) cc_final: 0.6381 (mtpt) REVERT: E 271 PHE cc_start: 0.7824 (m-80) cc_final: 0.6981 (m-80) REVERT: F 77 VAL cc_start: 0.8659 (t) cc_final: 0.8347 (m) REVERT: F 97 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7542 (pm20) REVERT: F 113 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7318 (mmtm) REVERT: F 157 HIS cc_start: 0.8812 (m90) cc_final: 0.8503 (m90) REVERT: F 160 LEU cc_start: 0.8944 (tp) cc_final: 0.8631 (tp) REVERT: F 230 LYS cc_start: 0.8159 (tppp) cc_final: 0.7717 (tppp) REVERT: F 254 LYS cc_start: 0.7937 (tmtt) cc_final: 0.7691 (tmtt) REVERT: F 261 TYR cc_start: 0.7021 (m-10) cc_final: 0.6816 (m-10) REVERT: G 110 PHE cc_start: 0.7468 (m-80) cc_final: 0.6994 (m-10) REVERT: G 155 ARG cc_start: 0.8441 (pmt170) cc_final: 0.7774 (tpt170) REVERT: H 63 TRP cc_start: 0.6758 (m100) cc_final: 0.6483 (m100) REVERT: H 85 LEU cc_start: 0.7804 (tp) cc_final: 0.7354 (tp) REVERT: H 132 MET cc_start: 0.7921 (tpt) cc_final: 0.7204 (tpt) REVERT: H 164 LEU cc_start: 0.8246 (mt) cc_final: 0.7982 (tp) REVERT: H 186 ASN cc_start: 0.8167 (m-40) cc_final: 0.7726 (p0) REVERT: H 198 MET cc_start: 0.8105 (mpp) cc_final: 0.7782 (mpp) REVERT: H 201 PHE cc_start: 0.8401 (t80) cc_final: 0.7980 (t80) REVERT: H 205 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8144 (mmmm) REVERT: H 206 GLU cc_start: 0.7326 (pp20) cc_final: 0.6784 (pp20) REVERT: H 262 LEU cc_start: 0.7226 (mm) cc_final: 0.6898 (mm) REVERT: R 367 ASN cc_start: 0.6512 (t0) cc_final: 0.6059 (t0) REVERT: R 413 MET cc_start: 0.6660 (mmm) cc_final: 0.6279 (mmm) REVERT: R 418 MET cc_start: 0.7475 (ppp) cc_final: 0.6974 (ppp) REVERT: Q 360 LYS cc_start: 0.5004 (ptpp) cc_final: 0.4796 (ptpp) REVERT: Q 418 MET cc_start: 0.7427 (ppp) cc_final: 0.6986 (ppp) REVERT: I 72 ASP cc_start: 0.7361 (t70) cc_final: 0.7032 (t70) REVERT: I 98 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6675 (mm-30) REVERT: I 165 GLU cc_start: 0.7185 (tp30) cc_final: 0.6981 (tp30) REVERT: J 92 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7730 (mtpp) REVERT: J 116 GLN cc_start: 0.6720 (tt0) cc_final: 0.6506 (tt0) REVERT: J 129 GLN cc_start: 0.7470 (tt0) cc_final: 0.6983 (mt0) REVERT: J 206 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7226 (tp30) REVERT: J 211 GLN cc_start: 0.6702 (tm-30) cc_final: 0.6466 (tm-30) REVERT: K 109 MET cc_start: 0.7903 (tpp) cc_final: 0.7352 (pmm) REVERT: L 104 MET cc_start: 0.5442 (mmp) cc_final: 0.5082 (mmp) REVERT: L 110 PHE cc_start: 0.7722 (m-80) cc_final: 0.7060 (t80) REVERT: L 133 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7979 (mmmt) REVERT: L 221 ILE cc_start: 0.6794 (mt) cc_final: 0.6456 (tt) REVERT: L 248 ASP cc_start: 0.6912 (p0) cc_final: 0.6689 (p0) REVERT: L 260 ARG cc_start: 0.6919 (mmm-85) cc_final: 0.6267 (mmm-85) REVERT: L 268 ASP cc_start: 0.7372 (p0) cc_final: 0.6930 (p0) REVERT: M 35 ASP cc_start: 0.6496 (m-30) cc_final: 0.6109 (m-30) REVERT: M 38 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7642 (tm-30) REVERT: M 44 GLN cc_start: 0.5777 (tp40) cc_final: 0.5493 (tp40) REVERT: M 61 ASP cc_start: 0.7239 (t70) cc_final: 0.6395 (t0) REVERT: M 80 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7096 (tm-30) REVERT: M 99 PHE cc_start: 0.8292 (m-80) cc_final: 0.7391 (m-80) REVERT: M 155 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7664 (mtt180) REVERT: M 224 CYS cc_start: 0.6443 (t) cc_final: 0.6130 (t) REVERT: N 61 ASP cc_start: 0.5797 (t70) cc_final: 0.5513 (t70) REVERT: N 113 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7448 (mmtm) REVERT: N 186 ASN cc_start: 0.5809 (m110) cc_final: 0.5453 (m-40) REVERT: N 200 ILE cc_start: 0.7079 (mm) cc_final: 0.6828 (pt) REVERT: N 252 VAL cc_start: 0.8143 (p) cc_final: 0.7887 (m) REVERT: N 260 ARG cc_start: 0.6852 (mtm-85) cc_final: 0.6284 (mtm-85) REVERT: O 11 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8139 (mm-30) REVERT: O 104 MET cc_start: 0.7256 (mmp) cc_final: 0.6401 (mmp) REVERT: O 110 PHE cc_start: 0.6964 (m-80) cc_final: 0.6643 (m-80) REVERT: O 132 MET cc_start: 0.8070 (mpp) cc_final: 0.7797 (mpp) REVERT: O 155 ARG cc_start: 0.8673 (pmt170) cc_final: 0.7950 (tpt170) REVERT: O 198 MET cc_start: 0.8244 (tpt) cc_final: 0.8015 (tpt) REVERT: O 200 ILE cc_start: 0.8588 (mm) cc_final: 0.8339 (mm) REVERT: O 201 PHE cc_start: 0.8616 (t80) cc_final: 0.8369 (t80) REVERT: O 208 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7593 (tm-30) REVERT: P 63 TRP cc_start: 0.6715 (m100) cc_final: 0.5560 (m100) REVERT: P 110 PHE cc_start: 0.7132 (m-80) cc_final: 0.6854 (m-80) REVERT: P 132 MET cc_start: 0.8079 (tpt) cc_final: 0.7263 (tpt) REVERT: P 201 PHE cc_start: 0.8402 (t80) cc_final: 0.7577 (t80) REVERT: P 202 ILE cc_start: 0.8697 (pt) cc_final: 0.8444 (pt) REVERT: P 205 LYS cc_start: 0.8301 (mmmm) cc_final: 0.7481 (mmmm) REVERT: P 206 GLU cc_start: 0.7152 (pp20) cc_final: 0.6094 (pp20) REVERT: P 261 TYR cc_start: 0.7147 (m-80) cc_final: 0.6868 (m-80) outliers start: 42 outliers final: 25 residues processed: 876 average time/residue: 0.4813 time to fit residues: 664.1811 Evaluate side-chains 848 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 822 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 0.9990 chunk 115 optimal weight: 0.0970 chunk 309 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 372 optimal weight: 0.9990 chunk 402 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 369 optimal weight: 3.9990 chunk 127 optimal weight: 50.0000 chunk 299 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN C 204 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 139 HIS E 208 GLN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS H 129 GLN I 17 GLN I 150 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 157 HIS ** M 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36705 Z= 0.280 Angle : 0.638 11.670 50248 Z= 0.343 Chirality : 0.045 0.245 5432 Planarity : 0.004 0.074 5969 Dihedral : 16.512 142.808 5791 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.23 % Allowed : 12.33 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 3971 helix: 1.20 (0.12), residues: 1874 sheet: 0.07 (0.19), residues: 746 loop : -1.23 (0.15), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP P 245 HIS 0.014 0.002 HIS M 12 PHE 0.031 0.002 PHE N 99 TYR 0.025 0.002 TYR A 134 ARG 0.014 0.001 ARG E 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 853 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6110 (tp30) REVERT: A 57 LYS cc_start: 0.7304 (tttm) cc_final: 0.7038 (ttmm) REVERT: A 72 ASP cc_start: 0.7347 (t70) cc_final: 0.7091 (t0) REVERT: A 76 LEU cc_start: 0.7648 (tp) cc_final: 0.7416 (tp) REVERT: A 98 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 109 MET cc_start: 0.7297 (tpp) cc_final: 0.7050 (tpt) REVERT: A 162 ASN cc_start: 0.8140 (t0) cc_final: 0.7613 (t0) REVERT: A 199 ASP cc_start: 0.6623 (t0) cc_final: 0.6237 (t70) REVERT: A 206 GLU cc_start: 0.7042 (tp30) cc_final: 0.6644 (tm-30) REVERT: A 223 PHE cc_start: 0.8221 (m-80) cc_final: 0.7406 (m-80) REVERT: A 262 LEU cc_start: 0.7014 (mm) cc_final: 0.6724 (mt) REVERT: B 124 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7570 (m) REVERT: B 140 THR cc_start: 0.8173 (m) cc_final: 0.7886 (t) REVERT: B 185 LEU cc_start: 0.7601 (mt) cc_final: 0.6967 (mp) REVERT: B 206 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6986 (tp30) REVERT: B 208 GLN cc_start: 0.7527 (tt0) cc_final: 0.7201 (tt0) REVERT: C 9 GLU cc_start: 0.7687 (tp30) cc_final: 0.7354 (tp30) REVERT: C 24 LEU cc_start: 0.7880 (mm) cc_final: 0.7568 (mp) REVERT: C 25 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7153 (tm-30) REVERT: C 30 ARG cc_start: 0.7432 (tpp80) cc_final: 0.7218 (tpp80) REVERT: C 104 MET cc_start: 0.6145 (ppp) cc_final: 0.5479 (ppp) REVERT: C 105 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7572 (ttpp) REVERT: C 186 ASN cc_start: 0.7969 (m-40) cc_final: 0.7700 (t0) REVERT: C 203 PHE cc_start: 0.7096 (t80) cc_final: 0.6648 (t80) REVERT: C 205 LYS cc_start: 0.8478 (mmmt) cc_final: 0.7983 (mmmt) REVERT: C 222 ARG cc_start: 0.4804 (ptm160) cc_final: 0.4054 (ptm160) REVERT: C 245 TRP cc_start: 0.7828 (m-90) cc_final: 0.7361 (m-90) REVERT: D 70 TYR cc_start: 0.6997 (t80) cc_final: 0.6621 (t80) REVERT: D 103 THR cc_start: 0.6990 (t) cc_final: 0.6232 (p) REVERT: D 104 MET cc_start: 0.6933 (mmp) cc_final: 0.6032 (mmp) REVERT: D 205 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7602 (tppt) REVERT: D 212 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6844 (tm-30) REVERT: D 236 GLU cc_start: 0.7298 (mp0) cc_final: 0.6795 (mp0) REVERT: D 238 GLN cc_start: 0.8763 (mt0) cc_final: 0.8321 (mt0) REVERT: D 254 LYS cc_start: 0.7346 (tppp) cc_final: 0.7069 (tppt) REVERT: E 61 ASP cc_start: 0.7722 (t70) cc_final: 0.7074 (t70) REVERT: E 89 GLU cc_start: 0.5754 (tm-30) cc_final: 0.5417 (tm-30) REVERT: E 103 THR cc_start: 0.8624 (t) cc_final: 0.8381 (p) REVERT: E 109 MET cc_start: 0.6436 (tpt) cc_final: 0.6204 (tpt) REVERT: E 157 HIS cc_start: 0.8505 (m90) cc_final: 0.7654 (m-70) REVERT: E 161 LYS cc_start: 0.8423 (mttt) cc_final: 0.7845 (mttt) REVERT: E 163 THR cc_start: 0.8058 (p) cc_final: 0.7758 (p) REVERT: E 181 THR cc_start: 0.8370 (p) cc_final: 0.8006 (p) REVERT: E 208 GLN cc_start: 0.7757 (tp40) cc_final: 0.7141 (tm-30) REVERT: E 212 GLN cc_start: 0.7624 (mp10) cc_final: 0.7001 (mp10) REVERT: E 270 LYS cc_start: 0.7085 (mtpt) cc_final: 0.6573 (mtpt) REVERT: E 271 PHE cc_start: 0.7963 (m-80) cc_final: 0.7127 (m-80) REVERT: F 70 TYR cc_start: 0.7435 (t80) cc_final: 0.7061 (t80) REVERT: F 77 VAL cc_start: 0.8600 (t) cc_final: 0.8325 (m) REVERT: F 97 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7763 (pm20) REVERT: F 113 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7437 (mmtm) REVERT: F 157 HIS cc_start: 0.8852 (m90) cc_final: 0.8534 (m-70) REVERT: F 230 LYS cc_start: 0.8242 (tppp) cc_final: 0.7802 (tppp) REVERT: F 254 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7682 (tptt) REVERT: G 110 PHE cc_start: 0.7272 (m-80) cc_final: 0.6860 (m-10) REVERT: H 63 TRP cc_start: 0.6859 (m100) cc_final: 0.6517 (m100) REVERT: H 87 TYR cc_start: 0.7127 (t80) cc_final: 0.6671 (t80) REVERT: H 132 MET cc_start: 0.7941 (tpt) cc_final: 0.7241 (tpt) REVERT: H 164 LEU cc_start: 0.8203 (mt) cc_final: 0.7918 (tp) REVERT: H 201 PHE cc_start: 0.8424 (t80) cc_final: 0.8016 (t80) REVERT: H 205 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8235 (mmmm) REVERT: H 206 GLU cc_start: 0.7372 (pp20) cc_final: 0.6827 (pp20) REVERT: R 418 MET cc_start: 0.7445 (ppp) cc_final: 0.6985 (ppp) REVERT: Q 360 LYS cc_start: 0.5161 (ptpp) cc_final: 0.4916 (ptpp) REVERT: Q 387 MET cc_start: 0.7068 (tpp) cc_final: 0.6823 (mmm) REVERT: Q 413 MET cc_start: 0.6487 (mmt) cc_final: 0.6248 (mmt) REVERT: Q 418 MET cc_start: 0.7447 (ppp) cc_final: 0.7006 (ppp) REVERT: I 35 ASP cc_start: 0.7234 (t70) cc_final: 0.6722 (t70) REVERT: I 72 ASP cc_start: 0.7473 (t70) cc_final: 0.7138 (t0) REVERT: I 98 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6988 (mm-30) REVERT: I 109 MET cc_start: 0.6832 (ttt) cc_final: 0.6274 (ttt) REVERT: I 126 GLU cc_start: 0.7279 (tp30) cc_final: 0.7019 (tp30) REVERT: I 