Starting phenix.real_space_refine on Mon Mar 25 19:31:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/03_2024/6ruo_10007.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/03_2024/6ruo_10007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/03_2024/6ruo_10007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/03_2024/6ruo_10007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/03_2024/6ruo_10007.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ruo_10007/03_2024/6ruo_10007.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 8 6.06 5 P 92 5.49 5 S 236 5.16 5 C 31988 2.51 5 N 8763 2.21 5 O 9705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q ARG 504": "NH1" <-> "NH2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "S ARG 44": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 221": "NH1" <-> "NH2" Residue "S ARG 257": "NH1" <-> "NH2" Residue "S PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 407": "NH1" <-> "NH2" Residue "S ARG 419": "NH1" <-> "NH2" Residue "S ARG 434": "NH1" <-> "NH2" Residue "S ARG 472": "NH1" <-> "NH2" Residue "S ARG 484": "NH1" <-> "NH2" Residue "S ARG 542": "NH1" <-> "NH2" Residue "S ARG 746": "NH1" <-> "NH2" Residue "S ARG 762": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R ARG 381": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "R ARG 441": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50792 Number of models: 1 Model: "" Number of chains: 26 Chain: "Q" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3572 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 11567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1465, 11567 Classifications: {'peptide': 1465} Link IDs: {'PTRANS': 59, 'TRANS': 1405} Chain breaks: 7 Chain: "B" Number of atoms: 9371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9371 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3807 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "T" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1000 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "U" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 901 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" 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 4867 SG CYS A 62 90.882 68.643 55.402 1.00206.29 S ATOM 4886 SG CYS A 65 89.578 65.457 57.326 1.00205.70 S ATOM 5212 SG CYS A 105 134.340 48.337 75.164 1.00154.29 S ATOM 6011 SG CYS A 233 135.160 47.348 78.508 1.00161.07 S ATOM 6033 SG CYS A 236 138.325 48.700 76.465 1.00166.28 S ATOM 24674 SG CYS B1107 96.660 52.213 61.717 1.00158.67 S ATOM 33644 SG CYS I 13 143.904 105.020 128.253 1.00115.67 S ATOM 33764 SG CYS I 30 145.997 103.005 126.084 1.00123.44 S ATOM 34192 SG CYS I 86 76.281 54.749 130.493 1.00225.37 S ATOM 34214 SG CYS I 89 77.100 52.066 133.433 1.00242.90 S ATOM 34431 SG CYS I 117 80.251 53.517 130.865 1.00251.09 S ATOM 34555 SG CYS J 7 49.375 96.408 110.539 1.00 70.94 S ATOM 34578 SG CYS J 10 45.423 95.930 110.617 1.00 66.58 S ATOM 34858 SG CYS J 45 48.117 94.746 113.566 1.00 69.06 S ATOM 34864 SG CYS J 46 46.232 98.565 113.791 1.00 72.08 S ATOM 35930 SG CYS L 31 73.782 121.659 83.281 1.00 76.67 S ATOM 35950 SG CYS L 34 72.689 125.018 84.119 1.00 80.79 S ATOM 36054 SG CYS L 48 73.546 123.447 80.102 1.00 77.73 S ATOM 36077 SG CYS L 51 76.187 124.354 83.963 1.00 71.94 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 22.77, per 1000 atoms: 0.45 Number of scatterers: 50792 At special positions: 0 Unit cell: (166.32, 215.16, 174.24, 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 8 29.99 S 236 16.00 P 92 15.00 O 9705 8.00 N 8763 7.00 C 31988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.54 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 117 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 12 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11548 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 65 sheets defined 35.8% alpha, 10.7% beta 11 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 17.32 Creating SS restraints... Processing helix chain 'Q' and resid 100 through 122 removed outlier: 3.819A pdb=" N SER Q 107 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Q 112 " --> pdb=" O PHE Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 147 removed outlier: 3.969A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE Q 135 " --> pdb=" O HIS Q 131 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE Q 136 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE Q 140 " --> pdb=" O ILE Q 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU Q 141 " --> pdb=" O TRP Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 172 removed outlier: 3.580A pdb=" N THR Q 161 " --> pdb=" O HIS Q 157 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE Q 162 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER Q 169 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 183 Processing helix chain 'Q' and resid 208 through 216 removed outlier: 3.559A pdb=" N ILE Q 214 " --> pdb=" O TYR Q 210 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU Q 216 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 237 removed outlier: 3.562A pdb=" N LYS Q 229 " --> pdb=" O GLN Q 225 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE Q 230 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 261 removed outlier: 3.570A pdb=" N LEU Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYS Q 255 " --> pdb=" O GLY Q 251 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU Q 256 " --> pdb=" O LEU Q 252 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 277 removed outlier: 4.015A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS Q 271 " --> pdb=" O TYR Q 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.942A pdb=" N LEU Q 307 " --> pdb=" O GLU Q 303 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER Q 308 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE Q 314 " --> pdb=" O PHE Q 310 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN Q 315 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 332 Processing helix chain 'Q' and resid 334 through 339 Processing helix chain 'Q' and resid 344 through 357 removed outlier: 3.519A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL Q 355 " --> pdb=" O ASN Q 351 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR Q 357 " --> pdb=" O VAL Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 369 Processing helix chain 'Q' and resid 372 through 386 removed outlier: 3.896A pdb=" N GLU Q 376 " --> pdb=" O GLU Q 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Q 378 " --> pdb=" O THR Q 374 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS Q 383 " --> pdb=" O LYS Q 379 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Q 384 " --> pdb=" O TRP Q 380 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE Q 385 " --> pdb=" O MET Q 381 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU Q 386 " --> pdb=" O GLU Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 407 through 414 Processing helix chain 'Q' and resid 441 through 446 Processing helix chain 'Q' and resid 471 through 491 removed outlier: 3.531A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU Q 479 " --> pdb=" O ALA Q 475 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA Q 484 " --> pdb=" O LEU Q 480 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Q 488 " --> pdb=" O ALA Q 484 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP Q 490 " --> pdb=" O