Starting phenix.real_space_refine on Tue Sep 15 17:49:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s28_54481/09_2026/9s28_54481.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s28_54481/09_2026/9s28_54481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s28_54481/09_2026/9s28_54481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s28_54481/09_2026/9s28_54481.map" model { file = "/net/cci-nas-00/data/ceres_data/9s28_54481/09_2026/9s28_54481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s28_54481/09_2026/9s28_54481.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.039 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 14 6.06 5 P 138 5.49 5 S 194 5.16 5 C 25996 2.51 5 N 7354 2.21 5 O 7994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41690 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2223 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 261} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1630 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2150 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1734 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2180 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 254} Chain breaks: 1 Chain: "F" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2010 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 4 Chain: "H" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2091 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain breaks: 2 Chain: "I" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2223 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 261} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1630 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "K" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2150 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1734 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "M" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2180 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 254} Chain breaks: 1 Chain: "N" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2010 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 4 Chain: "P" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2091 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain breaks: 2 Chain: "a" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "b" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 79} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "d" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 646 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "e" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "g" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 79} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "j" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 646 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "k" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "T" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} 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: "W" 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: "X" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} 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: 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: "H" 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} Chain: "P" 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 40 115.900 125.061 56.645 1.00 40.63 S ATOM 350 SG CYS A 43 112.723 122.846 57.426 1.00 38.81 S ATOM 2538 SG CYS B 40 24.850 140.439 75.182 1.00198.93 S ATOM 2559 SG CYS B 43 26.554 142.260 72.200 1.00191.23 S ATOM 4182 SG CYS C 40 55.495 164.599 46.565 1.00 42.21 S ATOM 4203 SG CYS C 43 52.580 162.577 48.231 1.00 32.68 S ATOM 8066 SG CYS E 40 134.082 133.940 82.771 1.00 86.18 S ATOM 8087 SG CYS E 43 131.841 135.986 85.264 1.00 83.17 S ATOM 10233 SG CYS F 40 115.454 167.002 47.962 1.00143.93 S ATOM 10254 SG CYS F 43 118.493 168.819 49.537 1.00148.04 S ATOM 12382 SG CYS G 40 139.364 190.874 86.240 1.00191.27 S ATOM 12403 SG CYS G 43 138.791 189.018 82.876 1.00200.03 S ATOM 14378 SG CYS H 40 106.974 220.711 62.268 1.00289.74 S ATOM 14399 SG CYS H 43 104.487 217.873 63.046 1.00295.79 S ATOM 16483 SG CYS I 40 57.001 108.646 56.638 1.00 38.76 S ATOM 16504 SG CYS I 43 60.179 110.864 57.408 1.00 35.92 S ATOM 18692 SG CYS J 40 148.080 93.269 75.253 1.00203.89 S ATOM 18713 SG CYS J 43 146.425 91.429 72.259 1.00195.22 S ATOM 20336 SG CYS K 40 117.411 69.084 46.584 1.00 43.13 S ATOM 20357 SG CYS K 43 120.315 71.107 48.263 1.00 32.22 S ATOM 24220 SG CYS M 40 38.839 99.763 82.778 1.00 86.80 S ATOM 24241 SG CYS M 43 41.077 97.711 85.274 1.00 83.54 S ATOM 26387 SG CYS N 40 57.549 66.699 47.985 1.00 59.22 S ATOM 26408 SG CYS N 43 54.514 64.871 49.554 1.00 52.46 S ATOM 28536 SG CYS O 40 33.608 42.831 86.262 1.00184.87 S ATOM 28557 SG CYS O 43 34.184 44.697 82.902 1.00196.06 S ATOM 30532 SG CYS P 40 66.037 12.988 62.331 1.00291.39 S ATOM 30553 SG CYS P 43 68.520 15.827 63.113 1.00297.74 S Time building chain proxies: 10.94, per 1000 atoms: 0.26 Number of scatterers: 41690 At special positions: 0 Unit cell: (174.8, 234.65, 120.65, 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 14 29.99 S 194 16.00 P 138 15.00 O 7994 8.00 N 7354 7.00 C 25996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 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 40 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 16 " 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=" ND1 HIS E 16 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 43 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 12 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 16 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " 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 H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " 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 40 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 43 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 16 " 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 40 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 43 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 12 " pdb="ZN ZN N 301 " - pdb=" ND1 HIS N 16 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 43 " 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 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 12 " pdb="ZN ZN P 301 " - pdb=" ND1 HIS P 16 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 40 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 43 " Number of angles added : 22 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9028 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 52 sheets defined 55.4% alpha, 14.2% beta 64 base pairs and 117 stacking pairs defined. Time for finding SS restraints: 4.92 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 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.519A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 196 through 214 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 removed outlier: 3.795A pdb=" N ASN B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.863A pdb=" N MET B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.540A pdb=" N GLN B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 196 through 215 removed outlier: 3.920A pdb=" N LYS B 215 " --> pdb=" O GLN B 211 " (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 removed outlier: 3.635A pdb=" N ASN C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 removed outlier: 3.550A pdb=" N TYR C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.888A pdb=" N GLN C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 166 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 Processing helix chain 'C' and resid 196 through 210 removed outlier: 3.979A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 removed outlier: 4.172A pdb=" N SER C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 173 through 187 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 215 through 220 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 39 Processing helix chain 'E' and resid 40 through 46 removed outlier: 3.702A pdb=" N GLU E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 125 through 135 Processing helix chain 'E' and resid 146 through 168 Processing helix chain 'E' and resid 173 through 187 Processing helix chain 'E' and resid 196 through 220 removed outlier: 3.526A pdb=" N GLN E 212 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS E 220 " --> pdb=" O SER E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 16 removed outlier: 3.572A pdb=" N ALA F 8 " --> pdb=" O ASN F 4 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 95 through 110 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'F' and resid 146 through 168 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 196 through 214 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 Processing helix chain 'G' and resid 95 through 109 removed outlier: 3.745A pdb=" N MET G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET G 109 " --> pdb=" O LYS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 134 removed outlier: 3.977A pdb=" N MET G 132 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 168 removed outlier: 3.503A pdb=" N GLN G 150 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 187 Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.545A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 