165 GLU cc_start: 0.7356 (tp30) cc_final: 0.7046 (tp30) REVERT: I 183 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7030 (mt) REVERT: I 238 GLN cc_start: 0.7571 (tm-30) cc_final: 0.6876 (tm-30) REVERT: I 262 LEU cc_start: 0.6377 (mm) cc_final: 0.6101 (mt) REVERT: J 10 GLU cc_start: 0.6992 (tp30) cc_final: 0.6789 (tp30) REVERT: J 92 LYS cc_start: 0.8284 (mtpp) cc_final: 0.8024 (mtpp) REVERT: J 94 GLU cc_start: 0.6577 (pp20) cc_final: 0.6281 (pp20) REVERT: J 105 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7696 (ttpt) REVERT: J 129 GLN cc_start: 0.7753 (tt0) cc_final: 0.7275 (mt0) REVERT: J 132 MET cc_start: 0.7689 (tpp) cc_final: 0.7337 (mmt) REVERT: J 206 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7230 (tp30) REVERT: J 211 GLN cc_start: 0.7010 (tm-30) cc_final: 0.6741 (tm-30) REVERT: K 109 MET cc_start: 0.8016 (tpp) cc_final: 0.7537 (pmm) REVERT: L 104 MET cc_start: 0.5549 (mmp) cc_final: 0.5132 (mmp) REVERT: L 110 PHE cc_start: 0.7829 (m-80) cc_final: 0.7187 (t80) REVERT: L 133 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8155 (mmmt) REVERT: L 220 LYS cc_start: 0.5294 (mmtm) cc_final: 0.4871 (mmtm) REVERT: L 248 ASP cc_start: 0.7227 (p0) cc_final: 0.6826 (p0) REVERT: L 260 ARG cc_start: 0.6842 (mmm-85) cc_final: 0.6490 (mmm-85) REVERT: L 268 ASP cc_start: 0.7680 (p0) cc_final: 0.6857 (p0) REVERT: M 7 LEU cc_start: 0.7568 (tt) cc_final: 0.7341 (tt) REVERT: M 35 ASP cc_start: 0.6758 (m-30) cc_final: 0.6427 (m-30) REVERT: M 61 ASP cc_start: 0.7375 (t70) cc_final: 0.6481 (t0) REVERT: M 62 HIS cc_start: 0.6819 (t70) cc_final: 0.6488 (t70) REVERT: M 63 TRP cc_start: 0.7161 (m100) cc_final: 0.6676 (m-10) REVERT: M 99 PHE cc_start: 0.8377 (m-80) cc_final: 0.7455 (m-80) REVERT: M 129 GLN cc_start: 0.8564 (mm110) cc_final: 0.8313 (mm-40) REVERT: M 195 THR cc_start: 0.8283 (m) cc_final: 0.7532 (t) REVERT: M 219 GLU cc_start: 0.7592 (mp0) cc_final: 0.7289 (mp0) REVERT: M 271 PHE cc_start: 0.7321 (m-80) cc_final: 0.6452 (m-80) REVERT: N 61 ASP cc_start: 0.5902 (t70) cc_final: 0.5601 (t70) REVERT: N 64 GLN cc_start: 0.6681 (tp40) cc_final: 0.5853 (tp40) REVERT: N 105 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7981 (mtmm) REVERT: N 113 LYS cc_start: 0.7686 (mmmt) cc_final: 0.7337 (mmtm) REVERT: N 165 GLU cc_start: 0.8229 (mp0) cc_final: 0.8007 (mp0) REVERT: N 166 LYS cc_start: 0.8759 (mppt) cc_final: 0.8457 (mppt) REVERT: N 186 ASN cc_start: 0.5972 (m110) cc_final: 0.5692 (m-40) REVERT: N 213 GLN cc_start: 0.7171 (pp30) cc_final: 0.6779 (pp30) REVERT: N 241 THR cc_start: 0.8268 (t) cc_final: 0.7826 (p) REVERT: N 252 VAL cc_start: 0.8292 (p) cc_final: 0.8014 (m) REVERT: N 254 LYS cc_start: 0.7608 (tptt) cc_final: 0.7367 (tptt) REVERT: N 260 ARG cc_start: 0.6861 (mtm-85) cc_final: 0.6316 (mtm-85) REVERT: O 11 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8174 (mm-30) REVERT: O 110 PHE cc_start: 0.6872 (m-80) cc_final: 0.6593 (m-80) REVERT: O 132 MET cc_start: 0.8214 (mpp) cc_final: 0.7888 (mpp) REVERT: O 198 MET cc_start: 0.8421 (tpt) cc_final: 0.8130 (tpt) REVERT: O 201 PHE cc_start: 0.8830 (t80) cc_final: 0.8504 (t80) REVERT: O 208 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7688 (tm-30) REVERT: P 63 TRP cc_start: 0.6758 (m100) cc_final: 0.5225 (m100) REVERT: P 87 TYR cc_start: 0.6317 (t80) cc_final: 0.6031 (t80) REVERT: P 110 PHE cc_start: 0.7090 (m-80) cc_final: 0.6749 (m-80) REVERT: P 132 MET cc_start: 0.8224 (tpt) cc_final: 0.7385 (tpt) REVERT: P 201 PHE cc_start: 0.8420 (t80) cc_final: 0.7887 (t80) REVERT: P 203 PHE cc_start: 0.8341 (t80) cc_final: 0.7751 (t80) REVERT: P 206 GLU cc_start: 0.7282 (pp20) cc_final: 0.6536 (tm-30) REVERT: P 207 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7845 (mm-40) REVERT: P 276 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7698 (mmtt) outliers start: 79 outliers final: 56 residues processed: 869 average time/residue: 0.5148 time to fit residues: 714.1259 Evaluate side-chains 885 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 826 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 157 HIS Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 230 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 0.9980 chunk 280 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 374 optimal weight: 8.9990 chunk 396 optimal weight: 3.9990 chunk 195 optimal weight: 0.0970 chunk 354 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 GLN A 39 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 213 GLN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 ASN F 162 ASN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS G 204 ASN H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 157 HIS ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36705 Z= 0.276 Angle : 0.619 10.898 50248 Z= 0.333 Chirality : 0.045 0.220 5432 Planarity : 0.004 0.059 5969 Dihedral : 16.656 144.341 5791 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.43 % Allowed : 15.13 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 3971 helix: 1.10 (0.12), residues: 1882 sheet: -0.03 (0.19), residues: 756 loop : -1.23 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP P 245 HIS 0.012 0.001 HIS E 139 PHE 0.032 0.002 PHE N 99 TYR 0.025 0.002 TYR I 134 ARG 0.010 0.001 ARG N 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 848 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7478 (mm110) cc_final: 0.7044 (mt0) REVERT: A 57 LYS cc_start: 0.7310 (tttm) cc_final: 0.7082 (ttmm) REVERT: A 72 ASP cc_start: 0.7389 (t70) cc_final: 0.7001 (t0) REVERT: A 76 LEU cc_start: 0.7642 (tp) cc_final: 0.7431 (tp) REVERT: A 165 GLU cc_start: 0.7546 (tp30) cc_final: 0.7157 (tp30) REVERT: A 199 ASP cc_start: 0.6586 (t0) cc_final: 0.6142 (t0) REVERT: A 223 PHE cc_start: 0.7921 (m-80) cc_final: 0.7015 (m-80) REVERT: A 238 GLN cc_start: 0.7791 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 262 LEU cc_start: 0.7170 (mm) cc_final: 0.6801 (mt) REVERT: B 124 VAL cc_start: 0.8049 (p) cc_final: 0.7710 (m) REVERT: B 140 THR cc_start: 0.8145 (m) cc_final: 0.7873 (t) REVERT: B 206 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6931 (tp30) REVERT: B 208 GLN cc_start: 0.7594 (tt0) cc_final: 0.7245 (tt0) REVERT: C 2 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8300 (mm) REVERT: C 9 GLU cc_start: 0.7696 (tp30) cc_final: 0.7365 (tp30) REVERT: C 24 LEU cc_start: 0.7905 (mm) cc_final: 0.7576 (mp) REVERT: C 25 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7132 (tm-30) REVERT: C 30 ARG cc_start: 0.7294 (tpp80) cc_final: 0.7093 (tpp80) REVERT: C 105 LYS cc_start: 0.7834 (ttpp) cc_final: 0.7628 (ttpp) REVERT: C 203 PHE cc_start: 0.7114 (t80) cc_final: 0.6670 (t80) REVERT: C 205 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8009 (mmmt) REVERT: C 222 ARG cc_start: 0.5028 (ptm160) cc_final: 0.4294 (ptm160) REVERT: C 245 TRP cc_start: 0.7835 (m-90) cc_final: 0.7395 (m-90) REVERT: C 267 LYS cc_start: 0.8297 (pttp) cc_final: 0.8008 (pttp) REVERT: D 70 TYR cc_start: 0.7097 (t80) cc_final: 0.6687 (t80) REVERT: D 103 THR cc_start: 0.7001 (t) cc_final: 0.6311 (p) REVERT: D 104 MET cc_start: 0.6953 (mmp) cc_final: 0.6084 (mmp) REVERT: D 205 LYS cc_start: 0.8052 (mmmt) cc_final: 0.6909 (mmmt) REVERT: D 208 GLN cc_start: 0.7609 (mt0) cc_final: 0.7377 (pp30) REVERT: D 220 LYS cc_start: 0.5274 (mmtm) cc_final: 0.4808 (mmtm) REVERT: D 236 GLU cc_start: 0.7355 (mp0) cc_final: 0.6811 (mp0) REVERT: D 238 GLN cc_start: 0.8756 (mt0) cc_final: 0.8283 (mt0) REVERT: D 254 LYS cc_start: 0.7452 (tppp) cc_final: 0.7149 (tppp) REVERT: E 38 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7836 (mm-40) REVERT: E 61 ASP cc_start: 0.7721 (t70) cc_final: 0.7137 (t70) REVERT: E 69 HIS cc_start: 0.7847 (t70) cc_final: 0.7624 (t70) REVERT: E 97 GLN cc_start: 0.8613 (pm20) cc_final: 0.8263 (pm20) REVERT: E 103 THR cc_start: 0.8599 (t) cc_final: 0.8354 (p) REVERT: E 157 HIS cc_start: 0.8618 (m90) cc_final: 0.7629 (m-70) REVERT: E 158 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8217 (mm-40) REVERT: E 161 LYS cc_start: 0.8348 (mttt) cc_final: 0.7824 (mttt) REVERT: E 195 THR cc_start: 0.8374 (m) cc_final: 0.7656 (t) REVERT: E 206 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6773 (tm-30) REVERT: E 208 GLN cc_start: 0.7801 (tp40) cc_final: 0.7287 (tm-30) REVERT: E 210 ILE cc_start: 0.8452 (mm) cc_final: 0.8212 (mt) REVERT: E 212 GLN cc_start: 0.7589 (mp10) cc_final: 0.7285 (mp10) REVERT: E 237 TRP cc_start: 0.6176 (m100) cc_final: 0.5637 (m100) REVERT: E 270 LYS cc_start: 0.7119 (mtpt) cc_final: 0.6481 (mtpt) REVERT: E 271 PHE cc_start: 0.7961 (m-80) cc_final: 0.7147 (m-80) REVERT: F 77 VAL cc_start: 0.8594 (t) cc_final: 0.8339 (m) REVERT: F 97 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7874 (pm20) REVERT: F 113 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7406 (mmtm) REVERT: F 129 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7220 (mt0) REVERT: F 157 HIS cc_start: 0.8831 (m90) cc_final: 0.8580 (m-70) REVERT: F 162 ASN cc_start: 0.8684 (m-40) cc_final: 0.8307 (p0) REVERT: F 188 LYS cc_start: 0.7420 (mtmm) cc_final: 0.7215 (pttt) REVERT: G 110 PHE cc_start: 0.7311 (m-80) cc_final: 0.6988 (m-10) REVERT: G 148 GLN cc_start: 0.7599 (tp40) cc_final: 0.7242 (mp10) REVERT: H 63 TRP cc_start: 0.6860 (m100) cc_final: 0.6454 (m100) REVERT: H 87 TYR cc_start: 0.7002 (t80) cc_final: 0.6498 (t80) REVERT: H 132 MET cc_start: 0.7901 (tpt) cc_final: 0.7203 (tpt) REVERT: H 161 LYS cc_start: 0.8536 (mttt) cc_final: 0.8179 (mttt) REVERT: H 164 LEU cc_start: 0.8156 (mt) cc_final: 0.7788 (tp) REVERT: H 201 PHE cc_start: 0.8449 (t80) cc_final: 0.8042 (t80) REVERT: H 205 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8326 (mmmm) REVERT: H 238 GLN cc_start: 0.5911 (mm-40) cc_final: 0.5617 (mm-40) REVERT: R 418 MET cc_start: 0.7413 (ppp) cc_final: 0.6986 (ppp) REVERT: Q 360 LYS cc_start: 0.5707 (ptpp) cc_final: 0.5348 (ptpp) REVERT: Q 387 MET cc_start: 0.7261 (tpp) cc_final: 0.6985 (mmm) REVERT: Q 413 MET cc_start: 0.6493 (mmt) cc_final: 0.6249 (mmt) REVERT: Q 418 MET cc_start: 0.7474 (ppp) cc_final: 0.7025 (ppp) REVERT: I 35 ASP cc_start: 0.7034 (t70) cc_final: 0.6763 (t70) REVERT: I 72 ASP cc_start: 0.7424 (t70) cc_final: 0.7078 (t0) REVERT: I 98 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6819 (mm-30) REVERT: I 109 MET cc_start: 0.6926 (ttt) cc_final: 0.6343 (ttt) REVERT: I 238 GLN cc_start: 0.7694 (tm-30) cc_final: 0.6903 (tm-30) REVERT: I 254 LYS cc_start: 0.8195 (tptp) cc_final: 0.7814 (tppt) REVERT: I 262 LEU cc_start: 0.6652 (mm) cc_final: 0.6335 (mt) REVERT: J 92 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7836 (mtpp) REVERT: J 94 GLU cc_start: 0.6853 (pp20) cc_final: 0.6446 (pp20) REVERT: J 105 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7704 (ttpt) REVERT: J 129 GLN cc_start: 0.7740 (tt0) cc_final: 0.7208 (mt0) REVERT: J 206 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7118 (tp30) REVERT: L 80 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6172 (tm-30) REVERT: L 104 MET cc_start: 0.5396 (mmp) cc_final: 0.5046 (mmp) REVERT: L 155 ARG cc_start: 0.8318 (ptp90) cc_final: 0.8091 (mtm110) REVERT: L 220 LYS cc_start: 