GLN Q 486 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE Q 491 " --> pdb=" O LEU Q 487 " (cutoff:3.500A) Processing helix chain 'Q' and resid 494 through 504 removed outlier: 3.700A pdb=" N CYS Q 501 " --> pdb=" O GLN Q 497 " (cutoff:3.500A) Processing helix chain 'Q' and resid 505 through 514 removed outlier: 3.893A pdb=" N HIS Q 511 " --> pdb=" O ASN Q 507 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Q 512 " --> pdb=" O ALA Q 508 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET Q 513 " --> pdb=" O CYS Q 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.679A pdb=" N LEU A 54 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.588A pdb=" N TYR A 95 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.681A pdb=" N VAL A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.900A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.615A pdb=" N ASN A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.592A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 4.027A pdb=" N ARG A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.560A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 removed outlier: 4.005A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.524A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.958A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 4.142A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.744A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 430 through 439 removed outlier: 3.629A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.920A pdb=" N VAL A 503 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.401A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.626A pdb=" N LYS A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 4.058A pdb=" N HIS A 571 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.527A pdb=" N THR A 621 " --> pdb=" O HIS A 617 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 622' Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.621A pdb=" N ALA A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.913A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.562A pdb=" N GLN A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.685A pdb=" N TRP A 760 " --> pdb=" O ASN A 757 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 761 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 794 through 799 removed outlier: 3.958A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.990A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.737A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.511A pdb=" N LYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 874 through 884 removed outlier: 4.019A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 912 removed outlier: 3.709A pdb=" N ILE A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 937 through 942 Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1008 through 1013 removed outlier: 3.806A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1024 removed outlier: 4.183A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS A1022 " --> pdb=" O TYR A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1077 Processing helix chain 'A' and resid 1085 through 1089 removed outlier: 3.661A pdb=" N LEU A1089 " --> pdb=" O ILE A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1108 removed outlier: 3.533A pdb=" N THR A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A1107 " --> pdb=" O LYS A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1149 removed outlier: 3.948A pdb=" N LEU A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1177 Processing helix chain 'A' and resid 1186 through 1191 Processing helix chain 'A' and resid 1195 through 1199 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.509A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A1225 " --> pdb=" O ARG A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1257 removed outlier: 3.622A pdb=" N SER A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 Processing helix chain 'A' and resid 1301 through 1306 removed outlier: 3.759A pdb=" N GLU A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.735A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1326 Processing helix chain 'A' and resid 1326 through 1334 removed outlier: 4.251A pdb=" N GLU A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1454 Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.664A pdb=" N ARG A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.156A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1530 Processing helix chain 'A' and resid 1545 through 1553 removed outlier: 4.063A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.636A pdb=" N ASN A1560 " --> pdb=" O GLU A1556 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A1562 " --> pdb=" O ALA A1558 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A1567 " --> pdb=" O VAL A1563 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.876A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.595A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.519A pdb=" N PHE A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A1626 " --> pdb=" O LEU A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.677A pdb=" N ILE A1641 " --> pdb=" O PRO A1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.306A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.586A pdb=" N ILE B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.923A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.557A pdb=" N GLN B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 removed outlier: 3.501A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.502A pdb=" N LYS B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.545A pdb=" N GLY B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.363A pdb=" N GLY B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 4.081A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 404 through 424 removed outlier: 3.725A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 424 " --> pdb=" O TYR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 433 removed outlier: 4.052A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.556A pdb=" N SER B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.626A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 465 " --> pdb=" O MET B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 597 through 613 removed outlier: 3.626A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 613 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.767A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.883A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.883A pdb=" N HIS B 735 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.562A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 795 removed outlier: 3.578A pdb=" N ASP B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 936 removed outlier: 3.577A pdb=" N MET B 936 " --> pdb=" O THR B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.567A pdb=" N PHE B 954 " --> pdb=" O PRO B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.830A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.557A pdb=" N GLY B 997 " --> pdb=" O ALA B 993 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1083 removed outlier: 3.987A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY B1081 " --> pdb=" O ASP B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1093 removed outlier: 3.667A pdb=" N LEU B1093 " --> pdb=" O GLN B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1193 removed outlier: 3.626A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.683A pdb=" N PHE C 40 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.572A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.621A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.030A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.616A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.854A pdb=" N VAL C 255 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 321 through 330 removed outlier: 3.855A pdb=" N GLU C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 removed outlier: 3.536A pdb=" N ASN D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.655A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.907A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.401A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 27 removed outlier: 3.560A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.905A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.546A pdb=" N TYR E 46 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.866A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 104 removed outlier: 3.609A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.847A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 161 through 168 removed outlier: 3.796A pdb=" N TYR E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'F' and resid 58 through 72 removed outlier: 5.193A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.821A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.758A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS G 21 " --> pdb=" O ILE G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.514A pdb=" N VAL G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'J' and resid 14 through 18 removed outlier: 4.047A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 31 through 40 removed outlier: 4.146A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 48 removed outlier: 4.001A pdb=" N ARG J 48 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.558A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.783A pdb=" N ASN K 74 " --> pdb=" O HIS K 70 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 121 removed outlier: 3.784A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 133 removed outlier: 3.554A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU K 127 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'N' and resid 149 through 154 removed outlier: 4.219A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 60 removed outlier: 3.525A pdb=" N ALA O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 78 removed outlier: 4.598A pdb=" N ILE O 74 " --> pdb=" O GLN O 70 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA O 75 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 103 removed outlier: 3.893A pdb=" N LEU O 97 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 112 No H-bonds generated for 'chain 'O' and resid 110 through 112' Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.732A pdb=" N SER O 118 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 147 removed outlier: 3.522A pdb=" N SER O 134 " --> pdb=" O PRO O 130 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE O 147 " --> pdb=" O LEU O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.661A pdb=" N VAL O 154 " --> pdb=" O TRP O 150 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER O 155 " --> pdb=" O TRP O 151 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL O 159 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 178 removed outlier: 4.205A pdb=" N ASP O 174 " --> pdb=" O VAL O 170 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS O 177 " --> pdb=" O HIS O 173 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 197 removed outlier: 4.463A pdb=" N LEU O 194 " --> pdb=" O ILE O 190 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.614A pdb=" N LYS O 207 " --> pdb=" O THR O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 217 removed outlier: 3.579A pdb=" N LEU O 215 " --> pdb=" O TYR O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 236 removed outlier: 3.757A pdb=" N SER O 231 " --> pdb=" O PHE O 227 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU O 233 " --> pdb=" O ILE O 229 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE O 234 " --> pdb=" O TRP O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 246 removed outlier: 4.370A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN O 245 " --> pdb=" O ASP O 241 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 334 removed outlier: 4.205A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 347 removed outlier: 3.881A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL O 339 " --> pdb=" O ILE O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 372 removed outlier: 3.910A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS O 369 " --> pdb=" O THR O 365 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR O 370 " --> pdb=" O THR O 366 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL O 372 " --> pdb=" O PHE O 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 389 removed outlier: 3.762A pdb=" N VAL O 388 " --> pdb=" O ILE O 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER O 389 " --> pdb=" O MET O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 408 removed outlier: 4.084A pdb=" N MET O 396 " --> pdb=" O GLN O 392 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER O 398 " --> pdb=" O GLU O 394 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL O 401 " --> pdb=" O ASP O 397 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR O 402 " --> pdb=" O SER O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 417 through 429 removed outlier: 3.730A pdb=" N GLY O 425 " --> pdb=" O LEU O 421 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 444 removed outlier: 3.735A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 450 Processing helix chain 'O' and resid 466 through 471 removed outlier: 4.228A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS O 471 " --> pdb=" O GLU O 468 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 485 removed outlier: 3.690A pdb=" N ALA O 476 " --> pdb=" O HIS O 472 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA O 479 " --> pdb=" O ALA O 475 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 509 removed outlier: 4.262A pdb=" N PHE O 506 " --> pdb=" O LEU O 502 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 522 through 535 removed outlier: 3.566A pdb=" N ARG O 530 " --> pdb=" O LEU O 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE O 531 " --> pdb=" O MET O 527 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA O 532 " --> pdb=" O PHE O 528 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU O 535 " --> pdb=" O ILE O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 545 Processing helix chain 'O' and resid 582 through 587 removed outlier: 3.714A pdb=" N ILE O 586 " --> pdb=" O ARG O 582 " (cutoff:3.500A) Processing helix chain 'O' and resid 601 through 605 Processing helix chain 'S' and resid 189 through 194 removed outlier: 3.954A pdb=" N ARG S 194 " --> pdb=" O ALA S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 576 removed outlier: 4.094A pdb=" N ALA S 575 " --> pdb=" O HIS S 571 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER S 576 " --> pdb=" O PRO S 