16 Processing helix chain 'H' and resid 18 through 27 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 95 through 109 removed outlier: 3.973A pdb=" N MET H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 135 Processing helix chain 'H' and resid 152 through 167 Processing helix chain 'H' and resid 173 through 187 Processing helix chain 'H' and resid 196 through 213 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 Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 125 through 136 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 removed outlier: 3.521A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 166 " --> pdb=" O ASN I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 187 Processing helix chain 'I' and resid 196 through 214 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 removed outlier: 3.803A pdb=" N ASN J 46 " --> pdb=" O VAL J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 110 removed outlier: 3.856A pdb=" N MET J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 146 through 168 removed outlier: 3.559A pdb=" N GLN J 150 " --> pdb=" O ASN J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'J' and resid 196 through 215 removed outlier: 3.936A pdb=" N LYS J 215 " --> pdb=" O GLN J 211 " (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 removed outlier: 3.651A pdb=" N ASN K 46 " --> pdb=" O VAL K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 107 removed outlier: 3.550A pdb=" N TYR K 107 " --> pdb=" O THR K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 136 Processing helix chain 'K' and resid 146 through 166 removed outlier: 3.884A pdb=" N GLN K 150 " --> pdb=" O ASN K 146 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS K 166 " --> pdb=" O ASN K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 Processing helix chain 'K' and resid 196 through 210 removed outlier: 3.969A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 removed outlier: 4.160A pdb=" N SER K 214 " --> pdb=" O ILE K 210 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU K 219 " --> pdb=" O LYS K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 269 No H-bonds generated for 'chain 'K' and resid 267 through 269' Processing helix chain 'L' and resid 95 through 110 Processing helix chain 'L' and resid 125 through 136 Processing helix chain 'L' and resid 146 through 168 Processing helix chain 'L' and resid 173 through 187 Processing helix chain 'L' and resid 197 through 211 Processing helix chain 'L' and resid 215 through 220 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 39 Processing helix chain 'M' and resid 40 through 46 removed outlier: 3.719A pdb=" N GLU M 45 " --> pdb=" O ASP M 41 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 110 Processing helix chain 'M' and resid 125 through 135 Processing helix chain 'M' and resid 146 through 168 Processing helix chain 'M' and resid 173 through 187 Processing helix chain 'M' and resid 196 through 220 removed outlier: 3.528A pdb=" N GLN M 212 " --> pdb=" O GLN M 208 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN M 213 " --> pdb=" O ARG M 209 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS M 220 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 16 removed outlier: 3.561A pdb=" N ALA N 8 " --> pdb=" O ASN N 4 " (cutoff:3.500A) 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 Processing helix chain 'N' and resid 95 through 110 Processing helix chain 'N' and resid 125 through 135 Processing helix chain 'N' and resid 146 through 168 Processing helix chain 'N' and resid 169 through 171 No H-bonds generated for 'chain 'N' and resid 169 through 171' Processing helix chain 'N' and resid 173 through 187 Processing helix chain 'N' and resid 196 through 214 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 Processing helix chain 'O' and resid 95 through 109 removed outlier: 3.741A pdb=" N MET O 104 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET O 109 " --> pdb=" O LYS O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 134 removed outlier: 3.975A pdb=" N MET O 132 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS O 133 " --> pdb=" O GLN O 129 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 168 removed outlier: 3.503A pdb=" N GLN O 150 " --> pdb=" O ASN O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 187 Processing helix chain 'O' and resid 196 through 211 removed outlier: 3.543A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 16 Processing helix chain 'P' and resid 18 through 27 Processing helix chain 'P' and resid 29 through 40 Processing helix chain 'P' and resid 40 through 45 Processing helix chain 'P' and resid 95 through 109 removed outlier: 3.975A pdb=" N MET P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 135 Processing helix chain 'P' and resid 152 through 167 Processing helix chain 'P' and resid 173 through 187 Processing helix chain 'P' and resid 196 through 213 removed outlier: 3.503A pdb=" N GLN P 213 " --> pdb=" O ARG P 209 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 363 Processing helix chain 'a' and resid 364 through 368 removed outlier: 3.666A pdb=" N LEU a 368 " --> pdb=" O ILE a 365 " (cutoff:3.500A) Processing helix chain 'a' and resid 369 through 382 Processing helix chain 'a' and resid 386 through 393 Processing helix chain 'a' and resid 393 through 404 Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'b' and resid 348 through 363 Processing helix chain 'b' and resid 364 through 368 removed outlier: 3.741A pdb=" N LEU b 368 " --> pdb=" O ILE b 365 " (cutoff:3.500A) Processing helix chain 'b' and resid 369 through 382 Processing helix chain 'b' and resid 386 through 393 Processing helix chain 'b' and resid 393 through 404 Processing helix chain 'b' and resid 409 through 425 Processing helix chain 'c' and resid 348 through 363 Processing helix chain 'c' and resid 364 through 368 removed outlier: 3.937A pdb=" N LEU c 368 " --> pdb=" O ILE c 365 " (cutoff:3.500A) Processing helix chain 'c' and resid 369 through 383 removed outlier: 3.521A pdb=" N LEU c 383 " --> pdb=" O GLU c 379 " (cutoff:3.500A) Processing helix chain 'c' and resid 386 through 393 Processing helix chain 'c' and resid 393 through 404 Processing helix chain 'c' and resid 409 through 426 Processing helix chain 'd' and resid 348 through 363 Processing helix chain 'd' and resid 364 through 368 removed outlier: 3.590A pdb=" N LEU d 368 " --> pdb=" O ILE d 365 " (cutoff:3.500A) Processing helix chain 'd' and resid 370 through 383 Processing helix chain 'd' and resid 386 through 393 Processing helix chain 'd' and resid 393 through 404 Processing helix chain 'd' and resid 409 through 424 Processing helix chain 'e' and resid 348 through 362 Processing helix chain 'e' and resid 369 through 382 Processing helix chain 'e' and resid 386 through 392 removed outlier: 3.542A pdb=" N LYS e 392 " --> pdb=" O GLN e 388 " (cutoff:3.500A) Processing helix chain 'e' and resid 393 through 404 Processing helix chain 'e' and resid 409 through 426 Processing helix chain 'g' and resid 348 through 363 Processing helix chain 'g' and resid 364 through 368 removed outlier: 3.670A pdb=" N LEU g 368 " --> pdb=" O ILE g 365 " (cutoff:3.500A) Processing helix chain 'g' and resid 369 through 382 Processing helix chain 'g' and resid 386 through 393 Processing helix chain 'g' and resid 393 through 404 Processing helix chain 'g' and resid 409 through 426 Processing helix chain 'h' and resid 348 through 363 Processing helix chain 'h' and resid 364 through 368 removed outlier: 3.739A pdb=" N LEU h 368 " --> pdb=" O ILE h 365 " (cutoff:3.500A) Processing helix chain 'h' and resid 369 through 382 Processing helix chain 'h' and resid 386 through 393 Processing helix chain 'h' and resid 393 through 404 Processing helix chain 'h' and resid 409 through 425 Processing helix chain 'i' and resid 348 through 363 Processing helix chain 'i' and resid 364 through 368 removed outlier: 3.941A pdb=" N LEU i 368 " --> pdb=" O ILE i 365 " (cutoff:3.500A) Processing helix chain 'i' and resid 369 through 383 Processing helix chain 'i' and resid 386 through 393 Processing helix chain 'i' and resid 393 through 404 Processing helix chain 'i' and resid 409 through 426 Processing helix chain 'j' and resid 348 through 363 Processing helix chain 'j' and resid 364 through 368 removed outlier: 3.592A pdb=" N LEU j 368 " --> pdb=" O ILE j 365 " (cutoff:3.500A) Processing helix chain 'j' and resid 370 through 383 Processing helix chain 'j' and resid 386 through 393 Processing helix chain 'j' and resid 393 through 404 Processing helix chain 'j' and resid 409 through 424 Processing helix chain 'k' and resid 348 through 362 Processing helix chain 'k' and resid 369 through 382 Processing helix chain 'k' and resid 386 through 392 removed outlier: 3.532A pdb=" N LYS k 392 " --> pdb=" O GLN k 388 " (cutoff:3.500A) Processing helix chain 'k' and resid 393 through 404 Processing helix chain 'k' and resid 409 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 91 removed outlier: 4.212A pdb=" N ILE A 74 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 115 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 265 removed outlier: 4.140A pdb=" N TRP A 245 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LYS A 254 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL A 243 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 