0.5407 (mmtm) cc_final: 0.5035 (mmtm) REVERT: L 238 GLN cc_start: 0.8514 (mt0) cc_final: 0.8191 (mt0) REVERT: L 248 ASP cc_start: 0.7265 (p0) cc_final: 0.6786 (p0) REVERT: L 259 ASP cc_start: 0.7759 (p0) cc_final: 0.7341 (p0) REVERT: L 260 ARG cc_start: 0.7067 (mmm-85) cc_final: 0.6689 (mmm-85) REVERT: L 268 ASP cc_start: 0.7603 (p0) cc_final: 0.7044 (p0) REVERT: M 1 TRP cc_start: 0.6161 (t-100) cc_final: 0.5835 (t-100) REVERT: M 7 LEU cc_start: 0.7609 (tt) cc_final: 0.7375 (tt) REVERT: M 30 ARG cc_start: 0.7821 (tpt-90) cc_final: 0.7128 (tpt-90) REVERT: M 35 ASP cc_start: 0.6971 (m-30) cc_final: 0.6260 (m-30) REVERT: M 61 ASP cc_start: 0.7363 (t70) cc_final: 0.6478 (t0) REVERT: M 62 HIS cc_start: 0.6801 (t70) cc_final: 0.6422 (t70) REVERT: M 99 PHE cc_start: 0.8346 (m-80) cc_final: 0.7394 (m-80) REVERT: M 155 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7608 (mtt180) REVERT: M 161 LYS cc_start: 0.8993 (mttt) cc_final: 0.8579 (mttt) REVERT: M 162 ASN cc_start: 0.8826 (p0) cc_final: 0.8609 (p0) REVERT: M 195 THR cc_start: 0.8125 (m) cc_final: 0.7507 (t) REVERT: M 215 LYS cc_start: 0.8526 (pttt) cc_final: 0.8273 (pttt) REVERT: M 271 PHE cc_start: 0.7435 (m-80) cc_final: 0.6512 (m-80) REVERT: N 61 ASP cc_start: 0.6152 (t70) cc_final: 0.5855 (t70) REVERT: N 104 MET cc_start: 0.8331 (tpt) cc_final: 0.8002 (tpt) REVERT: N 105 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7960 (mtmm) REVERT: N 107 TYR cc_start: 0.8075 (t80) cc_final: 0.7784 (t80) REVERT: N 110 PHE cc_start: 0.7151 (m-10) cc_final: 0.6772 (m-10) REVERT: N 158 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7595 (tm-30) REVERT: N 206 GLU cc_start: 0.7897 (tp30) cc_final: 0.7675 (tp30) REVERT: N 213 GLN cc_start: 0.7384 (pp30) cc_final: 0.6967 (pp30) REVERT: N 254 LYS cc_start: 0.7746 (tptt) cc_final: 0.7532 (tptt) REVERT: N 260 ARG cc_start: 0.6864 (mtm-85) cc_final: 0.6316 (mtm-85) REVERT: O 11 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8186 (mm-30) REVERT: O 110 PHE cc_start: 0.6934 (m-80) cc_final: 0.6587 (m-80) REVERT: O 132 MET cc_start: 0.8206 (mpp) cc_final: 0.7828 (mpp) REVERT: O 198 MET cc_start: 0.8474 (tpt) cc_final: 0.8165 (tpt) REVERT: O 201 PHE cc_start: 0.8896 (t80) cc_final: 0.8447 (t80) REVERT: O 208 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7654 (tm-30) REVERT: P 63 TRP cc_start: 0.6888 (m100) cc_final: 0.5301 (m100) REVERT: P 87 TYR cc_start: 0.6253 (t80) cc_final: 0.5902 (t80) REVERT: P 132 MET cc_start: 0.8301 (tpt) cc_final: 0.7451 (tpt) REVERT: P 186 ASN cc_start: 0.8700 (m-40) cc_final: 0.8450 (t0) REVERT: P 188 LYS cc_start: 0.7172 (mmtm) cc_final: 0.6674 (mmtm) REVERT: P 201 PHE cc_start: 0.8475 (t80) cc_final: 0.7986 (t80) REVERT: P 203 PHE cc_start: 0.8319 (t80) cc_final: 0.7766 (t80) REVERT: P 206 GLU cc_start: 0.7314 (pp20) cc_final: 0.6734 (tm-30) REVERT: P 207 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7961 (mm-40) outliers start: 86 outliers final: 70 residues processed: 875 average time/residue: 0.4725 time to fit residues: 652.8604 Evaluate side-chains 905 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 834 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 157 HIS Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 295 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 338 optimal weight: 7.9990 chunk 273 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 355 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN C 46 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 162 ASN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN H 207 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36705 Z= 0.233 Angle : 0.614 11.831 50248 Z= 0.324 Chirality : 0.044 0.193 5432 Planarity : 0.004 0.056 5969 Dihedral : 16.739 145.354 5791 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.88 % Allowed : 16.51 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 3971 helix: 1.10 (0.12), residues: 1876 sheet: 0.03 (0.19), residues: 736 loop : -1.14 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 1 HIS 0.015 0.001 HIS E 139 PHE 0.034 0.001 PHE N 99 TYR 0.021 0.001 TYR I 134 ARG 0.005 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 855 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7427 (t70) cc_final: 0.6996 (t0) REVERT: A 76 LEU cc_start: 0.7623 (tp) cc_final: 0.7396 (tp) REVERT: A 165 GLU cc_start: 0.7638 (tp30) cc_final: 0.7245 (tp30) REVERT: A 199 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6086 (t0) REVERT: A 223 PHE cc_start: 0.8217 (m-80) cc_final: 0.7224 (m-80) REVERT: A 238 GLN cc_start: 0.7740 (tm-30) cc_final: 0.6885 (tm-30) REVERT: A 254 LYS cc_start: 0.7938 (tppt) cc_final: 0.7523 (ttmt) REVERT: A 259 ASP cc_start: 0.6428 (t0) cc_final: 0.6170 (t0) REVERT: A 262 LEU cc_start: 0.7165 (mm) cc_final: 0.6763 (mt) REVERT: B 118 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7201 (p0) REVERT: B 124 VAL cc_start: 0.8102 (p) cc_final: 0.7785 (m) REVERT: B 140 THR cc_start: 0.8124 (m) cc_final: 0.7853 (t) REVERT: B 161 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7822 (mttp) REVERT: B 206 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7146 (tp30) REVERT: B 208 GLN cc_start: 0.7697 (tt0) cc_final: 0.7291 (tt0) REVERT: C 9 GLU cc_start: 0.7605 (tp30) cc_final: 0.7297 (tp30) REVERT: C 24 LEU cc_start: 0.7912 (mm) cc_final: 0.7585 (mp) REVERT: C 25 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7185 (tm-30) REVERT: C 104 MET cc_start: 0.6344 (ppp) cc_final: 0.5552 (ppp) REVERT: C 105 LYS cc_start: 0.7829 (ttpp) cc_final: 0.7529 (ttpp) REVERT: C 198 MET cc_start: 0.7917 (tpt) cc_final: 0.7657 (tpt) REVERT: C 203 PHE cc_start: 0.7112 (t80) cc_final: 0.6665 (t80) REVERT: C 207 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: C 222 ARG cc_start: 0.4943 (ptm160) cc_final: 0.4208 (ptm160) REVERT: C 245 TRP cc_start: 0.7838 (m-90) cc_final: 0.7378 (m-90) REVERT: C 267 LYS cc_start: 0.8092 (pttp) cc_final: 0.7878 (pttp) REVERT: D 70 TYR cc_start: 0.7116 (t80) cc_final: 0.6689 (t80) REVERT: D 103 THR cc_start: 0.6851 (t) cc_final: 0.6124 (p) REVERT: D 104 MET cc_start: 0.6918 (mmp) cc_final: 0.6060 (mmp) REVERT: D 208 GLN cc_start: 0.7746 (mt0) cc_final: 0.7407 (mt0) REVERT: D 220 LYS cc_start: 0.5308 (mmtm) cc_final: 0.4891 (mmtm) REVERT: D 236 GLU cc_start: 0.7381 (mp0) cc_final: 0.6799 (mp0) REVERT: D 238 GLN cc_start: 0.8731 (mt0) cc_final: 0.8260 (mt0) REVERT: D 254 LYS cc_start: 0.7453 (tppp) cc_final: 0.7193 (tppp) REVERT: D 260 ARG cc_start: 0.6793 (mmm-85) cc_final: 0.6477 (mmm-85) REVERT: E 35 ASP cc_start: 0.6763 (m-30) cc_final: 0.6376 (m-30) REVERT: E 38 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7901 (mm-40) REVERT: E 61 ASP cc_start: 0.7753 (t70) cc_final: 0.7070 (t70) REVERT: E 69 HIS cc_start: 0.7851 (t70) cc_final: 0.7633 (t70) REVERT: E 89 GLU cc_start: 0.6357 (tm-30) cc_final: 0.5701 (tm-30) REVERT: E 103 THR cc_start: 0.8543 (t) cc_final: 0.8297 (p) REVERT: E 157 HIS cc_start: 0.8622 (m90) cc_final: 0.7684 (m-70) REVERT: E 158 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8252 (mm-40) REVERT: E 161 LYS cc_start: 0.8338 (mttt) cc_final: 0.7824 (mttt) REVERT: E 195 THR cc_start: 0.8299 (m) cc_final: 0.7539 (t) REVERT: E 206 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6784 (tm-30) REVERT: E 208 GLN cc_start: 0.7741 (tp40) cc_final: 0.7125 (tm-30) REVERT: E 210 ILE cc_start: 0.8420 (mm) cc_final: 0.8187 (mt) REVERT: E 212 GLN cc_start: 0.7546 (mp10) cc_final: 0.6625 (mp10) REVERT: E 225 TYR cc_start: 0.6747 (t80) cc_final: 0.5393 (t80) REVERT: E 237 TRP cc_start: 0.6221 (m100) cc_final: 0.5833 (m100) REVERT: E 270 LYS cc_start: 0.6937 (mtpt) cc_final: 0.6410 (mtpt) REVERT: E 271 PHE cc_start: 0.7933 (m-80) cc_final: 0.7127 (m-80) REVERT: F 64 GLN cc_start: 0.6575 (tp40) cc_final: 0.6264 (tp-100) REVERT: F 129 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7335 (mt0) REVERT: F 156 THR cc_start: 0.8997 (p) cc_final: 0.8771 (p) REVERT: F 157 HIS cc_start: 0.8710 (m90) cc_final: 0.8429 (m90) REVERT: F 162 ASN cc_start: 0.8639 (m-40) cc_final: 0.8420 (p0) REVERT: F 188 LYS cc_start: 0.7457 (mtmm) cc_final: 0.7244 (pttt) REVERT: F 241 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7854 (p) REVERT: F 254 LYS cc_start: 0.8135 (tptt) cc_final: 0.7900 (tptt) REVERT: G 110 PHE cc_start: 0.7259 (m-80) cc_final: 0.6927 (m-10) REVERT: G 148 GLN cc_start: 0.7662 (tp40) cc_final: 0.7227 (mp10) REVERT: H 63 TRP cc_start: 0.6889 (m100) cc_final: 0.6458 (m100) REVERT: H 87 TYR cc_start: 0.7019 (t80) cc_final: 0.6430 (t80) REVERT: H 132 MET cc_start: 0.7884 (tpt) cc_final: 0.7183 (tpt) REVERT: H 161 LYS cc_start: 0.8535 (mttt) cc_final: 0.8173 (mttt) REVERT: H 164 LEU cc_start: 0.8109 (mt) cc_final: 0.7788 (tp) REVERT: H 201 PHE cc_start: 0.8426 (t80) cc_final: 0.7989 (t80) REVERT: H 205 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8248 (mmmm) REVERT: H 206 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6852 (pp20) REVERT: H 238 GLN cc_start: 0.5969 (mm-40) cc_final: 0.5745 (mm-40) REVERT: H 251 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6644 (mp) REVERT: H 262 LEU cc_start: 0.7350 (mm) cc_final: 0.6982 (mm) REVERT: R 418 MET cc_start: 0.7398 (ppp) cc_final: 0.6962 (ppp) REVERT: Q 360 LYS cc_start: 0.5744 (ptpp) cc_final: 0.5353 (ptpp) REVERT: Q 387 MET cc_start: 0.7275 (tpp) cc_final: 0.7029 (mmm) REVERT: Q 418 MET cc_start: 0.7480 (ppp) cc_final: 0.7029 (ppp) REVERT: I 35 ASP cc_start: 0.7238 (t70) cc_final: 0.7004 (t70) REVERT: I 72 ASP cc_start: 0.7401 (t70) cc_final: 0.7057 (t70) REVERT: I 109 MET cc_start: 0.6976 (ttt) cc_final: 0.6291 (ttt) REVERT: I 183 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7064 (mt) REVERT: I 238 GLN cc_start: 0.7657 (tm-30) cc_final: 0.6868 (tm-30) REVERT: I 254 LYS cc_start: 0.8121 (tptp) cc_final: 0.7625 (tppt) REVERT: I 262 LEU cc_start: 0.6697 (mm) cc_final: 0.6410 (mm) REVERT: J 92 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7763 (mtpp) REVERT: J 94 GLU cc_start: 0.6996 (pp20) cc_final: 0.6528 (pp20) REVERT: J 98 GLU cc_start: 0.7053 (tp30) cc_final: 0.6765 (tp30) REVERT: J 129 GLN cc_start: 0.7698 (tt0) cc_final: 0.7227 (mt0) REVERT: J 206 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7066 (tp30) REVERT: K 109 MET cc_start: 0.8090 (tpp) cc_final: 0.7385 (pmm) REVERT: K 198 MET cc_start: 0.7301 (pmm) cc_final: 0.7084 (pmm) REVERT: L 80 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6370 (tm-30) REVERT: L 104 MET cc_start: 0.5381 (mmp) cc_final: 0.5024 (mmp) REVERT: L 133 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7751 (mmmt) REVERT: L 155 ARG cc_start: 0.8330 (ptp90) cc_final: 0.8093 (mtm110) REVERT: L 220 LYS cc_start: 0.5472 (mmtm) cc_final: 0.5138 (mmtm) REVERT: L 238 GLN cc_start: 0.8575 (mt0) cc_final: 0.8226 (mt0) REVERT: L 248 ASP cc_start: 0.7234 (p0) cc_final: 0.6717 (p0) REVERT: L 260 ARG cc_start: 0.7108 (mmm-85) cc_final: 0.6745 (mmm-85) REVERT: L 268 ASP cc_start: 0.7639 (p0) cc_final: 0.6522 (p0) REVERT: M 30 ARG cc_start: 0.7433 (tpt-90) cc_final: 0.7225 (tpt-90) REVERT: M 35 ASP cc_start: 0.6726 (m-30) cc_final: 0.6424 (m-30) REVERT: M 61 ASP cc_start: 0.7397 (t70) cc_final: 0.6544 (t0) REVERT: M 62 HIS cc_start: 0.6658 (t70) cc_final: 0.6447 (t70) REVERT: M 63 TRP cc_start: 0.6144 (m100) cc_final: 0.5444 (m100) REVERT: M 99 PHE cc_start: 0.8289 (m-80) cc_final: 0.7315 (m-80) REVERT: M 132 MET cc_start: 0.8925 (ttt) cc_final: 0.8377 (ttt) REVERT: M 155 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7544 (mtt180) REVERT: M 158 GLN cc_start: 0.8654 (mm110) cc_final: 0.8009 (mm-40) REVERT: M 161 LYS cc_start: 0.8946 (mttt) cc_final: 0.8471 (mttt) REVERT: M 195 THR cc_start: 0.8169 (m) cc_final: 0.7460 (t) REVERT: M 211 GLN cc_start: 0.7902 (pp30) cc_final: 0.7256 (pp30) REVERT: M 259 ASP cc_start: 0.7639 (t0) cc_final: 0.7355 (t0) REVERT: M 267 LYS cc_start: 0.7712 (tptt) cc_final: 0.7510 (tppt) REVERT: N 61 ASP cc_start: 0.6474 (t70) cc_final: 0.6076 (t70) REVERT: N 64 GLN cc_start: 0.6494 (tp40) cc_final: 0.5778 (tp40) REVERT: N 105 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7920 (mtmm) REVERT: N 110 PHE cc_start: 0.7301 (m-10) cc_final: 0.6857 (m-10) REVERT: N 206 GLU cc_start: 0.7825 (tp30) cc_final: 0.7601 (tp30) REVERT: N 213 GLN cc_start: 0.7386 (pp30) cc_final: 0.6997 (pp30) REVERT: N 241 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7955 (p) REVERT: N 254 LYS cc_start: 0.7784 (tptt) cc_final: 0.7521 (tptt) REVERT: N 260 ARG cc_start: 0.6865 (mtm-85) cc_final: 0.6298 (mtm-85) REVERT: O 11 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8204 (mm-30) REVERT: O 110 PHE cc_start: 0.6910 (m-80) cc_final: 0.6533 (m-80) REVERT: O 132 MET cc_start: 0.8178 (mpp) cc_final: 0.7731 (mpp) REVERT: O 198 MET cc_start: 0.8472 (tpt) cc_final: 0.8117 (tpt) REVERT: O 201 PHE cc_start: 0.8801 (t80) cc_final: 0.8248 (t80) REVERT: O 208 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7611 (tm-30) REVERT: P 63 TRP cc_start: 0.6901 (m100) cc_final: 0.5357 (m100) REVERT: P 87 TYR cc_start: 0.6222 (t80) cc_final: 0.5793 (t80) REVERT: P 132 MET cc_start: 0.8297 (tpt) cc_final: 0.7448 (tpt) REVERT: P 186 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8380 (t0) REVERT: P 188 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6690 (mmtm) REVERT: P 201 PHE cc_start: 0.8509 (t80) cc_final: 0.8038 (t80) outliers start: 102 outliers final: 72 residues processed: 890 average time/residue: 0.4914 time to fit residues: 689.5344 Evaluate side-chains 926 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 845 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 156 THR Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 186 ASN Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 0.9990 chunk 356 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 97 optimal weight: 0.0980 chunk 396 optimal weight: 6.9990 chunk 329 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN E 162 ASN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36705 Z= 0.184 Angle : 0.600 15.589 50248 Z= 0.313 Chirality : 0.043 0.183 5432 Planarity : 0.004 0.052 5969 Dihedral : 16.759 145.738 5791 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.74 % Allowed : 17.42 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 3971 helix: 1.21 (0.12), residues: 1874 sheet: 0.09 (0.19), residues: 738 loop : -1.14 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 106 HIS 0.013 0.001 HIS N 16 PHE 0.036 0.001 PHE N 99 TYR 0.021 0.001 TYR M 226 ARG 0.007 0.000 ARG F 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 850 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7453 (t70) cc_final: 0.7010 (t0) REVERT: A 76 LEU cc_start: 0.7619 (tp) cc_final: 0.7379 (tp) REVERT: A 94 GLU cc_start: 0.7633 (mp0) cc_final: 0.7423 (mp0) REVERT: A 109 MET cc_start: 0.7282 (tpp) cc_final: 0.7035 (tpp) REVERT: A 138 GLU cc_start: 0.7086 (mp0) cc_final: 0.6624 (mp0) REVERT: A 165 GLU cc_start: 0.7669 (tp30) cc_final: 0.7274 (tp30) REVERT: A 183 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 199 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.6034 (t0) REVERT: A 223 PHE cc_start: 0.8250 (m-80) cc_final: 0.7378 (m-80) REVERT: A 238 GLN cc_start: 0.7791 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 254 LYS cc_start: 0.7904 (tppt) cc_final: 0.7485 (ttmt) REVERT: A 259 ASP cc_start: 0.6452 (t0) cc_final: 0.6188 (t0) REVERT: A 262 LEU cc_start: 0.7136 (mm) cc_final: 0.6736 (mt) REVERT: B 118 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7239 (p0) REVERT: B 124 VAL cc_start: 0.8154 (p) cc_final: 0.7812 (m) REVERT: B 140 THR cc_start: 0.8100 (m) cc_final: 0.7790 (t) REVERT: B 166 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8364 (tppt) REVERT: B 185 LEU cc_start: 0.7585 (mt) cc_final: 0.7149 (mp) REVERT: B 206 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7165 (tp30) REVERT: B 207 GLN cc_start: 0.8156 (tp40) cc_final: 0.7731 (tp40) REVERT: B 208 GLN cc_start: 0.7655 (tt0) cc_final: 0.7286 (tt0) REVERT: C 9 GLU cc_start: 0.7515 (tp30) cc_final: 0.7265 (tp30) REVERT: C 20 VAL cc_start: 0.8377 (m) cc_final: 0.8102 (t) REVERT: C 24 LEU cc_start: 0.7894 (mm) cc_final: 0.7558 (mp) REVERT: C 25 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7164 (tm-30) REVERT: C 30 ARG cc_start: 0.7155 (tpp80) cc_final: 0.6859 (tpp80) REVERT: C 104 MET cc_start: 0.6349 (ppp) cc_final: 0.5574 (ppp) REVERT: C 105 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7654 (ttpp) REVERT: C 198 MET cc_start: 0.8126 (tpt) cc_final: 0.7884 (tpp) REVERT: C 203 PHE cc_start: 0.7163 (t80) cc_final: 0.6688 (t80) REVERT: C 204 ASN cc_start: 0.8355 (m-40) cc_final: 0.8130 (p0) REVERT: C 207 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6672 (pm20) REVERT: C 222 ARG cc_start: 0.5079 (ptm160) cc_final: 0.4384 (ptm160) REVERT: C 245 TRP cc_start: 0.7879 (m-90) cc_final: 0.7371 (m-90) REVERT: D 70 TYR cc_start: 0.7251 (t80) cc_final: 0.6828 (t80) REVERT: D 103 THR cc_start: 0.6851 (t) cc_final: 0.6133 (p) REVERT: D 104 MET cc_start: 0.6905 (mmp) cc_final: 0.6043 (mmp) REVERT: D 220 LYS cc_start: 0.5389 (mmtm) cc_final: 0.5010 (mmtm) REVERT: D 236 GLU cc_start: 0.7368 (mp0) cc_final: 0.6773 (mp0) REVERT: D 254 LYS cc_start: 0.7403 (tppp) cc_final: 0.7126 (tppp) REVERT: D 260 ARG cc_start: 0.6946 (mmm-85) cc_final: 0.6559 (mmm-85) REVERT: E 61 ASP cc_start: 0.7720 (t70) cc_final: 0.7082 (t70) REVERT: E 69 HIS cc_start: 0.7828 (t70) cc_final: 0.7598 (t70) REVERT: E 132 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7526 (ttp) REVERT: E 139 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.7048 (p-80) REVERT: E 157 HIS cc_start: 0.8666 (m90) cc_final: 0.7689 (m-70) REVERT: E 158 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8171 (mm-40) REVERT: E 161 LYS cc_start: 0.8326 (mttt) cc_final: 0.7806 (mttt) REVERT: E 206 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6735 (tm-30) REVERT: E 208 GLN cc_start: 0.7634 (tp40) cc_final: 0.7056 (tm-30) REVERT: E 210 ILE cc_start: 0.8373 (mm) cc_final: 0.8099 (mt) REVERT: E 225 TYR cc_start: 0.6834 (t80) cc_final: 0.5600 (t80) REVERT: E 237 TRP cc_start: 0.6167 (m100) cc_final: 0.5712 (m100) REVERT: E 270 LYS cc_start: 0.6805 (mtpt) cc_final: 0.6310 (mtpt) REVERT: E 271 PHE cc_start: 0.7864 (m-80) cc_final: 0.7167 (m-80) REVERT: F 64 GLN cc_start: 0.6461 (tp40) cc_final: 0.6063 (tp-100) REVERT: F 98 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6935 (pt0) REVERT: F 129 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7355 (mt0) REVERT: F 156 THR cc_start: 0.8956 (p) cc_final: 0.8585 (p) REVERT: F 157 HIS cc_start: 0.8613 (m90) cc_final: 0.8355 (m90) REVERT: F 162 ASN cc_start: 0.8634 (m-40) cc_final: 0.8408 (p0) REVERT: F 241 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7736 (m) REVERT: F 254 LYS cc_start: 0.8099 (tptt) cc_final: 0.7861 (tptt) REVERT: G 110 PHE cc_start: 0.7205 (m-80) cc_final: 0.6908 (m-10) REVERT: H 63 TRP cc_start: 0.6886 (m100) cc_final: 0.6446 (m100) REVERT: H 87 TYR cc_start: 0.6946 (t80) cc_final: 0.6413 (t80) REVERT: H 132 MET cc_start: 0.7851 (tpt) cc_final: 0.7154 (tpt) REVERT: H 161 LYS cc_start: 0.8494 (mttt) cc_final: 0.8163 (ptpt) REVERT: H 164 LEU cc_start: 0.8091 (mt) cc_final: 0.7757 (tp) REVERT: H 201 PHE cc_start: 0.8458 (t80) cc_final: 0.8009 (t80) REVERT: H 205 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8232 (mmmm) REVERT: H 238 GLN cc_start: 0.5843 (mm-40) cc_final: 0.5640 (mm-40) REVERT: H 251 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6623 (mp) REVERT: H 262 LEU cc_start: 0.7393 (mm) cc_final: 0.7006 (mm) REVERT: R 418 MET cc_start: 0.7389 (ppp) cc_final: 0.6958 (ppp) REVERT: Q 360 LYS cc_start: 0.5734 (ptpp) cc_final: 0.5330 (ptpp) REVERT: Q 387 MET cc_start: 0.7262 (tpp) cc_final: 0.7035 (mmm) REVERT: Q 418 MET cc_start: 0.7490 (ppp) cc_final: 0.7033 (ppp) REVERT: I 35 ASP cc_start: 0.7197 (t70) cc_final: 0.6977 (t70) REVERT: I 72 ASP cc_start: 0.7374 (t70) cc_final: 0.7026 (t70) REVERT: I 80 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7309 (tm-30) REVERT: I 109 MET cc_start: 0.6975 (ttt) cc_final: 0.6372 (ttt) REVERT: I 183 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7061 (mt) REVERT: I 199 ASP cc_start: 0.6260 (t0) cc_final: 0.6052 (t0) REVERT: I 238 GLN cc_start: 0.7673 (tm-30) cc_final: 0.6859 (tm-30) REVERT: I 254 LYS cc_start: 0.8117 (tptp) cc_final: 0.7570 (tppt) REVERT: I 262 LEU cc_start: 0.6624 (mm) cc_final: 0.6315 (mm) REVERT: J 92 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7727 (mtpp) REVERT: J 94 GLU cc_start: 0.7041 (pp20) cc_final: 0.6568 (pp20) REVERT: J 98 GLU cc_start: 0.7008 (tp30) cc_final: 0.6730 (tp30) REVERT: J 129 GLN cc_start: 0.7839 (tt0) cc_final: 0.7381 (mt0) REVERT: J 206 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7015 (tp30) REVERT: K 109 MET cc_start: 0.7973 (tpp) cc_final: 0.7401 (pmm) REVERT: K 198 MET cc_start: 0.7280 (pmm) cc_final: 0.6965 (pmm) REVERT: L 80 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6379 (tm-30) REVERT: L 104 MET cc_start: 0.5383 (mmp) cc_final: 0.5032 (mmp) REVERT: L 133 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7802 (mmmt) REVERT: L 220 LYS cc_start: 0.5407 (mmtm) cc_final: 0.5054 (mmtm) REVERT: L 248 ASP cc_start: 0.7155 (p0) cc_final: 0.6627 (p0) REVERT: L 260 ARG cc_start: 0.7043 (mmm-85) cc_final: 0.6814 (mmm-85) REVERT: M 35 ASP cc_start: 0.6702 (m-30) cc_final: 0.6297 (m-30) REVERT: M 61 ASP cc_start: 0.7567 (t70) cc_final: 0.6858 (t0) REVERT: M 63 TRP cc_start: 0.6143 (m100) cc_final: 0.5434 (m100) REVERT: M 80 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7472 (tm-30) REVERT: M 99 PHE cc_start: 0.8245 (m-80) cc_final: 0.7282 (m-80) REVERT: M 132 MET cc_start: 0.8888 (ttt) cc_final: 0.8677 (ttt) REVERT: M 155 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7625 (mtt180) REVERT: M 195 THR cc_start: 0.7863 (m) cc_final: 0.7120 (t) REVERT: M 259 ASP cc_start: 0.7770 (t0) cc_final: 0.7473 (t0) REVERT: M 267 LYS cc_start: 0.7706 (tptt) cc_final: 0.7498 (tppt) REVERT: N 61 ASP cc_start: 0.6391 (t70) cc_final: 0.5967 (t70) REVERT: N 78 TRP cc_start: 0.7912 (m100) cc_final: 0.6802 (m100) REVERT: N 105 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7898 (mtmm) REVERT: N 110 PHE cc_start: 0.7163 (m-10) cc_final: 0.6835 (m-10) REVERT: N 206 GLU cc_start: 0.7794 (tp30) cc_final: 0.7493 (tp30) REVERT: N 213 GLN cc_start: 0.7368 (pp30) cc_final: 0.6985 (pp30) REVERT: N 241 THR cc_start: 0.8291 (t) cc_final: 0.7896 (p) REVERT: N 254 LYS cc_start: 0.7773 (tptt) cc_final: 0.7502 (tptt) REVERT: N 260 ARG cc_start: 0.6797 (mtm-85) cc_final: 0.6262 (mtm-85) REVERT: O 11 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8208 (mm-30) REVERT: O 110 PHE cc_start: 0.7020 (m-80) cc_final: 0.6697 (m-10) REVERT: O 132 MET cc_start: 0.8193 (mpp) cc_final: 0.7718 (mpp) REVERT: O 198 MET cc_start: 0.8475 (tpt) cc_final: 0.8130 (tpt) REVERT: O 201 PHE cc_start: 0.8786 (t80) cc_final: 0.8236 (t80) REVERT: O 208 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7452 (tm-30) REVERT: P 63 TRP cc_start: 0.6883 (m100) cc_final: 0.5332 (m100) REVERT: P 87 TYR cc_start: 0.6206 (t80) cc_final: 0.5802 (t80) REVERT: P 130 LEU cc_start: 0.8350 (mt) cc_final: 0.8079 (mt) REVERT: P 132 MET cc_start: 0.8291 (tpt) cc_final: 0.7438 (tpt) REVERT: P 186 ASN cc_start: 0.8659 (m-40) cc_final: 0.8377 (t0) REVERT: P 188 LYS cc_start: 0.7305 (mmtm) cc_final: 0.6786 (mmtm) REVERT: P 201 PHE cc_start: 0.8433 (t80) cc_final: 0.8052 (t80) outliers start: 97 outliers final: 70 residues processed: 887 average time/residue: 0.4791 time to fit residues: 670.1500 Evaluate side-chains 927 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 848 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 188 LYS Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 226 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 224 optimal weight: 0.3980 chunk 333 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 GLN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 204 ASN H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 GLN M 157 HIS ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36705 Z= 0.228 Angle : 0.624 14.825 50248 Z= 0.324 Chirality : 0.043 0.181 5432 Planarity : 0.004 0.080 5969 Dihedral : 16.815 145.549 5791 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.86 % Allowed : 18.12 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 3971 helix: 1.18 (0.12), residues: 1880 sheet: 0.02 (0.19), residues: 710 loop : -1.13 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 78 HIS 0.021 0.001 HIS N 16 PHE 0.038 0.001 PHE N 99 TYR 0.021 0.001 TYR I 134 ARG 0.007 0.000 ARG K 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 859 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7476 (t70) cc_final: 0.6990 (t0) REVERT: A 76 LEU cc_start: 0.7618 (tp) cc_final: 0.7400 (tp) REVERT: A 138 GLU cc_start: 0.7079 (mp0) cc_final: 0.6608 (mp0) REVERT: A 165 GLU cc_start: 0.7502 (tp30) cc_final: 0.7147 (tp30) REVERT: A 183 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7286 (mt) REVERT: A 223 PHE cc_start: 0.8214 (m-80) cc_final: 0.7419 (m-80) REVERT: A 238 GLN cc_start: 0.7760 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 259 ASP cc_start: 0.6520 (t0) cc_final: 0.6233 (t0) REVERT: A 262 LEU cc_start: 0.7203 (mm) cc_final: 0.6802 (mt) REVERT: B 109 MET cc_start: 0.7639 (ttm) cc_final: 0.7192 (ttm) REVERT: B 118 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7238 (p0) REVERT: B 124 VAL cc_start: 0.8219 (p) cc_final: 0.7910 (m) REVERT: B 140 THR cc_start: 0.8126 (m) cc_final: 0.7684 (t) REVERT: B 166 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8387 (tppt) REVERT: B 185 LEU cc_start: 0.7633 (mt) cc_final: 0.7412 (mp) REVERT: B 206 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7199 (tp30) REVERT: B 208 GLN cc_start: 0.7520 (tt0) cc_final: 0.7167 (tt0) REVERT: C 9 GLU cc_start: 0.7449 (tp30) cc_final: 0.7217 (tp30) REVERT: C 20 VAL cc_start: 0.8435 (m) cc_final: 0.8119 (t) REVERT: C 24 LEU cc_start: 0.7906 (mm) cc_final: 0.7568 (mp) REVERT: C 25 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 105 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7695 (ttpp) REVERT: C 198 MET cc_start: 0.8303 (tpt) cc_final: 0.8029 (tpt) REVERT: C 203 PHE cc_start: 0.7244 (t80) cc_final: 0.6793 (t80) REVERT: C 204 ASN cc_start: 0.8427 (m-40) cc_final: 0.7902 (m-40) REVERT: C 207 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: C 245 TRP cc_start: 0.7884 (m-90) cc_final: 0.7377 (m-90) REVERT: D 70 TYR cc_start: 0.7220 (t80) cc_final: 0.6756 (t80) REVERT: D 103 THR cc_start: 0.6889 (t) cc_final: 0.6185 (p) REVERT: D 104 MET cc_start: 0.6890 (mmp) cc_final: 0.6045 (mmp) REVERT: D 132 MET cc_start: 0.8343 (ppp) cc_final: 0.8021 (ppp) REVERT: D 162 ASN cc_start: 0.6932 (m110) cc_final: 0.6625 (p0) REVERT: D 220 LYS cc_start: 0.5415 (mmtm) cc_final: 0.5022 (mmtm) REVERT: D 236 GLU cc_start: 0.7371 (mp0) cc_final: 0.6772 (mp0) REVERT: D 254 LYS cc_start: 0.7428 (tppp) cc_final: 0.7192 (tppp) REVERT: D 260 ARG cc_start: 0.6985 (mmm-85) cc_final: 0.6607 (mmm-85) REVERT: E 30 ARG cc_start: 0.7442 (mmm-85) cc_final: 0.6724 (mmm-85) REVERT: E 61 ASP cc_start: 0.7781 (t70) cc_final: 0.7063 (t70) REVERT: E 69 HIS cc_start: 0.7772 (t70) cc_final: 0.7554 (t70) REVERT: E 132 MET cc_start: 0.8352 (ttp) cc_final: 0.7460 (ttp) REVERT: E 139 HIS cc_start: 0.7466 (p-80) cc_final: 0.7076 (p-80) REVERT: E 157 HIS cc_start: 0.8681 (m90) cc_final: 0.7635 (m-70) REVERT: E 158 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8163 (mm-40) REVERT: E 161 LYS cc_start: 0.8339 (mttt) cc_final: 0.7828 (mttt) REVERT: E 195 THR cc_start: 0.8286 (m) cc_final: 0.7534 (t) REVERT: E 206 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6596 (pp20) REVERT: E 208 GLN cc_start: 0.7745 (tp40) cc_final: 0.7172 (tm-30) REVERT: E 210 ILE cc_start: 0.8397 (mm) cc_final: 0.8140 (mt) REVERT: E 213 GLN cc_start: 0.7908 (pp30) cc_final: 0.7672 (pp30) REVERT: E 219 GLU cc_start: 0.8321 (mp0) cc_final: 0.8037 (pm20) REVERT: E 225 TYR cc_start: 0.6953 (t80) cc_final: 0.5848 (t80) REVERT: E 237 TRP cc_start: 0.6242 (m100) cc_final: 0.5792 (m100) REVERT: E 270 LYS cc_start: 0.6759 (mtpt) cc_final: 0.6272 (mtpt) REVERT: E 271 PHE cc_start: 0.7956 (m-80) cc_final: 0.7330 (m-80) REVERT: F 62 HIS cc_start: 0.7639 (m170) cc_final: 0.7162 (m170) REVERT: F 64 GLN cc_start: 0.6514 (tp40) cc_final: 0.6186 (tp40) REVERT: F 98 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6985 (pt0) REVERT: F 110 PHE cc_start: 0.7304 (m-10) cc_final: 0.6888 (m-80) REVERT: F 129 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7362 (mt0) REVERT: F 156 THR cc_start: 0.8990 (p) cc_final: 0.8758 (p) REVERT: F 157 HIS cc_start: 0.8661 (m90) cc_final: 0.8344 (m90) REVERT: F 162 ASN cc_start: 0.8702 (m-40) cc_final: 0.8448 (p0) REVERT: F 241 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7917 (m) REVERT: F 254 LYS cc_start: 0.8113 (tptt) cc_final: 0.7798 (tptt) REVERT: G 11 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8132 (tp30) REVERT: G 110 PHE cc_start: 0.7199 (m-80) cc_final: 0.6929 (m-10) REVERT: G 150 GLN cc_start: 0.8218 (mm110) cc_final: 0.7711 (mm110) REVERT: H 63 TRP cc_start: 0.6885 (m100) cc_final: 0.6440 (m100) REVERT: H 87 TYR cc_start: 0.6997 (t80) cc_final: 0.6496 (t80) REVERT: H 132 MET cc_start: 0.7838 (tpt) cc_final: 0.7151 (tpt) REVERT: H 161 LYS cc_start: 0.8524 (mttt) cc_final: 0.8163 (mttt) REVERT: H 164 LEU cc_start: 0.8095 (mt) cc_final: 0.7764 (tp) REVERT: H 188 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8103 (mmtm) REVERT: H 201 PHE cc_start: 0.8393 (t80) cc_final: 0.7947 (t80) REVERT: H 205 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8334 (mmmm) REVERT: H 238 GLN cc_start: 0.5865 (mm-40) cc_final: 0.5656 (mm-40) REVERT: H 251 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6632 (mp) REVERT: H 262 LEU cc_start: 0.7408 (mm) cc_final: 0.7013 (mm) REVERT: R 418 MET cc_start: 0.7386 (ppp) cc_final: 0.6955 (ppp) REVERT: Q 360 LYS cc_start: 0.5752 (ptpp) cc_final: 0.5333 (ptpp) REVERT: Q 387 MET cc_start: 0.7232 (tpp) cc_final: 0.6978 (mmm) REVERT: Q 418 MET cc_start: 0.7498 (ppp) cc_final: 0.7047 (ppp) REVERT: I 35 ASP cc_start: 0.7315 (t70) cc_final: 0.7093 (t70) REVERT: I 72 ASP cc_start: 0.7365 (t70) cc_final: 0.7024 (t70) REVERT: I 80 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7483 (tm-30) REVERT: I 89 GLU cc_start: 0.7058 (tp30) cc_final: 0.6780 (tp30) REVERT: I 109 MET cc_start: 0.7068 (ttt) cc_final: 0.6386 (ttt) REVERT: I 183 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7177 (mt) REVERT: I 238 GLN cc_start: 0.7635 (tm-30) cc_final: 0.6811 (tm-30) REVERT: I 254 LYS cc_start: 0.8112 (tptp) cc_final: 0.7575 (tppt) REVERT: I 262 LEU cc_start: 0.6721 (mm) cc_final: 0.6387 (mm) REVERT: J 92 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7742 (mtpp) REVERT: J 94 GLU cc_start: 0.7106 (pp20) cc_final: 0.6617 (pp20) REVERT: J 98 GLU cc_start: 0.7013 (tp30) cc_final: 0.6750 (tp30) REVERT: J 129 GLN cc_start: 0.7823 (tt0) cc_final: 0.7381 (mt0) REVERT: J 206 GLU cc_start: 0.7547 (tm-30) cc_final: 0.6995 (tp30) REVERT: K 198 MET cc_start: 0.7345 (pmm) cc_final: 0.7029 (pmm) REVERT: L 80 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6467 (tm-30) REVERT: L 104 MET cc_start: 0.5428 (mmp) cc_final: 0.5072 (mmp) REVERT: L 133 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7940 (mmmt) REVERT: L 155 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8110 (mtm110) REVERT: L 220 LYS cc_start: 0.5521 (mmtm) cc_final: 0.5197 (mmtm) REVERT: L 238 GLN cc_start: 0.8555 (mt0) cc_final: 0.8160 (mt0) REVERT: L 248 ASP cc_start: 0.7173 (p0) cc_final: 0.6585 (p0) REVERT: M 35 ASP cc_start: 0.6748 (m-30) cc_final: 0.6375 (m-30) REVERT: M 61 ASP cc_start: 0.7660 (t70) cc_final: 0.6953 (t0) REVERT: M 63 TRP cc_start: 0.6216 (m100) cc_final: 0.5401 (m100) REVERT: M 99 PHE cc_start: 0.8226 (m-80) cc_final: 0.7262 (m-80) REVERT: M 155 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7639 (mtt180) REVERT: M 195 THR cc_start: 0.8015 (m) cc_final: 0.7287 (t) REVERT: M 259 ASP cc_start: 0.7910 (t0) cc_final: 0.7551 (t0) REVERT: M 267 LYS cc_start: 0.7730 (tptt) cc_final: 0.7522 (tppt) REVERT: N 61 ASP cc_start: 0.6491 (t70) cc_final: 0.6041 (t70) REVERT: N 78 TRP cc_start: 0.7964 (m100) cc_final: 0.6810 (m100) REVERT: N 105 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7968 (mtmm) REVERT: N 110 PHE cc_start: 0.7238 (m-10) cc_final: 0.7018 (m-10) REVERT: N 165 GLU cc_start: 0.8279 (mp0) cc_final: 0.7608 (mp0) REVERT: N 206 GLU cc_start: 0.7764 (tp30) cc_final: 0.7422 (tp30) REVERT: N 213 GLN cc_start: 0.7360 (pp30) cc_final: 0.6985 (pp30) REVERT: N 241 THR cc_start: 0.8350 (t) cc_final: 0.8031 (p) REVERT: N 254 LYS cc_start: 0.7664 (tptt) cc_final: 0.7449 (tptt) REVERT: N 260 ARG cc_start: 0.6831 (mtm-85) cc_final: 0.6298 (mtm-85) REVERT: O 11 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8178 (mm-30) REVERT: O 110 PHE cc_start: 0.7004 (m-80) cc_final: 0.6675 (m-10) REVERT: O 132 MET cc_start: 0.8191 (mpp) cc_final: 0.7695 (mpp) REVERT: O 198 MET cc_start: 0.8495 (tpt) cc_final: 0.8150 (tpt) REVERT: O 201 PHE cc_start: 0.8809 (t80) cc_final: 0.8299 (t80) REVERT: O 208 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7499 (tm-30) REVERT: P 63 TRP cc_start: 0.6843 (m100) cc_final: 0.5261 (m100) REVERT: P 87 TYR cc_start: 0.6169 (t80) cc_final: 