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 571 through 576' Processing helix chain 'S' and resid 587 through 607 removed outlier: 4.210A pdb=" N LEU S 592 " --> pdb=" O SER S 588 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 596 " --> pdb=" O LEU S 592 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER S 605 " --> pdb=" O ARG S 601 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL S 607 " --> pdb=" O ARG S 603 " (cutoff:3.500A) Processing helix chain 'S' and resid 607 through 612 removed outlier: 3.646A pdb=" N GLU S 612 " --> pdb=" O GLN S 608 " (cutoff:3.500A) Processing helix chain 'S' and resid 617 through 644 removed outlier: 3.664A pdb=" N GLN S 624 " --> pdb=" O ASP S 620 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN S 635 " --> pdb=" O SER S 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU S 636 " --> pdb=" O ILE S 632 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU S 637 " --> pdb=" O ALA S 633 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU S 639 " --> pdb=" O ASN S 635 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 685 removed outlier: 3.629A pdb=" N SER S 676 " --> pdb=" O ILE S 672 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER S 677 " --> pdb=" O PRO S 673 " (cutoff:3.500A) Processing helix chain 'S' and resid 700 through 705 removed outlier: 4.413A pdb=" N LEU S 704 " --> pdb=" O LEU S 700 " (cutoff:3.500A) Processing helix chain 'S' and resid 710 through 720 removed outlier: 4.261A pdb=" N TYR S 715 " --> pdb=" O LEU S 711 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN S 716 " --> pdb=" O ASP S 712 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS S 717 " --> pdb=" O ILE S 713 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU S 718 " --> pdb=" O PHE S 714 " (cutoff:3.500A) Processing helix chain 'S' and resid 730 through 742 removed outlier: 3.832A pdb=" N GLU S 735 " --> pdb=" O LEU S 731 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE S 736 " --> pdb=" O LEU S 732 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL S 737 " --> pdb=" O THR S 733 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS S 738 " --> pdb=" O LYS S 734 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP S 739 " --> pdb=" O GLU S 735 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 766 removed outlier: 3.696A pdb=" N GLN S 757 " --> pdb=" O PHE S 753 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE S 760 " --> pdb=" O ILE S 756 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER S 761 " --> pdb=" O GLN S 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG S 762 " --> pdb=" O ASN S 758 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER S 763 " --> pdb=" O GLU S 759 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 38 removed outlier: 3.760A pdb=" N ARG R 17 " --> pdb=" O PHE R 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN R 22 " --> pdb=" O LYS R 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG R 33 " --> pdb=" O ARG R 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 34 " --> pdb=" O ARG R 30 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 130 removed outlier: 3.766A pdb=" N LYS R 129 " --> pdb=" O LYS R 126 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS R 130 " --> pdb=" O PHE R 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 126 through 130' Processing helix chain 'R' and resid 158 through 164 Processing helix chain 'R' and resid 166 through 173 Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.551A pdb=" N LEU R 177 " --> pdb=" O MET R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 192 removed outlier: 3.846A pdb=" N LEU R 186 " --> pdb=" O LYS R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 219 removed outlier: 3.744A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 225 Processing helix chain 'R' and resid 228 through 237 removed outlier: 4.445A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 253 removed outlier: 4.050A pdb=" N TRP R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 259 removed outlier: 3.877A pdb=" N LEU R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 278 removed outlier: 3.976A pdb=" N LEU R 271 " --> pdb=" O GLY R 267 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE R 277 " --> pdb=" O TRP R 273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR R 278 " --> pdb=" O MET R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 323 removed outlier: 3.642A pdb=" N SER R 316 " --> pdb=" O TYR R 312 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 317 " --> pdb=" O LEU R 313 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE R 318 " --> pdb=" O TRP R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 353 Processing helix chain 'R' and resid 362 through 379 removed outlier: 3.610A pdb=" N PHE R 366 " --> pdb=" O ALA R 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE R 367 " --> pdb=" O GLU R 363 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP R 377 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 403 through 421 removed outlier: 4.101A pdb=" N HIS R 407 " --> pdb=" O GLN R 403 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL R 411 " --> pdb=" O HIS R 407 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG R 412 " --> pdb=" O ILE R 408 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR R 413 " --> pdb=" O HIS R 409 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS R 421 " --> pdb=" O ILE R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 429 through 443 removed outlier: 3.816A pdb=" N ASN R 433 " --> pdb=" O ARG R 429 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER R 437 " --> pdb=" O ASN R 433 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE R 438 " --> pdb=" O GLN R 434 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU R 439 " --> pdb=" O LEU R 435 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER R 440 " --> pdb=" O LYS R 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 11 through 15 removed outlier: 3.978A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN M 82 " --> pdb=" O SER M 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 23 through 25 removed outlier: 6.493A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'M' and resid 38 through 42 removed outlier: 3.679A pdb=" N GLU M 61 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL M 101 " --> pdb=" O GLU M 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 11 through 14 removed outlier: 7.006A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 86 removed outlier: 10.330A pdb=" N LEU A 81 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N VAL A 361 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 85 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.808A pdb=" N HIS A 107 " --> pdb=" O CYS A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.831A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.204A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 479 through 483 removed outlier: 5.845A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 507 through 510 removed outlier: 7.039A pdb=" N TYR A 578 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB4, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.547A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS A 772 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.659A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 777 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 