91 removed outlier: 4.175A pdb=" N ILE B 74 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 91 removed outlier: 4.332A pdb=" N ILE C 74 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP C 63 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 115 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.169A pdb=" N CYS C 224 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 250 through 254 Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 91 removed outlier: 3.583A pdb=" N GLU D 89 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 76 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 140 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER D 117 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 242 removed outlier: 5.954A pdb=" N CYS D 224 " --> pdb=" O PRO D 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 245 through 246 removed outlier: 3.830A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 86 through 91 removed outlier: 4.293A pdb=" N ILE E 74 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU E 115 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 233 through 242 removed outlier: 5.649A pdb=" N LYS E 230 " --> pdb=" O PRO E 234 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLU E 236 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR E 228 " --> pdb=" O GLU E 236 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS E 224 " --> pdb=" O PRO E 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 245 through 246 removed outlier: 3.883A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 252 " --> pdb=" O TRP E 245 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG E 260 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 86 through 91 removed outlier: 4.071A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER F 117 " --> pdb=" O THR F 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 238 through 242 removed outlier: 6.171A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB8, first strand: chain 'F' and resid 245 through 246 removed outlier: 3.523A pdb=" N TRP F 245 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 63 through 70 removed outlier: 4.214A pdb=" N ILE G 74 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 114 through 117 Processing sheet with id=AC2, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.245A pdb=" N CYS G 224 " --> pdb=" O PRO G 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 251 through 255 Processing sheet with id=AC4, first strand: chain 'H' and resid 86 through 91 removed outlier: 4.173A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 241 through 242 removed outlier: 3.794A pdb=" N LYS H 270 " --> pdb=" O TYR H 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AC7, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.879A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 86 through 91 removed outlier: 4.221A pdb=" N ILE I 74 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU I 115 " --> pdb=" O THR I 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 260 through 265 removed outlier: 4.195A pdb=" N TRP I 245 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LYS I 254 " --> pdb=" O VAL I 243 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL I 243 " --> pdb=" O LYS I 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=AD2, first strand: chain 'J' and resid 86 through 91 removed outlier: 4.170A pdb=" N ILE J 74 " --> pdb=" O VAL J 91 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 86 through 91 removed outlier: 4.332A pdb=" N ILE K 74 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP K 63 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU K 115 " --> pdb=" O THR K 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 238 through 242 removed outlier: 6.182A pdb=" N CYS K 224 " --> pdb=" O PRO K 240 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 245 through 246 removed outlier: 4.004A pdb=" N TRP K 245 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.570A pdb=" N GLU L 89 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU L 76 " --> pdb=" O GLU L 89 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 140 " --> pdb=" O LEU L 115 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER L 117 " --> pdb=" O THR L 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 238 through 242 removed outlier: 5.956A pdb=" N CYS L 224 " --> pdb=" O PRO L 240 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 245 through 246 removed outlier: 3.824A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 86 through 91 removed outlier: 4.300A pdb=" N ILE M 74 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU M 115 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 233 through 242 removed outlier: 5.642A pdb=" N LYS M 230 " --> pdb=" O PRO M 234 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU M 236 " --> pdb=" O THR M 228 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR M 228 " --> pdb=" O GLU M 236 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS M 224 " --> pdb=" O PRO M 240 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 245 through 246 removed outlier: 3.882A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL M 252 " --> pdb=" O TRP M 245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG M 260 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 86 through 91 removed outlier: 4.073A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER N 117 " --> pdb=" O THR N 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 238 through 242 removed outlier: 6.183A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AE6, first strand: chain 'N' and resid 245 through 246 removed outlier: 3.527A pdb=" N TRP N 245 " --> pdb=" O VAL N 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 63 through 70 removed outlier: 4.213A pdb=" N ILE O 74 " --> pdb=" O VAL O 91 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 114 through 117 Processing sheet with id=AE9, first strand: chain 'O' and resid 238 through 241 removed outlier: 6.241A pdb=" N CYS O 224 " --> pdb=" O PRO O 240 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 251 through 255 Processing sheet with id=AF2, first strand: chain 'P' and resid 86 through 91 removed outlier: 4.174A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 241 through 242 removed outlier: 3.805A pdb=" N LYS P 270 " --> pdb=" O TYR P 225 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 229 through 230 Processing sheet with id=AF5, first strand: chain 'P' and resid 245 through 246 removed outlier: 3.886A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'e' and resid 363 through 364 removed outlier: 4.361A pdb=" N LYS e 364 " --> pdb=" O ASN e 367 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'k' and resid 363 through 364 removed outlier: 4.363A pdb=" N LYS k 364 " --> pdb=" O ASN k 367 " (cutoff:3.500A) 2165 hydrogen bonds defined for protein. 6345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 168 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 117 stacking parallelities Total time for adding SS restraints: 10.01 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10527 1.33 - 1.45: 8479 1.45 - 1.57: 23218 1.57 - 1.69: 272 1.69 - 1.81: 336 Bond restraints: 42832 Sorted by residual: bond pdb=" C3' DT U 19 " pdb=" C2' DT U 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT T 19 " pdb=" C2' DT T 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA Z 36 " pdb=" C2' DA Z 36 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 bond pdb=" C3' DA X 33 " pdb=" C2' DA X 33 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.93e+00 bond pdb=" C3' DA X 36 " pdb=" C2' DA X 36 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.68e+00 ... (remaining 42827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 57336 1.41 - 2.81: 954 2.81 - 4.22: 99 4.22 - 5.62: 30 5.62 - 7.03: 9 Bond angle restraints: 58428 Sorted by residual: angle pdb=" O4' DA X 19 " pdb=" C4' DA X 19 " pdb=" C3' DA X 19 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" O4' DA Z 19 " pdb=" C4' DA Z 19 " pdb=" C3' DA Z 19 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" N3 DT X 15 " pdb=" C4 DT X 15 " pdb=" O4 DT X 15 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT Z 15 " pdb=" C4 DT Z 15 " pdb=" O4 DT Z 15 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT Y 15 " pdb=" C4 DT Y 15 " pdb=" O4 DT Y 15 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 58423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 24546 29.56 - 59.13: 874 59.13 - 88.69: 34 88.69 - 118.26: 2 118.26 - 147.82: 2 Dihedral angle restraints: 25458 sinusoidal: 11556 harmonic: 13902 Sorted by residual: dihedral pdb=" CA PRO E 273 " pdb=" C PRO E 273 " pdb=" N PRO E 274 " pdb=" CA PRO E 274 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA PRO M 273 " pdb=" C PRO M 273 " pdb=" N PRO M 274 " pdb=" CA PRO M 274 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA CYS N 224 " pdb=" C CYS N 224 " pdb=" N TYR N 225 " pdb=" CA TYR N 225 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 25455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3897 0.028 - 0.056: 1521 0.056 - 0.083: 551 0.083 - 0.111: 362 0.111 - 0.139: 63 Chirality restraints: 6394 Sorted by residual: chirality pdb=" CA ILE I 251 " pdb=" N ILE I 251 " pdb=" C ILE I 251 " pdb=" CB ILE I 251 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE D 272 " pdb=" N