0.5746 (t80) REVERT: P 130 LEU cc_start: 0.8470 (mt) cc_final: 0.8241 (mt) REVERT: P 132 MET cc_start: 0.8314 (tpt) cc_final: 0.7445 (tpt) REVERT: P 186 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8345 (t0) REVERT: P 188 LYS cc_start: 0.7267 (mmtm) cc_final: 0.6729 (mmtm) REVERT: P 201 PHE cc_start: 0.8447 (t80) cc_final: 0.8078 (t80) REVERT: P 276 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7810 (mmtt) outliers start: 101 outliers final: 81 residues processed: 898 average time/residue: 0.5236 time to fit residues: 750.1187 Evaluate side-chains 928 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 840 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 156 THR Chi-restraints excluded: chain P residue 186 ASN Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 chunk 251 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 310 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 ASN K 207 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36705 Z= 0.209 Angle : 0.622 12.779 50248 Z= 0.322 Chirality : 0.043 0.172 5432 Planarity : 0.004 0.058 5969 Dihedral : 16.824 145.658 5791 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.25 % Allowed : 18.41 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 3971 helix: 1.23 (0.12), residues: 1868 sheet: 0.05 (0.19), residues: 722 loop : -1.11 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 78 HIS 0.017 0.001 HIS N 16 PHE 0.038 0.001 PHE N 99 TYR 0.017 0.001 TYR I 134 ARG 0.013 0.000 ARG L 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 856 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7483 (t70) cc_final: 0.7033 (t0) REVERT: A 138 GLU cc_start: 0.7072 (mp0) cc_final: 0.6595 (mp0) REVERT: A 165 GLU cc_start: 0.7488 (tp30) cc_final: 0.7158 (tp30) REVERT: A 183 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7303 (mt) REVERT: A 223 PHE cc_start: 0.8183 (m-80) cc_final: 0.7389 (m-80) REVERT: A 238 GLN cc_start: 0.7763 (tm-30) cc_final: 0.6889 (tm-30) REVERT: A 259 ASP cc_start: 0.6569 (t0) cc_final: 0.6278 (t0) REVERT: A 262 LEU cc_start: 0.7250 (mm) cc_final: 0.6848 (mt) REVERT: B 94 GLU cc_start: 0.7091 (pp20) cc_final: 0.6611 (pp20) REVERT: B 116 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: B 118 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7224 (p0) REVERT: B 124 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7788 (m) REVERT: B 140 THR cc_start: 0.8101 (m) cc_final: 0.7749 (p) REVERT: B 185 LEU cc_start: 0.7613 (mt) cc_final: 0.7190 (mp) REVERT: B 206 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7215 (tp30) REVERT: B 208 GLN cc_start: 0.7488 (tt0) cc_final: 0.7220 (tt0) REVERT: C 9 GLU cc_start: 0.7446 (tp30) cc_final: 0.7228 (tp30) REVERT: C 24 LEU cc_start: 0.7898 (mm) cc_final: 0.7607 (mp) REVERT: C 25 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7104 (tm-30) REVERT: C 104 MET cc_start: 0.6329 (ppp) cc_final: 0.5579 (ppp) REVERT: C 105 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7616 (ttpp) REVERT: C 198 MET cc_start: 0.8364 (tpt) cc_final: 0.8121 (tpt) REVERT: C 203 PHE cc_start: 0.7277 (t80) cc_final: 0.6838 (t80) REVERT: C 204 ASN cc_start: 0.8428 (m-40) cc_final: 0.7890 (m-40) REVERT: C 207 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: C 245 TRP cc_start: 0.7881 (m-90) cc_final: 0.7399 (m-90) REVERT: D 70 TYR cc_start: 0.7261 (t80) cc_final: 0.6785 (t80) REVERT: D 103 THR cc_start: 0.6950 (t) cc_final: 0.6258 (p) REVERT: D 104 MET cc_start: 0.6871 (mmp) cc_final: 0.6032 (mmp) REVERT: D 132 MET cc_start: 0.8371 (ppp) cc_final: 0.8108 (ppp) REVERT: D 220 LYS cc_start: 0.5434 (mmtm) cc_final: 0.5082 (mmtm) REVERT: D 236 GLU cc_start: 0.7370 (mp0) cc_final: 0.6766 (mp0) REVERT: D 254 LYS cc_start: 0.7438 (tppp) cc_final: 0.7204 (tppp) REVERT: D 260 ARG cc_start: 0.7003 (mmm-85) cc_final: 0.6614 (mmm-85) REVERT: E 24 LEU cc_start: 0.7690 (mp) cc_final: 0.7346 (mp) REVERT: E 30 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.6797 (mmm-85) REVERT: E 35 ASP cc_start: 0.7080 (m-30) cc_final: 0.6613 (m-30) REVERT: E 61 ASP cc_start: 0.7790 (t70) cc_final: 0.7086 (t70) REVERT: E 69 HIS cc_start: 0.7784 (t70) cc_final: 0.7553 (t70) REVERT: E 139 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.7043 (p-80) REVERT: E 157 HIS cc_start: 0.8658 (m90) cc_final: 0.7627 (m-70) REVERT: E 158 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8195 (mm-40) REVERT: E 161 LYS cc_start: 0.8332 (mttt) cc_final: 0.7842 (mttt) REVERT: E 195 THR cc_start: 0.8138 (m) cc_final: 0.7412 (t) REVERT: E 206 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6731 (tm-30) REVERT: E 208 GLN cc_start: 0.7740 (tp40) cc_final: 0.7166 (tm-30) REVERT: E 210 ILE cc_start: 0.8380 (mm) cc_final: 0.8046 (mt) REVERT: E 225 TYR cc_start: 0.7003 (t80) cc_final: 0.5999 (t80) REVERT: E 237 TRP cc_start: 0.6256 (m100) cc_final: 0.5857 (m100) REVERT: E 270 LYS cc_start: 0.6758 (mtpt) cc_final: 0.6284 (mtpt) REVERT: E 271 PHE cc_start: 0.7941 (m-80) cc_final: 0.7321 (m-80) REVERT: F 64 GLN cc_start: 0.6517 (tp40) cc_final: 0.6183 (tp40) REVERT: F 70 TYR cc_start: 0.7191 (t80) cc_final: 0.6851 (t80) REVERT: F 98 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6856 (pt0) REVERT: F 110 PHE cc_start: 0.7299 (m-10) cc_final: 0.6934 (m-80) REVERT: F 129 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7210 (mp10) REVERT: F 156 THR cc_start: 0.9004 (p) cc_final: 0.8633 (p) REVERT: F 157 HIS cc_start: 0.8657 (m90) cc_final: 0.8298 (m90) REVERT: F 162 ASN cc_start: 0.8701 (m-40) cc_final: 0.8387 (p0) REVERT: F 164 LEU cc_start: 0.9112 (mt) cc_final: 0.8872 (pp) REVERT: F 241 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7930 (m) REVERT: F 254 LYS cc_start: 0.8117 (tptt) cc_final: 0.7787 (tptt) REVERT: G 11 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8119 (tp30) REVERT: G 150 GLN cc_start: 0.8117 (mm110) cc_final: 0.7577 (mm110) REVERT: G 155 ARG cc_start: 0.8384 (pmt170) cc_final: 0.7818 (tpt170) REVERT: H 63 TRP cc_start: 0.6905 (m100) cc_final: 0.6466 (m100) REVERT: H 87 TYR cc_start: 0.6901 (t80) cc_final: 0.6285 (t80) REVERT: H 132 MET cc_start: 0.7809 (tpt) cc_final: 0.7103 (tpt) REVERT: H 161 LYS cc_start: 0.8510 (mttt) cc_final: 0.8151 (mttt) REVERT: H 164 LEU cc_start: 0.8102 (mt) cc_final: 0.7795 (tp) REVERT: H 188 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8097 (mmtm) REVERT: H 201 PHE cc_start: 0.8374 (t80) cc_final: 0.7992 (t80) REVERT: H 205 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8326 (mmmm) REVERT: H 238 GLN cc_start: 0.5906 (mm-40) cc_final: 0.5701 (mm-40) REVERT: H 251 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6569 (mp) REVERT: H 262 LEU cc_start: 0.7434 (mm) cc_final: 0.7022 (mm) REVERT: R 368 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.4057 (mm) REVERT: R 418 MET cc_start: 0.7384 (ppp) cc_final: 0.6953 (ppp) REVERT: Q 360 LYS cc_start: 0.5749 (ptpp) cc_final: 0.5326 (ptpp) REVERT: Q 387 MET cc_start: 0.7192 (tpp) cc_final: 0.6906 (mmm) REVERT: Q 418 MET cc_start: 0.7503 (ppp) cc_final: 0.7054 (ppp) REVERT: I 72 ASP cc_start: 0.7355 (t70) cc_final: 0.7022 (t70) REVERT: I 80 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7443 (tm-30) REVERT: I 109 MET cc_start: 0.7057 (ttt) cc_final: 0.6347 (ttt) REVERT: I 183 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7166 (mt) REVERT: I 206 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6757 (tm-30) REVERT: I 238 GLN cc_start: 0.7763 (tm-30) cc_final: 0.6825 (tm-30) REVERT: I 262 LEU cc_start: 0.6727 (mm) cc_final: 0.6391 (mm) REVERT: J 92 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7718 (mtpp) REVERT: J 94 GLU cc_start: 0.7140 (pp20) cc_final: 0.6641 (pp20) REVERT: J 98 GLU cc_start: 0.6966 (tp30) cc_final: 0.6719 (tp30) REVERT: J 129 GLN cc_start: 0.7795 (tt0) cc_final: 0.7381 (mt0) REVERT: J 206 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6960 (tp30) REVERT: K 11 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6425 (mm-30) REVERT: K 109 MET cc_start: 0.8076 (tpp) cc_final: 0.7346 (pmm) REVERT: K 198 MET cc_start: 0.7298 (pmm) cc_final: 0.6994 (pmm) REVERT: L 80 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6582 (tm-30) REVERT: L 104 MET cc_start: 0.5463 (mmp) cc_final: 0.5113 (mmp) REVERT: L 133 LYS cc_start: 0.8294 (mmmt) cc_final: 0.7973 (mmmt) REVERT: L 155 ARG cc_start: 0.8373 (ptp90) cc_final: 0.8128 (mtm110) REVERT: L 220 LYS cc_start: 0.5541 (mmtm) cc_final: 0.5273 (mmtm) REVERT: L 248 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6545 (p0) REVERT: L 260 ARG cc_start: 0.7133 (mmm-85) cc_final: 0.6718 (mmm-85) REVERT: M 15 TRP cc_start: 0.6910 (m100) cc_final: 0.6484 (m-10) REVERT: M 35 ASP cc_start: 0.6770 (m-30) cc_final: 0.6415 (m-30) REVERT: M 61 ASP cc_start: 0.7636 (t70) cc_final: 0.6913 (t0) REVERT: M 63 TRP cc_start: 0.6233 (m100) cc_final: 0.5502 (m100) REVERT: M 80 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7467 (tm-30) REVERT: M 99 PHE cc_start: 0.8147 (m-80) cc_final: 0.7169 (m-80) REVERT: M 132 MET cc_start: 0.8917 (ttt) cc_final: 0.8569 (ttt) REVERT: M 155 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7689 (mtt180) REVERT: M 195 THR cc_start: 0.7848 (m) cc_final: 0.7062 (t) REVERT: M 259 ASP cc_start: 0.7937 (t0) cc_final: 0.7562 (t0) REVERT: M 267 LYS cc_start: 0.7740 (tptt) cc_final: 0.7531 (tppt) REVERT: N 61 ASP cc_start: 0.6463 (t70) cc_final: 0.6032 (t70) REVERT: N 78 TRP cc_start: 0.7916 (m100) cc_final: 0.6895 (m100) REVERT: N 105 LYS cc_start: 0.8240 (mtpt) cc_final: 0.8006 (mtmm) REVERT: N 107 TYR cc_start: 0.8177 (t80) cc_final: 0.7185 (t80) REVERT: N 165 GLU cc_start: 0.8259 (mp0) cc_final: 0.7600 (mp0) REVERT: N 206 GLU cc_start: 0.7748 (tp30) cc_final: 0.7404 (tp30) REVERT: N 213 GLN cc_start: 0.7358 (pp30) cc_final: 0.6982 (pp30) REVERT: N 241 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8006 (p) REVERT: N 254 LYS cc_start: 0.7671 (tptt) cc_final: 0.7461 (tptt) REVERT: N 260 ARG cc_start: 0.6791 (mtm-85) cc_final: 0.6297 (mtm-85) REVERT: O 11 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8158 (mm-30) REVERT: O 110 PHE cc_start: 0.6974 (m-80) cc_final: 0.6672 (m-10) REVERT: O 132 MET cc_start: 0.8197 (mpp) cc_final: 0.7698 (mpp) REVERT: O 198 MET cc_start: 0.8511 (tpt) cc_final: 0.8195 (tpt) REVERT: O 201 PHE cc_start: 0.8806 (t80) cc_final: 0.8296 (t80) REVERT: P 63 TRP cc_start: 0.6816 (m100) cc_final: 0.5298 (m100) REVERT: P 87 TYR cc_start: 0.6173 (t80) cc_final: 0.5731 (t80) REVERT: P 132 MET cc_start: 0.8317 (tpt) cc_final: 0.7447 (tpt) REVERT: P 186 ASN cc_start: 0.8653 (m-40) cc_final: 0.8369 (t0) REVERT: P 188 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6741 (mmtm) REVERT: P 201 PHE cc_start: 0.8443 (t80) cc_final: 0.8095 (t80) REVERT: P 251 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6826 (mp) REVERT: P 276 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7843 (mmtt) outliers start: 115 outliers final: 86 residues processed: 898 average time/residue: 0.4792 time to fit residues: 678.5338 Evaluate side-chains 935 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 836 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 148 