774 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 949 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.659A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 777 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB8, first strand: chain 'A' and resid 1238 through 1239 Processing sheet with id=AB9, first strand: chain 'A' and resid 1460 through 1462 removed outlier: 4.016A pdb=" N CYS A1470 " --> pdb=" O MET A1294 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A1269 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1272 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A1274 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I 47 " --> pdb=" O GLU A1274 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1506 through 1508 removed outlier: 3.952A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 73 through 74 removed outlier: 4.700A pdb=" N ASP F 145 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.268A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.979A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.662A pdb=" N LEU B 403 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 214 through 215 removed outlier: 5.395A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 259 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.825A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 592 through 596 removed outlier: 6.229A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 661 through 664 Processing sheet with id=AD1, first strand: chain 'B' and resid 741 through 744 removed outlier: 3.817A pdb=" N ARG B 743 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 805 " --> pdb=" O TYR B 905 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 824 through 825 Processing sheet with id=AD3, first strand: chain 'B' and resid 857 through 859 removed outlier: 7.067A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.536A pdb=" N VAL B1103 " --> pdb=" O THR B1174 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD7, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.700A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.394A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS C 205 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE C 85 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N HIS C 207 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 83 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE C 209 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU C 81 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY C 211 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA C 79 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.322A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE4, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.592A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.506A pdb=" N ASN E 63 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 108 through 112 removed outlier: 3.747A pdb=" N GLU E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.513A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 132 through 140 removed outlier: 7.404A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 6 removed outlier: 6.509A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU H 142 " --> pdb=" O MET H 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 16 removed outlier: 6.744A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 116 through 117 Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF5, first strand: chain 'I' and resid 81 through 83 Processing sheet with id=AF6, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AF7, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.971A pdb=" N LYS K 48 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 86 through 92 removed outlier: 6.247A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 80 through 81 removed outlier: 3.732A pdb=" N MET N 80 " --> pdb=" O TYR N 87 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 110 through 111 Processing sheet with id=AG2, first strand: chain 'S' and resid 25 through 26 removed outlier: 6.937A pdb=" N LEU S 25 " --> pdb=" O LYS S 439 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASP S 441 " --> pdb=" O LEU S 25 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE S 421 " --> pdb=" O SER S 418 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER S 418 " --> pdb=" O ILE S 421 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 63 through 67 removed outlier: 6.082A pdb=" N LEU S 64 " --> pdb=" O TYR S 549 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR S 549 " --> pdb=" O LEU S 64 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 182 through 183 removed outlier: 3.800A pdb=" N VAL S 213 " --> pdb=" O SER S 207 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AG6, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.419A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL S 261 " --> pdb=" O PHE S 272 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET S 285 " --> pdb=" O GLU S 275 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 300 through 303 removed outlier: 6.551A pdb=" N ASP S 319 " --> pdb=" O GLN S 301 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TRP S 324 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU S 347 " --> pdb=" O TRP S 324 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE S 326 " --> pdb=" O ASP S 345 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 362 through 365 removed outlier: 3.729A pdb=" N ARG S 362 " --> pdb=" O PHE S 375 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 449 through 457 removed outlier: 3.615A pdb=" N VAL S 465 " --> pdb=" O GLN S 454 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 478 through 479 Processing sheet with id=AH2, first strand: chain 'S' and resid 504 through 510 removed outlier: 6.578A pdb=" N LYS S 540 " --> pdb=" O THR S 506 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE S 508 " --> pdb=" O LEU S 538 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU S 538 " --> pdb=" O ILE S 508 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 23.33 Time building geometry restraints manager: 21.23 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: 13883 1.33 - 1.45: 10652 1.45 - 1.58: 26921 1.58 - 1.70: 181 1.70 - 1.82: 370 Bond restraints: 52007 Sorted by residual: bond pdb=" C THR A 659 " pdb=" N PRO A 660 " ideal model delta sigma weight residual 1.331 1.285 0.046 7.90e-03 1.60e+04 3.43e+01 bond pdb=" N MET Q 236 " pdb=" CA MET Q 236 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.20e-02 6.94e+03 1.22e+01 bond pdb=" N ILE O 237 " pdb=" CA ILE O 237 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N LEU Q 152 " pdb=" CA LEU Q 152 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.79e+00 bond pdb=" CA THR C 61 " pdb=" C THR C 61 " ideal model delta sigma weight residual 1.522 1.477 0.044 1.72e-02 3.38e+03 6.66e+00 ... (remaining 52002 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.19: 1019 104.19 - 111.76: 23222 111.76 - 119.33: 19962 119.33 - 126.90: 25622 126.90 - 134.46: 834 Bond angle restraints: 70659 Sorted by residual: angle pdb=" N ILE O 237 " pdb=" CA ILE O 237 " pdb=" C ILE O 237 " ideal model delta sigma weight residual 112.96 102.65 10.31 1.00e+00 1.00e+00 1.06e+02 angle pdb=" C LYS O 236 " pdb=" N ILE O 237 " pdb=" CA ILE O 237 " ideal model delta sigma weight residual 121.84 129.80 -7.96 1.13e+00 