ILE D 272 " pdb=" C ILE D 272 " pdb=" CB ILE D 272 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 6391 not shown) Planarity restraints: 6998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 272 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO M 273 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO M 273 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 273 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 272 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO E 273 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 273 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 273 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C LEU A 160 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 161 " 0.013 2.00e-02 2.50e+03 ... (remaining 6995 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 20264 2.99 - 3.47: 41806 3.47 - 3.95: 68000 3.95 - 4.42: 76395 4.42 - 4.90: 119788 Nonbonded interactions: 326253 Sorted by model distance: nonbonded pdb=" O5' DG Z 23 " pdb=" O4' DG Z 23 " model vdw 2.516 2.432 nonbonded pdb=" O5' DG W 21 " pdb=" O4' DG W 21 " model vdw 2.579 2.432 nonbonded pdb=" O5' DG X 23 " pdb=" O4' DG X 23 " model vdw 2.580 2.432 nonbonded pdb=" O TYR I 107 " pdb=" O PHE I 110 " model vdw 2.585 3.040 nonbonded pdb=" O TYR A 107 " pdb=" O PHE A 110 " model vdw 2.586 3.040 ... (remaining 326248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 71 or resid 301)) selection = (chain 'C' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 271 o \ r resid 301)) selection = (chain 'E' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 71 or resid 301)) selection = (chain 'F' and (resid 2 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 71 or resid 301)) selection = (chain 'G' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or re \ sid 271 through 301)) selection = (chain 'H' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 213 or resid 223 through \ 231 or resid 234 through 265 or resid 267 through 269 or (resid 270 and (name N \ or name CA or name C or name O or name CB )) or resid 271 or resid 301)) selection = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 71 or resid 301)) selection = (chain 'K' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 271 o \ r resid 301)) selection = (chain 'M' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 71 or resid 301)) selection = (chain 'N' and (resid 2 through 45 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 71 or resid 301)) selection = (chain 'O' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 145 or resid 151 through \ 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or re \ sid 271 through 301)) selection = (chain 'P' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 45 or resid 60 through 213 or resid 223 through \ 231 or resid 234 through 265 or resid 267 through 269 or (resid 270 and (name N \ or name CA or name C or name O or name CB )) or resid 271 or resid 301)) } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'X' selection = chain 'Z' } ncs_group { reference = (chain 'a' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'b' and resid 347 through 425) selection = (chain 'c' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'd' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'e' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'g' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'h' and resid 347 through 425) selection = (chain 'i' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'j' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'k' and (resid 347 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 or (resid 407 and (name N or name CA o \ r name C or name O or name CB )) or resid 408 through 425)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 49.690 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.008 0.305 42888 Z= 0.258 Angle : 0.469 10.694 58450 Z= 0.313 Chirality : 0.040 0.139 6394 Planarity : 0.003 0.062 6998 Dihedral : 13.266 147.820 16430 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.14 % Allowed : 4.57 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.13), residues: 4694 helix: 2.75 (0.11), residues: 2452 sheet: 0.93 (0.19), residues: 836 loop : -0.59 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 53 TYR 0.009 0.001 TYR N 225 PHE 0.006 0.001 PHE H 174 TRP 0.013 0.001 TRP I 106 HIS 0.004 0.000 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.21 (42832) covalent geometry : angle 0.44580 / 0.31 (58428) hydrogen bonds : bond 0.12626 / 8.14 ( 2333) hydrogen bonds : angle 4.94879 / 3.58 ( 6681) metal coordination : bond 0.19767 / 13.10 ( 56) metal coordination : angle 7.53173 / 5.44 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 976 time to evaluate : 1.601 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: A 48 MET cc_start: 0.7722 (ptt) cc_final: 0.7305 (mmp) REVERT: A 133 LYS cc_start: 0.8253 (mmmm) cc_final: 0.8028 (mttp) REVERT: B 113 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8672 (mptt) REVERT: B 207 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7136 (mp10) REVERT: C 14 LYS cc_start: 0.7794 (mtpt) cc_final: 0.6392 (ttpt) REVERT: C 61 ASP cc_start: 0.6377 (m-30) cc_final: 0.6156 (m-30) REVERT: D 256 ARG cc_start: 0.7314 (mtp85) cc_final: 0.7097 (mtm-85) REVERT: E 74 ILE cc_start: 0.8999 (mp) cc_final: 0.8734 (mm) REVERT: E 226 TYR cc_start: 0.7573 (p90) cc_final: 0.7192 (p90) REVERT: E 237 TRP cc_start: 0.7175 (m100) cc_final: 0.6065 (m100) REVERT: E 268 ASP cc_start: 0.6697 (m-30) cc_final: 0.6239 (m-30) REVERT: F 70 TYR cc_start: 0.8160 (t80) cc_final: 0.7859 (t80) REVERT: F 162 ASN cc_start: 0.8623 (m110) cc_final: 0.8327 (m-40) REVERT: F 251 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8327 (mm) REVERT: G 132 MET cc_start: 0.7939 (mpp) cc_final: 0.7652 (mtp) REVERT: G 167 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6184 (tt) REVERT: I 48 MET cc_start: 0.7785 (ptt) cc_final: 0.7358 (mmp) REVERT: I 133 LYS cc_start: 0.8282 (mmmm) cc_final: 0.8072 (mtpt) REVERT: J 113 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8675 (mptt) REVERT: J 162 ASN cc_start: 0.7390 (m-40) cc_final: 0.7186 (t0) REVERT: J 207 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: J 212 GLN cc_start: 0.6622 (tt0) cc_final: 0.6407 (tm130) REVERT: K 14 LYS cc_start: 0.7816 (mtpt) cc_final: 0.6476 (ttpt) REVERT: L 256 ARG cc_start: 0.7515 (mtp85) cc_final: 0.7219 (mtm-85) REVERT: M 74 ILE cc_start: 0.8948 (mp) cc_final: 0.8595 (mm) REVERT: M 225 TYR cc_start: 0.7290 (m-80) cc_final: 0.6957 (m-10) REVERT: M 226 TYR cc_start: 0.7538 (p90) cc_final: 0.7178 (p90) REVERT: M 237 TRP cc_start: 0.6990 (m100) cc_final: 0.5937 (m100) REVERT: M 268 ASP cc_start: 0.6739 (m-30) cc_final: 0.6275 (m-30) REVERT: N 251 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8196 (mm) REVERT: O 132 MET cc_start: 0.7982 (mpp) cc_final: 0.7366 (ptp) REVERT: O 167 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.5992 (tm) REVERT: P 182 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9173 (pp) REVERT: a 420 TYR cc_start: 0.8667 (t80) cc_final: 0.8326 (t80) REVERT: c 404 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7623 (ttm170) REVERT: e 379 GLU cc_start: 0.7695 (tt0) cc_final: 0.7005 (tm-30) REVERT: e 402 LYS cc_start: 0.8015 (mttt) cc_final: 0.7543 (mmtm) REVERT: e 407 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7107 (pmtt) REVERT: g 419 LEU cc_start: 0.9235 (mm) cc_final: 0.8775 (mm) REVERT: g 420 TYR cc_start: 0.8566 (t80) cc_final: 0.8286 (t80) REVERT: i 404 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7587 (ttm170) REVERT: k 379 GLU cc_start: 0.7617 (tt0) cc_final: 0.7005 (tm-30) REVERT: k 402 LYS cc_start: 0.7895 (mttt) cc_final: 0.7428 (mmtt) REVERT: k 407 LYS cc_start: 0.7724 (mmtm) cc_final: 0.6989 (pmtt) REVERT: k 415 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8169 (mmmt) outliers start: 48 outliers final: 11 residues processed: 1014 average time/residue: 0.8060 time to fit residues: 989.9380 Evaluate side-chains 655 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 637 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 182 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0980 chunk 470 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 69 HIS A 129 GLN A 157 HIS A 208 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 62 HIS F 116 GLN F 157 HIS G 150 GLN G 212 GLN ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN I 69 HIS I 129 GLN I 157 HIS I 208 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN K 23 HIS ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 238 GLN M 211 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN N 44 GLN N 62 HIS ** N 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 GLN O 212 GLN ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 356 HIS ** k 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.284938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.257572 restraints weight = 50231.449| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 2.02 r_work: 0.4541 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.4507 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 42888 Z= 0.209 Angle : 0.688 14.533 58450 Z= 0.364 Chirality : 0.047 0.384 6394 Planarity : 0.005 0.066 6998 Dihedral : 16.088 143.852 6639 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.05 % Allowed : 12.49 