GLN Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 207 GLN Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 248 ASP Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 1.9990 chunk 378 optimal weight: 0.0070 chunk 345 optimal weight: 1.9990 chunk 368 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 289 optimal weight: 0.0270 chunk 113 optimal weight: 0.8980 chunk 332 optimal weight: 3.9990 chunk 348 optimal weight: 0.6980 chunk 366 optimal weight: 0.3980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 GLN ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 HIS ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36705 Z= 0.184 Angle : 0.635 19.066 50248 Z= 0.325 Chirality : 0.043 0.181 5432 Planarity : 0.004 0.056 5969 Dihedral : 16.800 145.606 5791 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.86 % Allowed : 19.23 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 3971 helix: 1.22 (0.12), residues: 1874 sheet: 0.08 (0.19), residues: 720 loop : -1.08 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 78 HIS 0.014 0.001 HIS N 16 PHE 0.040 0.001 PHE N 99 TYR 0.031 0.001 TYR F 70 ARG 0.008 0.000 ARG L 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 824 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 TRP cc_start: 0.4521 (m100) cc_final: 0.3877 (m100) REVERT: A 72 ASP cc_start: 0.7485 (t70) cc_final: 0.7045 (t70) REVERT: A 138 GLU cc_start: 0.7059 (mp0) cc_final: 0.6577 (mp0) REVERT: A 165 GLU cc_start: 0.7489 (tp30) cc_final: 0.7165 (tp30) REVERT: A 183 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7315 (mt) REVERT: A 223 PHE cc_start: 0.8187 (m-80) cc_final: 0.7388 (m-80) REVERT: A 238 GLN cc_start: 0.7781 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 262 LEU cc_start: 0.7286 (mm) cc_final: 0.6903 (mt) REVERT: B 94 GLU cc_start: 0.7082 (pp20) cc_final: 0.6599 (pp20) REVERT: B 118 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7216 (p0) REVERT: B 124 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7800 (m) REVERT: B 140 THR cc_start: 0.8090 (m) cc_final: 0.7579 (p) REVERT: B 185 LEU cc_start: 0.7620 (mt) cc_final: 0.7215 (mp) REVERT: B 206 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7098 (tp30) REVERT: B 208 GLN cc_start: 0.7490 (tt0) cc_final: 0.7203 (tt0) REVERT: C 9 GLU cc_start: 0.7435 (tp30) cc_final: 0.7221 (tp30) REVERT: C 24 LEU cc_start: 0.7900 (mm) cc_final: 0.7597 (mp) REVERT: C 25 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7099 (tm-30) REVERT: C 104 MET cc_start: 0.6313 (ppp) cc_final: 0.5575 (ppp) REVERT: C 105 LYS cc_start: 0.7918 (ttpp) cc_final: 0.7634 (ttpp) REVERT: C 198 MET cc_start: 0.8373 (tpt) cc_final: 0.8135 (tpt) REVERT: C 203 PHE cc_start: 0.7285 (t80) cc_final: 0.6850 (t80) REVERT: C 204 ASN cc_start: 0.8479 (m-40) cc_final: 0.7922 (m-40) REVERT: C 207 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: C 245 TRP cc_start: 0.7879 (m-90) cc_final: 0.7437 (m-90) REVERT: D 70 TYR cc_start: 0.7321 (t80) cc_final: 0.6841 (t80) REVERT: D 103 THR cc_start: 0.6972 (t) cc_final: 0.6291 (p) REVERT: D 104 MET cc_start: 0.6788 (mmp) cc_final: 0.5864 (mmp) REVERT: D 109 MET cc_start: 0.7137 (tpt) cc_final: 0.6761 (tmm) REVERT: D 132 MET cc_start: 0.8373 (ppp) cc_final: 0.8117 (ppp) REVERT: D 162 ASN cc_start: 0.6905 (m110) cc_final: 0.6602 (p0) REVERT: D 220 LYS cc_start: 0.5447 (mmtm) cc_final: 0.5102 (mmtm) REVERT: D 236 GLU cc_start: 0.7360 (mp0) cc_final: 0.6754 (mp0) REVERT: D 254 LYS cc_start: 0.7396 (tppp) cc_final: 0.7122 (tppt) REVERT: E 24 LEU cc_start: 0.7631 (mp) cc_final: 0.7269 (mp) REVERT: E 30 ARG cc_start: 0.6979 (mmm-85) cc_final: 0.6713 (mmm-85) REVERT: E 35 ASP cc_start: 0.7071 (m-30) cc_final: 0.6434 (m-30) REVERT: E 61 ASP cc_start: 0.7808 (t70) cc_final: 0.7132 (t70) REVERT: E 69 HIS cc_start: 0.7769 (t70) cc_final: 0.7542 (t70) REVERT: E 157 HIS cc_start: 0.8642 (m90) cc_final: 0.7632 (m-70) REVERT: E 158 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8092 (mm-40) REVERT: E 161 LYS cc_start: 0.8381 (mttt) cc_final: 0.7861 (mttt) REVERT: E 162 ASN cc_start: 0.8663 (m110) cc_final: 0.8319 (p0) REVERT: E 195 THR cc_start: 0.8104 (m) cc_final: 0.7370 (t) REVERT: E 206 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6707 (tm-30) REVERT: E 210 ILE cc_start: 0.8362 (mm) cc_final: 0.8072 (mt) REVERT: E 225 TYR cc_start: 0.6987 (t80) cc_final: 0.5986 (t80) REVERT: E 226 TYR cc_start: 0.6658 (p90) cc_final: 0.5951 (p90) REVERT: E 237 TRP cc_start: 0.6234 (m100) cc_final: 0.5848 (m100) REVERT: E 270 LYS cc_start: 0.6745 (mtpt) cc_final: 0.6278 (mtpt) REVERT: E 271 PHE cc_start: 0.7912 (m-80) cc_final: 0.7298 (m-80) REVERT: F 64 GLN cc_start: 0.6561 (tp40) cc_final: 0.6224 (tp40) REVERT: F 70 TYR cc_start: 0.7342 (t80) cc_final: 0.7088 (t80) REVERT: F 98 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7178 (pt0) REVERT: F 129 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7364 (mp10) REVERT: F 157 HIS cc_start: 0.8634 (m90) cc_final: 0.8399 (m90) REVERT: F 162 ASN cc_start: 0.8774 (m-40) cc_final: 0.8431 (p0) REVERT: F 164 LEU cc_start: 0.9114 (mt) cc_final: 0.8820 (pp) REVERT: F 206 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7385 (tp30) REVERT: F 241 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7834 (m) REVERT: F 254 LYS cc_start: 0.8116 (tptt) cc_final: 0.7877 (tptt) REVERT: G 11 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8109 (tp30) REVERT: G 150 GLN cc_start: 0.8140 (mm110) cc_final: 0.7603 (mm110) REVERT: G 155 ARG cc_start: 0.8405 (pmt170) cc_final: 0.7860 (tpt170) REVERT: H 63 TRP cc_start: 0.6883 (m100) cc_final: 0.6413 (m100) REVERT: H 87 TYR cc_start: 0.6982 (t80) cc_final: 0.6374 (t80) REVERT: H 132 MET cc_start: 0.7800 (tpt) cc_final: 0.7094 (tpt) REVERT: H 161 LYS cc_start: 0.8486 (mttt) cc_final: 0.8161 (ptpt) REVERT: H 164 LEU cc_start: 0.8088 (mt) cc_final: 0.7768 (tp) REVERT: H 188 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8109 (mmtm) REVERT: H 201 PHE cc_start: 0.8363 (t80) cc_final: 0.7981 (t80) REVERT: H 205 LYS cc_start: 0.8829 (mmmm) cc_final: 0.8332 (mmmm) REVERT: H 251 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6532 (mp) REVERT: H 262 LEU cc_start: 0.7416 (mm) cc_final: 0.7002 (mm) REVERT: R 368 LEU cc_start: 0.4379 (OUTLIER) cc_final: 0.4085 (mm) REVERT: R 418 MET cc_start: 0.7385 (ppp) cc_final: 0.6952 (ppp) REVERT: Q 360 LYS cc_start: 0.5742 (ptpp) cc_final: 0.5317 (ptpp) REVERT: Q 387 MET cc_start: 0.7189 (tpp) cc_final: 0.6891 (mmm) REVERT: Q 418 MET cc_start: 0.7507 (ppp) cc_final: 0.7055 (ppp) REVERT: I 72 ASP cc_start: 0.7342 (t70) cc_final: 0.7030 (t70) REVERT: I 80 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7403 (tm-30) REVERT: I 109 MET cc_start: 0.7095 (ttt) cc_final: 0.6409 (ttt) REVERT: I 183 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7160 (mt) REVERT: I 206 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6758 (tm-30) REVERT: I 238 GLN cc_start: 0.7746 (tm-30) cc_final: 0.6761 (tm-30) REVERT: I 242 GLN cc_start: 0.6875 (tt0) cc_final: 0.6650 (tt0) REVERT: I 262 LEU cc_start: 0.6716 (mm) cc_final: 0.6399 (mm) REVERT: J 92 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7708 (mtpp) REVERT: J 94 GLU cc_start: 0.7150 (pp20) cc_final: 0.6657 (pp20) REVERT: J 98 GLU cc_start: 0.6939 (tp30) cc_final: 0.6711 (tp30) REVERT: J 129 GLN cc_start: 0.7757 (tt0) cc_final: 0.7200 (mt0) REVERT: J 206 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6941 (tp30) REVERT: K 11 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6409 (mm-30) REVERT: K 109 MET cc_start: 0.8066 (tpp) cc_final: 0.7399 (pmm) REVERT: K 198 MET cc_start: 0.7287 (pmm) cc_final: 0.7029 (pmm) REVERT: L 104 MET cc_start: 0.5428 (mmp) cc_final: 0.5075 (mmp) REVERT: L 133 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7991 (mmmt) REVERT: L 155 ARG cc_start: 0.8371 (ptp90) cc_final: 0.8121 (mtm110) REVERT: L 220 LYS cc_start: 0.5547 (mmtm) cc_final: 0.5272 (mmtm) REVERT: L 248 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6504 (p0) REVERT: L 260 ARG cc_start: 0.7157 (mmm-85) cc_final: 0.6720 (mmm-85) REVERT: M 35 ASP cc_start: 0.6738 (m-30) cc_final: 0.6373 (m-30) REVERT: M 61 ASP cc_start: 0.7560 (t70) cc_final: 0.6844 (t0) REVERT: M 63 TRP cc_start: 0.6193 (m100) cc_final: 0.5494 (m100) REVERT: M 80 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7457 (tm-30) REVERT: M 99 PHE cc_start: 0.8128 (m-80) cc_final: 0.7148 (m-80) REVERT: M 132 MET cc_start: 0.8950 (ttt) cc_final: 0.8407 (ttt) REVERT: M 195 THR cc_start: 0.7815 (m) cc_final: 0.7073 (t) REVERT: M 259 ASP cc_start: 0.7921 (t0) cc_final: 0.7521 (t0) REVERT: M 267 LYS cc_start: 0.7723 (tptt) cc_final: 0.7515 (tppt) REVERT: N 61 ASP cc_start: 0.6423 (t70) cc_final: 0.5988 (t70) REVERT: N 78 TRP cc_start: 0.7902 (m100) cc_final: 0.6859 (m100) REVERT: N 107 TYR cc_start: 0.8135 (t80) cc_final: 0.7126 (t80) REVERT: N 165 GLU cc_start: 0.8244 (mp0) cc_final: 0.7582 (mp0) REVERT: N 206 GLU cc_start: 0.7790 (tp30) cc_final: 0.7537 (tp30) REVERT: N 213 GLN cc_start: 0.7376 (pp30) cc_final: 0.7047 (pp30) REVERT: N 241 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7918 (p) REVERT: N 254 LYS cc_start: 0.7673 (tptt) cc_final: 0.7460 (tptt) REVERT: N 260 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.6279 (mtm-85) REVERT: O 11 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8146 (mm-30) REVERT: O 110 PHE cc_start: 0.6796 (m-80) cc_final: 0.6319 (m-80) REVERT: O 132 MET cc_start: 0.8197 (mpp) cc_final: 0.7696 (mpp) REVERT: O 198 MET cc_start: 0.8504 (tpt) cc_final: 0.8193 (tpt) REVERT: O 201 PHE cc_start: 0.8796 (t80) cc_final: 0.8272 (t80) REVERT: P 63 TRP cc_start: 0.6792 (m100) cc_final: 0.5266 (m100) REVERT: P 87 TYR cc_start: 0.6103 (t80) cc_final: 0.5669 (t80) REVERT: P 132 MET cc_start: 0.8170 (tpt) cc_final: 0.7282 (tpt) REVERT: P 186 ASN cc_start: 0.8702 (m-40) cc_final: 0.8448 (t0) REVERT: P 188 LYS cc_start: 0.7354 (mmtm) cc_final: 0.6799 (mmtm) REVERT: P 201 PHE cc_start: 0.8420 (t80) cc_final: 0.8117 (t80) REVERT: P 230 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.5364 (tptm) REVERT: P 251 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6819 (mp) REVERT: P 276 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7829 (mmtt) outliers start: 101 outliers final: 79 residues processed: 871 average time/residue: 0.4861 time to fit residues: 665.9656 Evaluate side-chains 915 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 824 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 211 GLN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 198 MET Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 248 ASP Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 3.9990 chunk 389 optimal weight: 0.0870 chunk 237 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 270 optimal weight: 20.0000 chunk 408 optimal weight: 1.9990 chunk 375 optimal weight: 6.9990 chunk 325 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 199 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS D 208 GLN D 213 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36705 Z= 0.226 Angle : 0.653 17.664 50248 Z= 0.335 Chirality : 0.044 0.176 5432 Planarity : 0.004 0.051 5969 Dihedral : 16.829 145.424 5791 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.77 % Allowed : 19.65 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3971 helix: 1.18 (0.12), residues: 1874 sheet: 0.06 (0.19), residues: 722 loop : -1.12 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 78 HIS 0.016 0.001 HIS M 139 PHE 0.040 0.001 PHE N 99 TYR 0.029 0.001 TYR F 70 ARG 0.009 0.000 ARG K 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 838 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 TRP cc_start: 0.4793 (m100) cc_final: 0.4154 (m100) REVERT: A 72 ASP cc_start: 0.7503 (t70) cc_final: 0.7075 (t70) REVERT: A 138 GLU cc_start: 0.7071 (mp0) cc_final: 0.6607 (mp0) REVERT: A 165 GLU cc_start: 0.7499 (tp30) cc_final: 0.7163 (tp30) REVERT: A 183 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7294 (mt) REVERT: A 223 PHE cc_start: 0.8151 (m-80) cc_final: 0.7345 (m-80) REVERT: A 238 GLN cc_start: 0.7772 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 262 LEU cc_start: 0.7328 (mm) cc_final: 0.6928 (mt) REVERT: B 94 GLU cc_start: 0.7102 (pp20) cc_final: 0.6607 (pp20) REVERT: B 118 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7221 (p0) REVERT: B 124 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7830 (m) REVERT: B 140 THR cc_start: 0.8108 (m) cc_final: 0.7603 (p) REVERT: B 185 LEU cc_start: 0.7640 (mt) cc_final: 0.7209 (mp) REVERT: B 206 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7108 (tp30) REVERT: B 208 GLN cc_start: 0.7498 (tt0) cc_final: 0.7238 (tt0) REVERT: C 9 GLU cc_start: 0.7430 (tp30) cc_final: 0.7223 (tp30) REVERT: C 24 LEU cc_start: 0.7906 (mm) cc_final: 0.7613 (mp) REVERT: C 25 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7104 (tm-30) REVERT: C 104 MET cc_start: 0.6334 (ppp) cc_final: 0.5599 (ppp) REVERT: C 105 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7594 (ttpp) REVERT: C 198 MET cc_start: 0.8390 (tpt) cc_final: 0.8152 (tpt) REVERT: C 203 PHE cc_start: 0.7290 (t80) cc_final: 0.6867 (t80) REVERT: C 204 ASN cc_start: 0.8500 (m-40) cc_final: 0.7924 (m-40) REVERT: C 207 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6588 (pm20) REVERT: C 245 TRP cc_start: 0.7894 (m-90) cc_final: 0.7445 (m-90) REVERT: D 70 TYR cc_start: 0.7306 (t80) cc_final: 0.7076 (t80) REVERT: D 103 THR cc_start: 0.6999 (t) cc_final: 0.6336 (p) REVERT: D 104 MET cc_start: 0.6817 (mmp) cc_final: 0.5909 (mmp) REVERT: D 109 MET cc_start: 0.7176 (tpt) cc_final: 0.6808 (tmm) REVERT: D 132 MET cc_start: 0.8395 (ppp) cc_final: 0.8148 (ppp) REVERT: D 162 ASN cc_start: 0.7109 (m110) cc_final: 0.6793 (p0) REVERT: D 220 LYS cc_start: 0.5482 (mmtm) cc_final: 0.5160 (mmtm) REVERT: D 236 GLU cc_start: 0.7368 (mp0) cc_final: 0.6769 (mp0) REVERT: D 254 LYS cc_start: 0.7464 (tppp) cc_final: 0.7203 (tppt) REVERT: E 24 LEU cc_start: 0.7574 (mp) cc_final: 0.7339 (mp) REVERT: E 30 ARG cc_start: 0.7188 (mmm-85) cc_final: 0.6885 (mmm-85) REVERT: E 35 ASP cc_start: 0.7083 (m-30) cc_final: 0.6465 (m-30) REVERT: E 61 ASP cc_start: 0.7850 (t70) cc_final: 0.7214 (t70) REVERT: E 69 HIS cc_start: 0.7775 (t70) cc_final: 0.7544 (t70) REVERT: E 97 GLN cc_start: 0.8826 (pm20) cc_final: 0.8604 (pm20) REVERT: E 157 HIS cc_start: 0.8637 (m90) cc_final: 0.7586 (m-70) REVERT: E 158 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8095 (mm-40) REVERT: E 161 LYS cc_start: 0.8401 (mttt) cc_final: 0.7796 (mttt) REVERT: E 195 THR cc_start: 0.8107 (m) cc_final: 0.7376 (t) REVERT: E 206 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6807 (tm-30) REVERT: E 225 TYR cc_start: 0.7036 (t80) cc_final: 0.6047 (t80) REVERT: E 226 TYR cc_start: 0.6708 (p90) cc_final: 0.6366 (p90) REVERT: E 237 TRP cc_start: 0.6257 (m100) cc_final: 0.5794 (m100) REVERT: E 270 LYS cc_start: 0.6723 (mtpt) cc_final: 0.6271 (mtpt) REVERT: E 271 PHE cc_start: 0.7943 (m-80) cc_final: 0.7480 (m-80) REVERT: F 64 GLN cc_start: 0.6558 (tp40) cc_final: 0.6221 (tp40) REVERT: F 70 TYR cc_start: 0.7434 (t80) cc_final: 0.7117 (t80) REVERT: F 98 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7200 (pt0) REVERT: F 129 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7358 (mp10) REVERT: F 157 HIS cc_start: 0.8775 (m90) cc_final: 0.8459 (m90) REVERT: F 162 ASN cc_start: 0.8778 (m-40) cc_final: 0.8432 (p0) REVERT: F 164 LEU cc_start: 0.9120 (mt) cc_final: 0.8879 (pp) REVERT: F 241 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7986 (m) REVERT: F 254 LYS cc_start: 0.8112 (tptt) cc_final: 0.7768 (tptt) REVERT: G 150 GLN cc_start: 0.8194 (mm110) cc_final: 0.7644 (mm110) REVERT: G 155 ARG cc_start: 0.8406 (pmt170) cc_final: 0.7892 (tpt170) REVERT: H 63 TRP cc_start: 0.6873 (m100) cc_final: 0.6384 (m100) REVERT: H 87 TYR cc_start: 0.7043 (t80) cc_final: 0.6516 (t80) REVERT: H 132 MET cc_start: 0.7810 (tpt) cc_final: 0.7097 (tpt) REVERT: H 161 LYS cc_start: 0.8510 (mttt) cc_final: 0.8157 (mttt) REVERT: H 164 LEU cc_start: 0.8104 (mt) cc_final: 0.7798 (tp) REVERT: H 188 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8101 (mmtm) REVERT: H 201 PHE cc_start: 0.8375 (t80) cc_final: 0.7994 (t80) REVERT: H 205 LYS cc_start: 0.8837 (mmmm) cc_final: 0.8335 (mmmm) REVERT: H 208 GLN cc_start: 0.8175 (tp40) cc_final: 0.7810 (tp40) REVERT: H 251 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6606 (mp) REVERT: H 262 LEU cc_start: 0.7433 (mm) cc_final: 0.7017 (mm) REVERT: R 368 LEU cc_start: 0.4393 (OUTLIER) cc_final: 0.4096 (mm) REVERT: R 418 MET cc_start: 0.7390 (ppp) cc_final: 0.6954 (ppp) REVERT: Q 360 LYS cc_start: 0.5751 (ptpp) cc_final: 0.5328 (ptpp) REVERT: Q 387 MET cc_start: 0.7208 (tpp) cc_final: 0.6897 (mmm) REVERT: Q 418 MET cc_start: 0.7512 (ppp) cc_final: 0.7063 (ppp) REVERT: I 72 ASP cc_start: 0.7352 (t70) cc_final: 0.7024 (t70) REVERT: I 80 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7435 (tm-30) REVERT: I 109 MET cc_start: 0.7102 (ttt) cc_final: 0.6393 (ttt) REVERT: I 183 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7165 (mt) REVERT: I 238 GLN cc_start: 0.7769 (tm-30) cc_final: 0.6829 (tm-30) REVERT: I 262 LEU cc_start: 0.6804 (mm) cc_final: 0.6491 (mm) REVERT: J 6 PRO cc_start: 0.5829 (Cg_exo) cc_final: 0.5559 (Cg_endo) REVERT: J 92 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7712 (mtpp) REVERT: J 94 GLU cc_start: 0.7149 (pp20) cc_final: 0.6643 (pp20) REVERT: J 98 GLU cc_start: 0.6970 (tp30) cc_final: 0.6741 (tp30) REVERT: J 129 GLN cc_start: 0.7752 (tt0) cc_final: 0.7303 (mt0) REVERT: J 206 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6962 (tp30) REVERT: K 11 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6444 (mm-30) REVERT: K 109 MET cc_start: 0.8094 (tpp) cc_final: 0.7463 (pmm) REVERT: K 198 MET cc_start: 0.7246 (pmm) cc_final: 0.6991 (pmm) REVERT: L 104 MET cc_start: 0.5498 (mmp) cc_final: 0.5157 (mmp) REVERT: L 133 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8131 (mmmt) REVERT: L 155 ARG cc_start: 0.8382 (ptp90) cc_final: 0.8129 (mtm110) REVERT: L 220 LYS cc_start: 0.5579 (mmtm) cc_final: 0.5300 (mmtm) REVERT: L 238 GLN cc_start: 0.8560 (mt0) cc_final: 0.8167 (mt0) REVERT: L 248 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6494 (p0) REVERT: L 260 ARG cc_start: 0.7181 (mmm-85) cc_final: 0.6677 (mmm-85) REVERT: M 15 TRP cc_start: 0.7038 (m100) cc_final: 0.6776 (m-10) REVERT: M 35 ASP cc_start: 0.6845 (m-30) cc_final: 0.6511 (m-30) REVERT: M 61 ASP cc_start: 0.7429 (t70) cc_final: 0.6736 (t0) REVERT: M 63 TRP cc_start: 0.6548 (m100) cc_final: 0.5664 (m100) REVERT: M 80 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7401 (tm-30) REVERT: M 99 PHE cc_start: 0.8134 (m-80) cc_final: 0.7160 (m-80) REVERT: M 132 MET cc_start: 0.8924 (ttt) cc_final: 0.8563 (ttt) REVERT: M 195 THR cc_start: 0.7982 (m) cc_final: 0.7149 (t) REVERT: M 206 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6653 (tm-30) REVERT: M 259 ASP cc_start: 0.7964 (t0) cc_final: 0.7581 (t0) REVERT: M 267 LYS cc_start: 0.7731 (tptt) cc_final: 0.7526 (tppt) REVERT: N 61 ASP cc_start: 0.6486 (t70) cc_final: 0.6040 (t70) REVERT: N 78 TRP cc_start: 0.7960 (m100) cc_final: 0.6883 (m100) REVERT: N 165 GLU cc_start: 0.8251 (mp0) cc_final: 0.7846 (mp0) REVERT: N 166 LYS cc_start: 0.8828 (mppt) cc_final: 0.7885 (mppt) REVERT: N 206 GLU cc_start: 0.7809 (tp30) cc_final: 0.7518 (tp30) REVERT: N 213 GLN cc_start: 0.7386 (pp30) cc_final: 0.7053 (pp30) REVERT: N 241 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7966 (p) REVERT: N 254 LYS cc_start: 0.7666 (tptt) cc_final: 0.7447 (tptt) REVERT: N 260 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6286 (mtm-85) REVERT: O 11 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8147 (mm-30) REVERT: O 110 PHE cc_start: 0.6840 (m-80) cc_final: 0.6428 (m-10) REVERT: O 132 MET cc_start: 0.8194 (mpp) cc_final: 0.7694 (mpp) REVERT: O 198 MET cc_start: 0.8479 (tpt) cc_final: 0.8228 (tpt) REVERT: O 201 PHE cc_start: 0.8818 (t80) cc_final: 0.8339 (t80) REVERT: P 63 TRP cc_start: 0.6747 (m100) cc_final: 0.5188 (m100) REVERT: P 87 TYR cc_start: 0.6107 (t80) cc_final: 0.5666 (t80) REVERT: P 132 MET cc_start: 0.8257 (tpt) cc_final: 0.7354 (tpt) REVERT: P 186 ASN cc_start: 0.8692 (m-40) cc_final: 0.8467 (t0) REVERT: P 188 LYS cc_start: 0.7334 (mmtm) cc_final: 0.6773 (mmtm) REVERT: P 201 PHE cc_start: 0.8372 (t80) cc_final: 0.8150 (t80) REVERT: P 230 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.5391 (tptm) REVERT: P 276 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7902 (mmtt) outliers start: 98 outliers final: 82 residues processed: 881 average time/residue: 0.4842 time to fit residues: 672.7828 Evaluate side-chains 921 residues out of total 3537 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 828 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 148 GLN Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 198 MET Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 248 ASP Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 0.7980 chunk 346 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 0.0770 chunk 325 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 334 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.240653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.183428 restraints weight = 63947.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.189000 restraints weight = 29466.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.189471 restraints weight = 20290.249| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 36705 Z= 0.321 Angle : 0.771 58.914 50248 Z= 0.426 Chirality : 0.045 0.671 5432 Planarity : 0.005 0.143 5969 Dihedral : 16.830 145.418 5791 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.80 % Allowed : 19.71 % Favored : 77.50 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 3971 helix: 1.18 (0.12), residues: 1874 sheet: 0.05 (0.19), residues: 722 loop : -1.12 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 78 HIS 0.216 0.002 HIS F 69 PHE 0.037 0.001 PHE N 99 TYR 0.023 0.002 TYR F 70 ARG 0.007 0.000 ARG K 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10416.33 seconds wall clock time: 186 minutes 15.32 seconds (11175.32 seconds total)