7.83e-01 4.97e+01 angle pdb=" C HIS S 230 " pdb=" N ASN S 231 " pdb=" CA ASN S 231 " ideal model delta sigma weight residual 122.46 130.59 -8.13 1.41e+00 5.03e-01 3.33e+01 angle pdb=" N ILE Q 281 " pdb=" CA ILE Q 281 " pdb=" C ILE Q 281 " ideal model delta sigma weight residual 110.62 116.92 -6.30 1.14e+00 7.69e-01 3.05e+01 angle pdb=" N ILE A1329 " pdb=" CA ILE A1329 " pdb=" C ILE A1329 " ideal model delta sigma weight residual 111.90 107.55 4.35 8.10e-01 1.52e+00 2.89e+01 ... (remaining 70654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 30775 35.28 - 70.56: 525 70.56 - 105.85: 39 105.85 - 141.13: 5 141.13 - 176.41: 6 Dihedral angle restraints: 31350 sinusoidal: 13543 harmonic: 17807 Sorted by residual: dihedral pdb=" CA GLU A 23 " pdb=" C GLU A 23 " pdb=" N ILE A 24 " pdb=" CA ILE A 24 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ASP B 15 " pdb=" C ASP B 15 " pdb=" N PHE B 16 " pdb=" CA PHE B 16 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LYS B 894 " pdb=" C LYS B 894 " pdb=" N PHE B 895 " pdb=" CA PHE B 895 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 31347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 7282 0.104 - 0.207: 560 0.207 - 0.311: 25 0.311 - 0.415: 7 0.415 - 0.518: 4 Chirality restraints: 7878 Sorted by residual: chirality pdb=" CB ILE K 47 " pdb=" CA ILE K 47 " pdb=" CG1 ILE K 47 " pdb=" CG2 ILE K 47 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 7875 not shown) Planarity restraints: 8735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 659 " -0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO A 660 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 660 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 660 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 295 " 0.059 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO R 296 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO R 296 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 296 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 712 " 0.054 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 713 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 713 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 713 " 0.045 5.00e-02 4.00e+02 ... (remaining 8732 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2847 2.72 - 3.26: 48115 3.26 - 3.81: 82172 3.81 - 4.35: 102707 4.35 - 4.90: 167596 Nonbonded interactions: 403437 Sorted by model distance: nonbonded pdb=" O THR Q 12 " pdb="ZN ZN Q 601 " model vdw 2.170 2.230 nonbonded pdb=" O ASP Q 13 " pdb="ZN ZN Q 601 " model vdw 2.176 2.230 nonbonded pdb=" O THR Q 279 " pdb=" O ASP Q 280 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 618 " pdb=" O GLY B 780 " model vdw 2.219 2.440 nonbonded pdb=" OE1 GLU A 646 " pdb=" OG1 THR B1084 " model vdw 2.221 2.440 ... (remaining 403432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.740 Check model and map are aligned: 0.710 Set scattering table: 0.420 Process input model: 146.350 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2898 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 : 0.007 0.080 52007 Z= 0.478 Angle : 1.048 11.404 70659 Z= 0.574 Chirality : 0.060 0.518 7878 Planarity : 0.007 0.087 8735 Dihedral : 13.248 176.412 19802 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.52 % Favored : 89.43 % Rotamer: Outliers : 0.40 % Allowed : 2.93 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.08), residues: 5986 helix: -4.09 (0.06), residues: 1897 sheet: -3.11 (0.18), residues: 646 loop : -2.95 (0.09), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP N 54 HIS 0.016 0.003 HIS B 183 PHE 0.042 0.003 PHE A 628 TYR 0.046 0.003 TYR R 368 ARG 0.020 0.001 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1324 time to evaluate : 5.411 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: Q 35 MET cc_start: 0.4662 (ttp) cc_final: 0.2435 (mmp) REVERT: Q 209 ASN cc_start: 0.3140 (p0) cc_final: 0.2857 (p0) REVERT: Q 360 LYS cc_start: 0.4659 (ptpt) cc_final: 0.4311 (mmmt) REVERT: A 22 LYS cc_start: 0.6954 (mmpt) cc_final: 0.6315 (tmtt) REVERT: A 199 ASP cc_start: 0.5801 (m-30) cc_final: 0.5535 (m-30) REVERT: A 345 LEU cc_start: 0.2355 (mp) cc_final: 0.2070 (mp) REVERT: A 424 MET cc_start: 0.2821 (mmp) cc_final: 0.2235 (ppp) REVERT: A 458 GLN cc_start: 0.7224 (mm110) cc_final: 0.6715 (tm-30) REVERT: A 572 THR cc_start: 0.4483 (m) cc_final: 0.4262 (p) REVERT: A 758 GLU cc_start: 0.5581 (mp0) cc_final: 0.5379 (pt0) REVERT: A 1439 MET cc_start: 0.2096 (mtm) cc_final: 0.1059 (tpt) REVERT: A 1441 LYS cc_start: 0.5962 (tttm) cc_final: 0.5717 (mmtp) REVERT: A 1535 PHE cc_start: 0.4321 (m-80) cc_final: 0.4110 (m-10) REVERT: A 1620 GLN cc_start: 0.7380 (tp40) cc_final: 0.6552 (mp10) REVERT: A 1632 GLU cc_start: 0.4158 (tp30) cc_final: 0.3607 (tp30) REVERT: B 39 GLN cc_start: 0.4520 (mp10) cc_final: 0.4081 (mp10) REVERT: B 315 LYS cc_start: 0.7176 (tttm) cc_final: 0.6734 (mmtt) REVERT: B 358 VAL cc_start: 0.1022 (OUTLIER) cc_final: -0.0232 (p) REVERT: B 650 LEU cc_start: 0.1471 (mt) cc_final: 0.1169 (mt) REVERT: B 1097 ASP cc_start: 0.6892 (p0) cc_final: 0.6473 (p0) REVERT: E 65 THR cc_start: 0.4166 (p) cc_final: 0.3325 (t) REVERT: G 84 TYR cc_start: 0.4710 (p90) cc_final: 0.3499 (p90) REVERT: G 238 THR cc_start: 0.3496 (m) cc_final: 0.3084 (p) REVERT: G 241 ARG cc_start: 0.4199 (mtm-85) cc_final: 0.3873 (mpt180) REVERT: H 111 LEU cc_start: 0.5143 (mt) cc_final: 0.4914 (tp) REVERT: N 156 PRO cc_start: 0.5057 (Cg_endo) cc_final: 0.4844 (Cg_exo) REVERT: O 177 LYS cc_start: 0.6262 (ttpt) cc_final: 0.5456 (tptp) REVERT: O 218 LEU cc_start: 0.5515 (tp) cc_final: 0.4914 (tp) REVERT: O 229 ILE cc_start: 0.4194 (mm) cc_final: 0.3915 (pt) REVERT: O 385 MET cc_start: 0.2289 (tpp) cc_final: 0.1575 (tpt) REVERT: O 467 MET cc_start: 0.4521 (mmp) cc_final: 0.4005 (mmt) REVERT: O 608 GLU cc_start: 0.2948 (tm-30) cc_final: 0.2121 (pm20) REVERT: S 46 VAL cc_start: 0.1764 (p) cc_final: 0.1135 (p) REVERT: S 305 PHE cc_start: 0.5773 (m-10) cc_final: 0.5258 (t80) REVERT: S 323 ASN cc_start: 0.5467 (p0) cc_final: 0.4724 (p0) REVERT: S 344 ILE cc_start: 0.3913 (mm) cc_final: 0.3623 (pt) REVERT: S 389 TRP cc_start: 0.5553 (t60) cc_final: 0.2711 (t60) REVERT: S 416 LEU cc_start: 0.3392 (tp) cc_final: 0.3087 (tp) REVERT: S 622 TYR cc_start: 0.6568 (t80) cc_final: 0.6361 (t80) REVERT: S 639 GLU cc_start: 0.2003 (mm-30) cc_final: 0.1698 (mm-30) REVERT: S 730 GLU cc_start: 0.2301 (tp30) cc_final: 0.1686 (mm-30) REVERT: R 2 PHE cc_start: 0.3361 (m-80) cc_final: 0.2481 (m-10) REVERT: R 173 MET cc_start: 0.4863 (tpt) cc_final: 0.4633 (mmt) REVERT: R 297 PHE cc_start: 0.5046 (m-80) cc_final: 0.4713 (m-80) REVERT: R 401 ILE cc_start: 0.3353 (OUTLIER) cc_final: 0.2870 (tt) outliers start: 22 outliers final: 1 residues processed: 1340 average time/residue: 0.6907 time to fit residues: 1488.4595 Evaluate side-chains 637 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 634 time to evaluate : 5.