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.12), residues: 4694 helix: 2.36 (0.10), residues: 2454 sheet: 0.63 (0.18), residues: 874 loop : -0.78 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG e 404 TYR 0.017 0.002 TYR B 107 PHE 0.038 0.002 PHE c 423 TRP 0.021 0.002 TRP D 78 HIS 0.023 0.002 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (42832) covalent geometry : angle 0.67148 / 0.36 (58428) hydrogen bonds : bond 0.05073 / 3.35 ( 2333) hydrogen bonds : angle 4.28128 / 3.09 ( 6681) metal coordination : bond 0.05673 / 4.30 ( 56) metal coordination : angle 7.69322 / 5.58 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 670 time to evaluate : 1.567 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: A 30 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7833 (tpt90) REVERT: B 207 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: C 14 LYS cc_start: 0.8256 (mtpt) cc_final: 0.6438 (mttm) REVERT: C 104 MET cc_start: 0.3136 (pp-130) cc_final: 0.2882 (pp-130) REVERT: E 61 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6438 (m-30) REVERT: F 251 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8355 (mm) REVERT: G 229 ARG cc_start: 0.3668 (tpp-160) cc_final: 0.2133 (mmp-170) REVERT: I 30 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7843 (tpt90) REVERT: J 207 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: K 14 LYS cc_start: 0.8240 (mtpt) cc_final: 0.6430 (mttm) REVERT: K 39 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: M 30 ARG cc_start: 0.7430 (tpt-90) cc_final: 0.7134 (tpt-90) REVERT: N 251 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8364 (mm) REVERT: O 229 ARG cc_start: 0.3807 (tpp-160) cc_final: 0.2134 (mmp-170) REVERT: e 358 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6422 (tp30) REVERT: e 407 LYS cc_start: 0.6960 (mmtm) cc_final: 0.5636 (mmtm) REVERT: i 407 LYS cc_start: 0.7706 (tptp) cc_final: 0.7236 (ttpp) REVERT: k 358 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6432 (tp30) REVERT: k 407 LYS cc_start: 0.6966 (mmtm) cc_final: 0.5714 (mmtm) outliers start: 171 outliers final: 59 residues processed: 775 average time/residue: 0.7678 time to fit residues: 725.2336 Evaluate side-chains 646 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 579 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 146 ASN Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 172 ASN Chi-restraints excluded: chain N residue 176 SER Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain b residue 366 ASP Chi-restraints excluded: chain d residue 396 MET Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain k residue 358 GLU Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 184 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 463 optimal weight: 0.6980 chunk 417 optimal weight: 20.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN G 212 GLN ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN H 162 ASN H 204 ASN I 129 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 HIS ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 GLN ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN P 162 ASN P 204 ASN ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 356 HIS k 389 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.284136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.254170 restraints weight = 50227.696| |-----------------------------------------------------------------------------| r_work (start): 0.4820 rms_B_bonded: 2.23 r_work: 0.4510 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.4478 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 42888 Z= 0.178 Angle : 0.669 15.963 58450 Z= 0.349 Chirality : 0.046 0.368 6394 Planarity : 0.005 0.072 6998 Dihedral : 16.157 142.481 6621 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.19 % Allowed : 14.45 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 4694 helix: 2.11 (0.10), residues: 2462 sheet: 0.52 (0.18), residues: 868 loop : -0.88 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG c 404 TYR 0.059 0.002 TYR C 225 PHE 0.046 0.002 PHE i 423 TRP 0.019 0.002 TRP N 15 HIS 0.022 0.002 HIS G 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (42832) covalent geometry : angle 0.65157 / 0.35 (58428) hydrogen bonds : bond 0.04513 / 2.99 ( 2333) hydrogen bonds : angle 4.24276 / 3.07 ( 6681) metal coordination : bond 0.04239 / 3.19 ( 56) metal coordination : angle 7.74740 / 5.55 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 608 time to evaluate : 1.858 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: A 18 ASP cc_start: 0.7910 (p0) cc_final: 0.7627 (p0) REVERT: A 30 ARG cc_start: 0.8028 (ttt-90) cc_final: 0.7816 (tpt90) REVERT: A 162 ASN cc_start: 0.8106 (t0) cc_final: 0.7893 (m-40) REVERT: B 137 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.7997 (pp) REVERT: B 207 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: C 14 LYS cc_start: 0.8301 (mtpt) cc_final: 0.6456 (ttpt) REVERT: C 41 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6652 (p0) REVERT: C 104 MET cc_start: 0.3330 (pp-130) cc_final: 0.3074 (pp-130) REVERT: F 251 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8367 (mm) REVERT: G 229 ARG cc_start: 0.3304 (tpp-160) cc_final: 0.1732 (mmp-170) REVERT: I 9 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8069 (mt-10) REVERT: I 18 ASP cc_start: 0.7986 (p0) cc_final: 0.7708 (p0) REVERT: I 30 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7861 (tpt90) REVERT: I 162 ASN cc_start: 0.8092 (t0) cc_final: 0.7874 (m-40) REVERT: J 137 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.7966 (pp) REVERT: J 207 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: K 14 LYS cc_start: 0.8314 (mtpt) cc_final: 0.6123 (ttpt) REVERT: K 41 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6738 (p0) REVERT: M 30 ARG cc_start: 0.7468 (tpt-90) cc_final: 0.7232 (tpt-90) REVERT: M 61 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6421 (m-30) REVERT: N 251 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8376 (mm) REVERT: O 229 ARG cc_start: 0.3554 (tpp-160) cc_final: 0.2123 (mmp-170) REVERT: c 426 MET cc_start: 0.0822 (ttt) cc_final: 0.0008 (ptt) REVERT: e 358 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6334 (tp30) REVERT: i 407 LYS cc_start: 0.7677 (tptp) cc_final: 0.7207 (ttpp) REVERT: k 358 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6325 (tp30) outliers start: 177 outliers final: 73 residues processed: 728 average time/residue: 0.7198 time to fit residues: 641.5210 Evaluate side-chains 665 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 581 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 225 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 176 SER Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 256 ARG Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain a residue 355 ILE Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain k residue 358 GLU Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 464 optimal weight: 7.9990 chunk 471 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 434 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 185 optimal weight: 30.0000 chunk 405 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 363 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 148 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN G 82 ASN ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN I 129 GLN I 148 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 HIS ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 GLN ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN P 212 GLN d 361 ASN ** e 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 389 GLN k 393 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.282156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.253312 restraints weight = 49704.574| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 2.10 r_work: 0.4509 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.4479 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 42888 Z= 0.286 Angle : 0.767 13.735 58450 Z= 0.405 Chirality : 0.052 0.594 6394 Planarity : 0.005 0.086 6998 Dihedral : 16.416 142.417 6621 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.38 % Allowed : 15.38 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.12), residues: 4694 helix: 1.78 (0.10), residues: 2462 sheet: 0.27 (0.18), residues: 858 loop : -1.05 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 227 TYR 0.027 0.002 TYR H 226 PHE 0.047 0.002 PHE c 423 TRP 0.026 0.002 TRP D 78 HIS 0.025 0.002 HIS K 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.29 (42832) covalent geometry : angle 0.75322 / 0.40 (58428) hydrogen bonds : bond 0.05695 / 3.79 ( 2333) hydrogen bonds : angle 4.40471 / 3.19 ( 6681) metal coordination : bond 0.03945 / 2.71 ( 56) metal coordination : angle 7.43986 / 5.18 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 606 time to evaluate : 1.574 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 48 MET cc_start: 0.8087 (mmp) cc_final: 0.7868 (mmp) REVERT: A 133 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8078 (mtpt) REVERT: A 184 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 208 GLN cc_start: 0.8401 (tt0) cc_final: 0.8052 (mt0) REVERT: C 14 LYS cc_start: 0.8329 (mtpt) cc_final: 0.6465 (ttmt) REVERT: C 41 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6874 (p0) REVERT: C 104 MET cc_start: 0.3222 (pp-130) cc_final: 0.2998 (pp-130) REVERT: E 61 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: F 251 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8376 (mm) REVERT: G 227 ARG cc_start: 0.1895 (mmm160) cc_final: -0.0031 (mpp-170) REVERT: G 229 ARG cc_start: 0.3218 (tpp-160) cc_final: 0.1730 (mmp-170) REVERT: H 139 HIS cc_start: 0.6053 (t-90) cc_final: 0.5681 (t-90) REVERT: I 133 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8057 (mtpt) REVERT: I 184 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8705 (p) REVERT: J 207 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: K 14 LYS cc_start: 0.8293 (mtpt) cc_final: 0.6317 (ttpt) REVERT: K 18 ASP cc_start: 0.7222 (m-30) cc_final: 0.7014 (m-30) REVERT: K 41 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6635 (p0) REVERT: K 104 MET cc_start: 0.3129 (pp-130) cc_final: 0.2918 (pp-130) REVERT: M 61 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: N 251 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8385 (mm) REVERT: O 227 ARG cc_start: 0.1875 (mmm160) cc_final: 0.0323 (mpp-170) REVERT: O 229 ARG cc_start: 0.3157 (tpp-160) cc_final: 0.1880 (mmp-170) REVERT: e 348 MET cc_start: 0.4524 (tmm) cc_final: 0.4174 (tmm) REVERT: e 358 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6414 (tp30) REVERT: i 407 LYS cc_start: 0.7708 (tptp) cc_final: 0.7176 (ttpp) REVERT: k 358 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6387 (tp30) outliers start: 185 outliers final: 97 residues processed: 732 average time/residue: 0.7462 time to fit residues: 665.7157 Evaluate side-chains 677 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 567 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 184 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 205 LYS Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 256 ARG Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain a residue 386 THR Chi-restraints excluded: chain a residue 419 LEU Chi-restraints excluded: chain c residue 394 THR Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain e residue 407 LYS Chi-restraints excluded: chain g residue 419 LEU Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain j residue 361 ASN Chi-restraints excluded: chain k residue 358 GLU Chi-restraints excluded: chain k residue 374 ILE Chi-restraints excluded: chain k residue 407 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 178 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 336 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 301 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 372 optimal weight: 8.9990 chunk 383 optimal weight: 0.9980 chunk 349 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 432 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN I 46 ASN I 129 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN ** M 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN P 162 ASN ** a 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 356 HIS e 393 HIS j 361 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.282363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.254703 restraints weight = 49846.968| |-----------------------------------------------------------------------------| r_work (start): 0.4820 rms_B_bonded: 1.99 r_work: 0.4512 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.4481 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 42888 Z= 0.292 Angle : 0.777 14.803 58450 Z= 0.407 Chirality : 0.053 0.648 6394 Planarity : 0.005 0.071 6998 Dihedral : 16.468 134.701 6621 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.57 % Allowed : 16.52 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 4694 helix: 1.62 (0.10), residues: 2476 sheet: 0.19 (0.18), residues: 858 loop : -1.12 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG c 404 TYR 0.039 0.002 TYR C 225 PHE 0.035 0.002 PHE g 423 TRP 0.022 0.002 TRP A 78 HIS 0.018 0.002 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.29 (42832) covalent geometry : angle 0.76429 / 0.41 (58428) hydrogen bonds : bond 0.05656 / 3.78 ( 2333) hydrogen bonds : angle 4.44396 / 3.23 ( 6681) metal coordination : bond 0.03685 / 2.54 ( 56) metal coordination : angle 7.11231 / 4.92 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 591 time to evaluate : 1.418 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: A 48 MET cc_start: 0.8136 (mmp) cc_final: 0.7926 (mmp) REVERT: A 184 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8702 (p) REVERT: C 14 LYS cc_start: 0.8277 (mtpt) cc_final: 0.6243 (ttpt) REVERT: C 104 MET cc_start: 0.3226 (pp-130) cc_final: 0.2999 (pp-130) REVERT: C 225 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.4967 (t80) REVERT: D 104 MET cc_start: 0.3214 (pp-130) cc_final: 0.2782 (pp-130) REVERT: E 61 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.6557 (m-30) REVERT: F 80 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6415 (tt0) REVERT: F 251 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8410 (mm) REVERT: H 139 HIS cc_start: 0.6055 (t-90) cc_final: 0.5664 (t-90) REVERT: I 184 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8701 (p) REVERT: K 14 LYS cc_start: 0.8291 (mtpt) cc_final: 0.6249 (ttpt) REVERT: K 104 MET cc_start: 0.3126 (pp-130) cc_final: 0.2891 (pp-130) REVERT: M 61 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: N 133 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7742 (tppt) REVERT: N 251 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8386 (mm) REVERT: c 426 MET cc_start: -0.0320 (ptt) cc_final: -0.0623 (ttt) REVERT: e 358 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6488 (tp30) REVERT: i 426 MET cc_start: 0.1325 (tmt) cc_final: 0.0009 (ptt) REVERT: k 358 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6433 (tp30) outliers start: 193 outliers final: 106 residues processed: 729 average time/residue: 0.7367 time to fit residues: 656.5931 Evaluate side-chains 675 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 558 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 184 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 205 LYS Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain a residue 355 ILE Chi-restraints excluded: chain a residue 359 ILE Chi-restraints excluded: chain a residue 386 THR Chi-restraints excluded: chain b residue 366 ASP Chi-restraints excluded: chain c residue 394 THR Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain e residue 374 ILE Chi-restraints excluded: chain g residue 355 ILE Chi-restraints excluded: chain g residue 359 ILE Chi-restraints excluded: chain i residue 386 THR Chi-restraints excluded: chain i residue 408 VAL Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain k residue 358 GLU Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 10 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 398 optimal weight: 50.0000 chunk 95 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 312 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN I 129 GLN I 207 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 162 ASN ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN ** a 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.282865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.255293 restraints weight = 50077.911| |-----------------------------------------------------------------------------| r_work (start): 0.4822 rms_B_bonded: 1.97 r_work: 0.4519 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.4481 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 42888 Z= 0.227 Angle : 0.745 14.804 58450 Z= 0.386 Chirality : 0.049 0.547 6394 Planarity : 0.005 0.085 6998 Dihedral : 16.402 125.452 6621 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.48 % Allowed : 17.70 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.12), residues: 4694 helix: 1.65 (0.10), residues: 2474 sheet: 0.16 (0.18), residues: 862 loop : -1.11 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 209 TYR 0.022 0.002 TYR a 420 PHE 0.051 0.002 PHE c 423 TRP 0.025 0.002 TRP N 15 HIS 0.012 0.002 HIS K 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (42832) covalent geometry : angle 0.73366 / 0.39 (58428) hydrogen bonds : bond 0.05015 / 3.34 ( 2333) hydrogen bonds : angle 4.38650 / 3.19 ( 6681) metal coordination : bond 0.03375 / 2.48 ( 56) metal coordination : angle 6.57168 / 4.58 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 579 time to evaluate : 1.597 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: A 10 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7412 (pp20) REVERT: C 14 LYS cc_start: 0.8282 (mtpt) cc_final: 0.6339 (ttpt) REVERT: C 104 MET cc_start: 0.3225 (pp-130) cc_final: 0.3006 (pp-130) REVERT: D 104 MET cc_start: 0.3149 (pp-130) cc_final: 0.2948 (pp-130) REVERT: E 61 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: F 61 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: F 133 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7756 (tppt) REVERT: F 251 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8412 (mm) REVERT: H 139 HIS cc_start: 0.5981 (t-90) cc_final: 0.5608 (t-90) REVERT: I 222 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6819 (mtm-85) REVERT: K 14 LYS cc_start: 0.8245 (mtpt) cc_final: 0.6321 (ttpt) REVERT: K 41 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6579 (p0) REVERT: K 104 MET cc_start: 0.3193 (pp-130) cc_final: 0.2936 (pp-130) REVERT: M 30 ARG cc_start: 0.7477 (tpt-90) cc_final: 0.7276 (tpt90) REVERT: M 61 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: N 61 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: N 80 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: N 133 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7722 (tppt) REVERT: N 251 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8402 (mm) REVERT: c 426 MET cc_start: -0.0449 (ptt) cc_final: -0.0930 (ttt) REVERT: e 358 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6440 (tp30) REVERT: i 426 MET cc_start: 0.1036 (tmt) cc_final: -0.0161 (ptt) REVERT: k 358 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6422 (tp30) outliers start: 189 outliers final: 105 residues processed: 711 average time/residue: 0.7470 time to fit residues: 651.1385 Evaluate side-chains 665 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 546 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 222 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 205 LYS Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain a residue 355 ILE Chi-restraints excluded: chain c residue 386 THR Chi-restraints excluded: chain c residue 394 THR Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain e residue 374 ILE Chi-restraints excluded: chain e residue 407 LYS Chi-restraints excluded: chain g residue 355 ILE Chi-restraints excluded: chain i residue 386 THR Chi-restraints excluded: chain i residue 394 THR Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain k residue 358 GLU Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 116 optimal weight: 20.0000 chunk 445 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 421 optimal weight: 9.9990 chunk 451 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 208 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 GLN I 129 GLN I 208 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 HIS ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN ** c 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.270716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.258601 restraints weight = 47522.507| |-----------------------------------------------------------------------------| r_work (start): 0.4808 rms_B_bonded: 0.73 r_work: 0.4570 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.4544 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.4473 rms_B_bonded: 2.69 restraints_weight: 0.1250 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 42888 Z= 0.343 Angle : 0.850 14.438 58450 Z= 0.441 Chirality : 0.055 0.660 6394 Planarity : 0.006 0.074 6998 Dihedral : 16.535 116.673 6621 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.57 % Allowed : 18.55 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.12), residues: 4694 helix: 1.47 (0.11), residues: 2464 sheet: 0.04 (0.18), residues: 878 loop : -1.18 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 209 TYR 0.032 0.002 TYR P 107 PHE 0.047 0.003 PHE g 423 TRP 0.032 0.003 TRP N 15 HIS 0.019 0.002 HIS G 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.34 (42832) covalent geometry : angle 0.83974 / 0.44 (58428) hydrogen bonds : bond 0.06126 / 4.10 ( 2333) hydrogen bonds : angle 4.54832 / 3.30 ( 6681) metal coordination : bond 0.03678 / 2.45 ( 56) metal coordination : angle 6.84131 / 4.62 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 547 time to evaluate : 1.578 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: A 184 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8688 (p) REVERT: D 104 MET cc_start: 0.2883 (pp-130) cc_final: 0.2673 (pp-130) REVERT: E 164 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6654 (tt) REVERT: F 80 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6221 (mm-30) REVERT: F 133 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7289 (tppt) REVERT: F 251 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8333 (mm) REVERT: I 184 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8692 (p) REVERT: I 222 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6832 (mtm-85) REVERT: K 14 LYS cc_start: 0.8261 (mtpt) cc_final: 0.6191 (ttpt) REVERT: M 61 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6450 (m-30) REVERT: M 164 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6666 (tt) REVERT: N 61 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: N 80 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6192 (mm-30) REVERT: N 133 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7274 (tppt) REVERT: N 251 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8341 (mm) REVERT: e 358 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6312 (tp30) outliers start: 193 outliers final: 121 residues processed: 683 average time/residue: 0.7422 time to fit residues: 621.4418 Evaluate side-chains 668 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 533 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 123 PHE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 156 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 184 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 222 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 205 LYS Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 256 ARG Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain a residue 353 GLN Chi-restraints excluded: chain c residue 370 VAL Chi-restraints excluded: chain c residue 386 THR Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain e residue 374 ILE Chi-restraints excluded: chain e residue 407 LYS Chi-restraints excluded: chain e residue 419 LEU Chi-restraints excluded: chain g residue 353 GLN Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain k residue 370 VAL Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 202 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 335 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 456 optimal weight: 40.0000 chunk 388 optimal weight: 20.0000 chunk 286 optimal weight: 0.0870 chunk 459 optimal weight: 7.9990 chunk 294 optimal weight: 7.9990 overall best weight: 1.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 208 GLN I 129 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.283423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.258210 restraints weight = 49041.333| |-----------------------------------------------------------------------------| r_work (start): 0.4873 rms_B_bonded: 1.70 r_work: 0.4602 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4570 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.4570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 42888 Z= 0.217 Angle : 0.783 17.228 58450 Z= 0.401 Chirality : 0.050 0.519 6394 Planarity : 0.005 0.085 6998 Dihedral : 16.425 121.660 6621 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.03 % Allowed : 19.55 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 4694 helix: 1.52 (0.10), residues: 2462 sheet: 0.12 (0.18), residues: 876 loop : -1.14 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG K 209 TYR 0.032 0.002 TYR P 107 PHE 0.058 0.002 PHE C 110 TRP 0.040 0.002 TRP N 15 HIS 0.013 0.001 HIS K 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (42832) covalent geometry : angle 0.77376 / 0.40 (58428) hydrogen bonds : bond 0.04911 / 3.26 ( 2333) hydrogen bonds : angle 4.46377 / 3.24 ( 6681) metal coordination : bond 0.03109 / 2.24 ( 56) metal coordination : angle 6.39325 / 4.41 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 578 time to evaluate : 1.662 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: B 72 ASP cc_start: 0.7537 (p0) cc_final: 0.7334 (p0) REVERT: C 14 LYS cc_start: 0.8253 (mtpt) cc_final: 0.6154 (ttpt) REVERT: D 104 MET cc_start: 0.3126 (pp-130) cc_final: 0.2857 (pp-130) REVERT: F 61 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: F 80 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: F 133 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7652 (tppt) REVERT: F 251 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8375 (mm) REVERT: I 222 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6834 (mtm-85) REVERT: K 14 LYS cc_start: 0.8245 (mtpt) cc_final: 0.6310 (ttpt) REVERT: M 61 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: N 61 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: N 80 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: N 133 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7697 (tppt) REVERT: N 251 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8403 (mm) REVERT: O 227 ARG cc_start: 0.1539 (mmm160) cc_final: -0.0251 (mpp-170) REVERT: e 358 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6450 (tp30) outliers start: 170 outliers final: 111 residues processed: 701 average time/residue: 0.7027 time to fit residues: 605.2492 Evaluate side-chains 667 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 545 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 222 ARG Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 205 LYS Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 256 ARG Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain a residue 353 GLN Chi-restraints excluded: chain b residue 366 ASP Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain e residue 399 THR Chi-restraints excluded: chain e residue 407 LYS Chi-restraints excluded: chain e residue 419 LEU Chi-restraints excluded: chain g residue 353 GLN Chi-restraints excluded: chain i residue 394 THR Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 122 optimal weight: 0.0570 chunk 265 optimal weight: 0.0570 chunk 