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain R residue 401 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 515 optimal weight: 5.9990 chunk 463 optimal weight: 9.9990 chunk 256 optimal weight: 0.0980 chunk 158 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 247 optimal weight: 0.5980 chunk 478 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 356 optimal weight: 3.9990 chunk 554 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 33 HIS Q 238 HIS Q 283 ASN ** Q 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 435 GLN Q 514 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 322 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN A 590 ASN A 620 ASN A 706 HIS A 748 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A1026 GLN A1072 ASN A1088 HIS A1162 ASN A1180 ASN A1320 GLN A1336 GLN A1447 GLN A1461 ASN A1487 ASN A1564 ASN A1568 ASN ** A1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 282 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 439 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 673 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN B 952 HIS B1008 HIS B1041 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 161 HIS C 172 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN G 20 HIS G 23 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 95 ASN J 53 HIS K 64 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN O 66 ASN O 94 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 391 GLN O 472 HIS S 346 ASN S 483 HIS S 705 HIS R 184 ASN R 207 ASN R 223 ASN ** R 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 246 GLN R 289 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 382 GLN R 407 HIS ** R 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3598 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 52007 Z= 0.263 Angle : 0.752 16.008 70659 Z= 0.396 Chirality : 0.046 0.293 7878 Planarity : 0.006 0.074 8735 Dihedral : 14.538 177.805 7615 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 2.45 % Allowed : 10.06 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.09), residues: 5986 helix: -3.10 (0.08), residues: 2057 sheet: -2.40 (0.19), residues: 649 loop : -2.57 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Q 380 HIS 0.010 0.001 HIS A 673 PHE 0.028 0.002 PHE R 383 TYR 0.031 0.002 TYR Q 446 ARG 0.027 0.001 ARG A1572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 781 time to evaluate : 5.421 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: Q 35 MET cc_start: 0.4081 (ttp) cc_final: 0.2060 (mmp) REVERT: Q 252 LEU cc_start: 0.3821 (OUTLIER) cc_final: 0.3510 (tt) REVERT: Q 317 MET cc_start: 0.5539 (mmt) cc_final: 0.4631 (tpt) REVERT: Q 360 LYS cc_start: 0.5329 (ptpt) cc_final: 0.5003 (mmmt) REVERT: M 30 PHE cc_start: 0.3498 (t80) cc_final: 0.2300 (t80) REVERT: A 80 GLU cc_start: 0.6200 (mm-30) cc_final: 0.4850 (tm-30) REVERT: A 199 ASP cc_start: 0.6022 (m-30) cc_final: 0.5478 (m-30) REVERT: A 348 LYS cc_start: 0.5270 (mtmm) cc_final: 0.4929 (tttp) REVERT: A 424 MET cc_start: 0.2989 (mmp) cc_final: 0.2448 (ppp) REVERT: A 458 GLN cc_start: 0.7001 (mm110) cc_final: 0.6623 (tm-30) REVERT: A 481 ARG cc_start: 0.5281 (ptm160) cc_final: 0.4735 (ptp-170) REVERT: A 509 GLU cc_start: 0.5193 (tt0) cc_final: 0.4886 (tm-30) REVERT: A 603 HIS cc_start: 0.6117 (m-70) cc_final: 0.5675 (m90) REVERT: A 780 ILE cc_start: 0.3439 (OUTLIER) cc_final: 0.3217 (pp) REVERT: A 1063 MET cc_start: 0.4729 (tpp) cc_final: 0.4491 (tpp) REVERT: A 1120 TYR cc_start: 0.5235 (OUTLIER) cc_final: 0.4909 (t80) REVERT: A 1175 MET cc_start: 0.7372 (ttp) cc_final: 0.7149 (ttp) REVERT: A 1294 MET cc_start: 0.4714 (mtt) cc_final: 0.4461 (ttm) REVERT: A 1337 LYS cc_start: 0.6815 (pptt) cc_final: 0.6239 (mptt) REVERT: A 1439 MET cc_start: 0.2198 (mtm) cc_final: 0.1423 (tpt) REVERT: A 1620 GLN cc_start: 0.6903 (tp40) cc_final: 0.6306 (mp10) REVERT: A 1656 VAL cc_start: 0.5804 (p) cc_final: 0.5498 (p) REVERT: B 39 GLN cc_start: 0.4903 (mp10) cc_final: 0.3925 (mp10) REVERT: B 205 MET cc_start: 0.3729 (mpp) cc_final: 0.2914 (mtm) REVERT: B 234 ILE cc_start: 0.5766 (mm) cc_final: 0.5496 (mm) REVERT: B 268 GLU cc_start: 0.7786 (mp0) cc_final: 0.7312 (mp0) REVERT: B 315 LYS cc_start: 0.6802 (tttm) cc_final: 0.6518 (mmtt) REVERT: B 411 MET cc_start: 0.3828 (tpt) cc_final: 0.2161 (ttp) REVERT: B 502 MET cc_start: 0.3763 (ttt) cc_final: 0.3293 (ttm) REVERT: B 593 ILE cc_start: 0.2431 (OUTLIER) cc_final: 0.2118 (tt) REVERT: C 298 PHE cc_start: 0.3826 (m-10) cc_final: 0.3294 (m-10) REVERT: C 308 MET cc_start: 0.3227 (tpt) cc_final: 0.1630 (mtm) REVERT: E 87 SER cc_start: 0.5962 (t) cc_final: 0.5670 (m) REVERT: E 94 LYS cc_start: 0.6371 (mttt) cc_final: 0.6057 (ptpp) REVERT: G 52 MET cc_start: 0.6685 (tmm) cc_final: 0.6458 (tmm) REVERT: G 238 THR cc_start: 0.3482 (OUTLIER) cc_final: 0.3207 (p) REVERT: G 241 ARG cc_start: 0.5639 (mtm-85) cc_final: 0.4001 (mpt180) REVERT: H 10 PHE cc_start: 0.4529 (m-10) cc_final: 0.3934 (m-10) REVERT: H 146 ARG cc_start: 0.5186 (mtt-85) cc_final: 0.4673 (ttm-80) REVERT: K 74 ASN cc_start: 0.5544 (t0) cc_final: 0.4777 (p0) REVERT: N 107 MET cc_start: 0.5026 (mmp) cc_final: 0.4279 (mmt) REVERT: O 182 MET cc_start: 0.0958 (ttt) cc_final: -0.0681 (tmm) REVERT: O 190 ILE cc_start: 0.4904 (mt) cc_final: 0.4368 (mt) REVERT: O 230 TRP cc_start: 0.4576 (m100) cc_final: 0.3817 (m100) REVERT: O 467 MET cc_start: 0.4413 (mmp) cc_final: 0.3788 (mmt) REVERT: O 608 GLU cc_start: 0.2702 (tm-30) cc_final: 0.1685 (pm20) REVERT: S 16 LEU cc_start: 0.3823 (OUTLIER) cc_final: 0.3467 (mp) REVERT: S 21 GLN cc_start: 0.5095 (tt0) cc_final: 0.4775 (mm-40) REVERT: S 43 LEU cc_start: 0.3008 (OUTLIER) cc_final: 0.2777 (tt) REVERT: S 305 PHE cc_start: 0.5832 (m-10) cc_final: 0.5246 (t80) REVERT: S 344 ILE cc_start: 0.3568 (mm) cc_final: 0.3273 (pt) REVERT: S 360 TRP cc_start: 0.3393 (OUTLIER) cc_final: 0.2542 (t-100) REVERT: S 419 ARG cc_start: 0.6113 (ptt90) cc_final: 0.5465 (ptm160) REVERT: S 478 MET cc_start: 0.3328 (OUTLIER) cc_final: 0.3084 (ptm) REVERT: S 614 GLU cc_start: 0.5575 (mt-10) cc_final: 0.5369 (tm-30) REVERT: S 639 GLU cc_start: 0.2269 (mm-30) cc_final: 0.2052 (mm-30) REVERT: S 686 TYR cc_start: 0.0490 (m-80) cc_final: 0.0040 (m-80) REVERT: S 730 GLU cc_start: 0.1979 (tp30) cc_final: 0.1448 (mm-30) REVERT: S 777 MET cc_start: 0.1651 (ppp) cc_final: 0.1020 (ttt) REVERT: R 173 MET cc_start: 0.4668 (tpt) cc_final: 0.4061 (tpt) REVERT: R 274 MET cc_start: 0.3686 (ptt) cc_final: 0.2759 (tpp) outliers start: 134 outliers final: 60 residues processed: 880 average time/residue: 0.6192 time to fit residues: 902.3334 Evaluate side-chains 652 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 583 time to evaluate : 5.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 252 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 366 TYR Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 986 PHE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 986 PHE Chi-restraints excluded: chain B residue 1178 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain G residue 16 PHE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 360 TRP Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 478 MET Chi-restraints excluded: chain S residue 608 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 461 optimal weight: 3.9990 chunk 377 optimal weight: 0.5980 chunk 153 optimal weight: 0.4980 chunk 555 optimal weight: 6.9990 chunk 600 optimal weight: 0.6980 chunk 495 optimal weight: 0.5980 chunk 551 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 445 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 507 ASN ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 559 ASN A 590 ASN A 693 GLN A 819 ASN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN A1503 HIS A1509 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1581 HIS B 50 ASN B 212 ASN B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN B1165 