166 optimal weight: 7.9990 chunk 425 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 overall best weight: 1.1418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN A 207 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 208 GLN I 129 GLN I 207 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.284549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.259583 restraints weight = 49096.194| |-----------------------------------------------------------------------------| r_work (start): 0.4881 rms_B_bonded: 1.74 r_work: 0.4611 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4584 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 42888 Z= 0.176 Angle : 0.786 17.396 58450 Z= 0.397 Chirality : 0.048 0.412 6394 Planarity : 0.005 0.080 6998 Dihedral : 16.357 128.165 6621 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.22 % Allowed : 20.83 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4694 helix: 1.52 (0.10), residues: 2472 sheet: 0.16 (0.18), residues: 882 loop : -1.06 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG a 404 TYR 0.033 0.002 TYR P 107 PHE 0.051 0.002 PHE i 423 TRP 0.050 0.002 TRP N 15 HIS 0.018 0.001 HIS O 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (42832) covalent geometry : angle 0.77664 / 0.40 (58428) hydrogen bonds : bond 0.04449 / 2.95 ( 2333) hydrogen bonds : angle 4.42080 / 3.21 ( 6681) metal coordination : bond 0.02848 / 2.15 ( 56) metal coordination : angle 6.11615 / 4.24 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 563 time to evaluate : 1.582 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: C 14 LYS cc_start: 0.8201 (mtpt) cc_final: 0.6417 (ttpt) REVERT: D 104 MET cc_start: 0.3093 (pp-130) cc_final: 0.2857 (pp-130) REVERT: F 80 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6479 (tt0) REVERT: F 133 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7641 (tppt) REVERT: F 251 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8332 (mm) REVERT: I 184 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8640 (p) REVERT: K 14 LYS cc_start: 0.8183 (mtpt) cc_final: 0.6177 (ttpt) REVERT: M 61 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6450 (m-30) REVERT: N 61 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: N 80 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6310 (mm-30) REVERT: N 133 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7715 (tppt) REVERT: N 251 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8355 (mm) REVERT: e 358 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6379 (tp30) REVERT: k 370 VAL cc_start: 0.8151 (t) cc_final: 0.7943 (m) outliers start: 136 outliers final: 91 residues processed: 665 average time/residue: 0.7465 time to fit residues: 608.7684 Evaluate side-chains 646 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 545 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 256 ARG Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 184 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 69 HIS Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 256 ARG Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain a residue 353 GLN Chi-restraints excluded: chain b residue 366 ASP Chi-restraints excluded: chain c residue 370 VAL Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain e residue 358 GLU Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain e residue 399 THR Chi-restraints excluded: chain e residue 407 LYS Chi-restraints excluded: chain e residue 419 LEU Chi-restraints excluded: chain g residue 353 GLN Chi-restraints excluded: chain i residue 394 THR Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 96 optimal weight: 1.9990 chunk 232 optimal weight: 0.1980 chunk 408 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 452 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 467 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 406 optimal weight: 7.9990 chunk 428 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 208 GLN I 129 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN d 356 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.277815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.250940 restraints weight = 49300.945| |-----------------------------------------------------------------------------| r_work (start): 0.4860 rms_B_bonded: 1.89 r_work: 0.4568 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4539 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 42888 Z= 0.217 Angle : 0.830 16.851 58450 Z= 0.421 Chirality : 0.050 0.447 6394 Planarity : 0.005 0.123 6998 Dihedral : 16.408 128.877 6621 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.96 % Allowed : 21.23 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 4694 helix: 1.41 (0.10), residues: 2474 sheet: 0.10 (0.18), residues: 876 loop : -1.09 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG C 209 TYR 0.033 0.002 TYR P 107 PHE 0.049 0.002 PHE a 423 TRP 0.058 0.002 TRP N 15 HIS 0.011 0.001 HIS K 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (42832) covalent geometry : angle 0.82182 / 0.42 (58428) hydrogen bonds : bond 0.04910 / 3.26 ( 2333) hydrogen bonds : angle 4.49282 / 3.27 ( 6681) metal coordination : bond 0.03019 / 2.18 ( 56) metal coordination : angle 6.22148 / 4.23 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 566 time to evaluate : 1.637 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: C 14 LYS cc_start: 0.8213 (mtpt) cc_final: 0.6296 (ttpt) REVERT: D 104 MET cc_start: 0.3157 (pp-130) cc_final: 0.2902 (pp-130) REVERT: F 80 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6579 (tt0) REVERT: F 251 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8343 (mm) REVERT: I 184 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8658 (p) REVERT: K 14 LYS cc_start: 0.8152 (mtpt) cc_final: 0.6342 (ttpt) REVERT: M 61 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6481 (m-30) REVERT: N 61 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: N 80 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6300 (mm-30) REVERT: N 133 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7751 (tppt) REVERT: N 251 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8362 (mm) REVERT: g 353 GLN cc_start: 0.6593 (pp30) cc_final: 0.6301 (pp30) outliers start: 125 outliers final: 99 residues processed: 662 average time/residue: 0.7671 time to fit residues: 618.4851 Evaluate side-chains 644 residues out of total 4246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 537 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 172 ASN Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 114 SER Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 184 THR Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 205 LYS Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 171 PHE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 269 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 46 ASN Chi-restraints excluded: chain M residue 61 ASP Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 69 HIS Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 256 ARG Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 123 PHE Chi-restraints excluded: chain O residue 162 ASN Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain a residue 353 GLN Chi-restraints excluded: chain b residue 366 ASP Chi-restraints excluded: chain c residue 370 VAL Chi-restraints excluded: chain c residue 409 SER Chi-restraints excluded: chain e residue 370 VAL Chi-restraints excluded: chain e residue 399 THR Chi-restraints excluded: chain e residue 407 LYS Chi-restraints excluded: chain e residue 419 LEU Chi-restraints excluded: chain i residue 409 SER Chi-restraints excluded: chain k residue 374 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 467 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 374 optimal weight: 8.9990 chunk 436 optimal weight: 9.9990 chunk 391 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN H 208 GLN I 129 GLN I 207 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 HIS ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN ** O 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.277978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.251317 restraints weight = 49576.184| |-----------------------------------------------------------------------------| r_work (start): 0.4868 rms_B_bonded: 1.88 r_work: 0.4576 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4548 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 42888 Z= 0.203 Angle : 0.830 17.116 58450 Z= 0.422 Chirality : 0.050 0.415 6394 Planarity : 0.005 0.086 6998 Dihedral : 16.402 129.649 6621 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 3.20 % Allowed : 21.26 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4694 helix: 1.37 (0.10), residues: 2476 sheet: 0.10 (0.18), residues: 876 loop : -1.10 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG a 404 TYR 0.034 0.002 TYR P 107 PHE 0.057 0.002 PHE g 423 TRP 0.059 0.002 TRP N 15 HIS 0.018 0.001 HIS G 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (42832) covalent geometry : angle 0.82134 / 0.42 (58428) hydrogen bonds : bond 0.04774 / 3.17 ( 2333) hydrogen bonds : angle 4.52344 / 3.29 ( 6681) metal coordination : bond 0.03128 / 2.34 ( 56) metal coordination : angle 6.12773 / 4.24 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17387.51 seconds wall clock time: 296 minutes 35.13 seconds (17795.13 seconds total)