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 301 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 GLN H 11 GLN K 106 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 HIS ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 434 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3948 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 52007 Z= 0.210 Angle : 0.663 14.113 70659 Z= 0.345 Chirality : 0.044 0.240 7878 Planarity : 0.005 0.071 8735 Dihedral : 14.219 179.008 7610 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.02 % Allowed : 11.91 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.10), residues: 5986 helix: -2.44 (0.09), residues: 2076 sheet: -2.05 (0.19), residues: 692 loop : -2.25 (0.10), residues: 3218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 314 HIS 0.012 0.001 HIS A1503 PHE 0.026 0.002 PHE B 313 TYR 0.028 0.002 TYR A 97 ARG 0.012 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 687 time to evaluate : 5.079 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: Q 35 MET cc_start: 0.4053 (ttp) cc_final: 0.2000 (mmp) REVERT: Q 317 MET cc_start: 0.5578 (mmt) cc_final: 0.4863 (tpt) REVERT: Q 350 ARG cc_start: 0.7208 (mmm160) cc_final: 0.6870 (tpt170) REVERT: M 30 PHE cc_start: 0.3214 (t80) cc_final: 0.2431 (t80) REVERT: M 47 GLU cc_start: -0.1933 (OUTLIER) cc_final: -0.2602 (mt-10) REVERT: A 130 ILE cc_start: 0.4851 (mp) cc_final: 0.3412 (mp) REVERT: A 199 ASP cc_start: 0.5997 (m-30) cc_final: 0.5661 (m-30) REVERT: A 424 MET cc_start: 0.2504 (mmp) cc_final: 0.1997 (ppp) REVERT: A 458 GLN cc_start: 0.7015 (mm110) cc_final: 0.6614 (tm-30) REVERT: A 481 ARG cc_start: 0.5348 (ptm160) cc_final: 0.4239 (ptp-170) REVERT: A 573 LEU cc_start: 0.5109 (mt) cc_final: 0.4864 (mt) REVERT: A 1057 ILE cc_start: 0.6509 (mp) cc_final: 0.6234 (mt) REVERT: A 1120 TYR cc_start: 0.5651 (OUTLIER) cc_final: 0.5017 (t80) REVERT: A 1439 MET cc_start: 0.2245 (mtm) cc_final: 0.1706 (tpp) REVERT: A 1441 LYS cc_start: 0.5822 (tptp) cc_final: 0.5274 (mmmt) REVERT: A 1501 ILE cc_start: 0.3847 (tp) cc_final: 0.3414 (mm) REVERT: A 1620 GLN cc_start: 0.6742 (tp40) cc_final: 0.6404 (mp10) REVERT: B 39 GLN cc_start: 0.4848 (mp10) cc_final: 0.4053 (mp10) REVERT: B 143 TRP cc_start: 0.5394 (OUTLIER) cc_final: 0.5065 (m100) REVERT: B 268 GLU cc_start: 0.7730 (mp0) cc_final: 0.7373 (mp0) REVERT: B 315 LYS cc_start: 0.6646 (tttm) cc_final: 0.6419 (mmtt) REVERT: B 316 ARG cc_start: 0.5070 (tpt90) cc_final: 0.4395 (ptp-170) REVERT: B 411 MET cc_start: 0.3237 (tpt) cc_final: 0.2550 (ttp) REVERT: B 451 MET cc_start: 0.5670 (tpt) cc_final: 0.5111 (ptm) REVERT: B 502 MET cc_start: 0.4243 (ttt) cc_final: 0.3843 (ttm) REVERT: B 650 LEU cc_start: 0.4211 (mt) cc_final: 0.3784 (mp) REVERT: B 702 ASN cc_start: 0.5507 (t0) cc_final: 0.4736 (t0) REVERT: B 721 MET cc_start: 0.5020 (tpp) cc_final: 0.4744 (tpp) REVERT: B 783 MET cc_start: 0.2466 (mmt) cc_final: 0.1954 (mtt) REVERT: B 1010 ASN cc_start: 0.3770 (OUTLIER) cc_final: 0.3309 (m110) REVERT: B 1053 ASN cc_start: 0.6468 (t0) cc_final: 0.6246 (t0) REVERT: C 74 GLU cc_start: 0.5965 (mp0) cc_final: 0.5188 (tp30) REVERT: C 192 LEU cc_start: 0.6651 (tt) cc_final: 0.6426 (tp) REVERT: C 298 PHE cc_start: 0.4102 (m-10) cc_final: 0.3731 (m-10) REVERT: C 308 MET cc_start: 0.3617 (tpt) cc_final: 0.2419 (mtm) REVERT: D 37 LEU cc_start: 0.8506 (tt) cc_final: 0.8021 (mt) REVERT: E 87 SER cc_start: 0.5424 (t) cc_final: 0.5082 (m) REVERT: E 93 MET cc_start: 0.4008 (OUTLIER) cc_final: 0.3070 (tmm) REVERT: E 121 MET cc_start: 0.4771 (tpt) cc_final: 0.3658 (mmt) REVERT: E 215 MET cc_start: 0.2774 (ptp) cc_final: 0.1630 (mtt) REVERT: G 52 MET cc_start: 0.6609 (tmm) cc_final: 0.6292 (tmm) REVERT: G 62 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.5283 (ttp) REVERT: G 241 ARG cc_start: 0.5537 (mtm-85) cc_final: 0.3988 (mpt180) REVERT: H 130 ARG cc_start: 0.4478 (ptp-170) cc_final: 0.3749 (ptp-170) REVERT: H 146 ARG cc_start: 0.5143 (mtt-85) cc_final: 0.4779 (ttp-170) REVERT: K 74 ASN cc_start: 0.5955 (t0) cc_final: 0.5279 (p0) REVERT: N 117 GLU cc_start: 0.2027 (pm20) cc_final: 0.1431 (tt0) REVERT: O 182 MET cc_start: 0.0832 (ttt) cc_final: -0.0670 (tmm) REVERT: O 205 ARG cc_start: 0.4573 (mmm-85) cc_final: 0.4321 (mmm-85) REVERT: O 230 TRP cc_start: 0.3973 (m100) cc_final: 0.3736 (m100) REVERT: O 396 MET cc_start: 0.5848 (mtp) cc_final: 0.5527 (mtp) REVERT: O 467 MET cc_start: 0.4687 (mmp) cc_final: 0.4003 (mmt) REVERT: O 472 HIS cc_start: 0.3024 (OUTLIER) cc_final: 0.2634 (m90) REVERT: O 608 GLU cc_start: 0.3093 (tm-30) cc_final: 0.2091 (pm20) REVERT: S 43 LEU cc_start: 0.2675 (OUTLIER) cc_final: 0.2453 (tt) REVERT: S 305 PHE cc_start: 0.5836 (m-10) cc_final: 0.5410 (t80) REVERT: S 344 ILE cc_start: 0.3599 (mm) cc_final: 0.3322 (pt) REVERT: S 360 TRP cc_start: 0.2803 (OUTLIER) cc_final: 0.2418 (t-100) REVERT: S 419 ARG cc_start: 0.6179 (ptt90) cc_final: 0.5582 (ptm160) REVERT: S 478 MET cc_start: 0.3434 (OUTLIER) cc_final: 0.3215 (ptm) REVERT: S 614 GLU cc_start: 0.5589 (mt-10) cc_final: 0.5266 (tm-30) REVERT: S 706 GLU cc_start: 0.5453 (tp30) cc_final: 0.4053 (mt-10) REVERT: S 730 GLU cc_start: 0.2485 (tp30) cc_final: 0.1655 (mm-30) REVERT: R 168 ILE cc_start: 0.5019 (OUTLIER) cc_final: 0.4352 (mp) outliers start: 165 outliers final: 85 residues processed: 800 average time/residue: 0.5899 time to fit residues: 800.7740 Evaluate side-chains 657 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 561 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 1010 ASN Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 360 TRP Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 478 MET Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 644 THR Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 253 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 549 optimal weight: 5.9990 chunk 417 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 373 optimal weight: 2.9990 chunk 557 optimal weight: 10.0000 chunk 590 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 528 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 514 ASN ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN A1564 ASN B 282 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 492 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN B 695 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN B 770 ASN B 824 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 29 GLN E 8 ASN E 146 HIS ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN S 58 HIS S 346 ASN S 665 ASN R 221 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4930 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 52007 Z= 0.344 Angle : 0.814 16.444 70659 Z= 0.420 Chirality : 0.049 0.418 7878 Planarity : 0.006 0.095 8735 Dihedral : 14.345 179.149 7610 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.93 % Allowed : 12.64 % Favored : 83.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.10), residues: 5986 helix: -2.14 (0.10), residues: 2067 sheet: -2.04 (0.19), residues: 679 loop : -2.20 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 314 HIS 0.069 0.002 HIS O 472 PHE 0.065 0.003 PHE R 366 TYR 0.030 0.003 TYR H 95 ARG 0.019 0.001 ARG S 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 797 time to evaluate : 4.966 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: Q 35 MET cc_start: 0.4180 (ttp) cc_final: 0.2214 (mmp) REVERT: Q 412 LYS cc_start: 0.7428 (mtmt) cc_final: 0.7124 (tptp) REVERT: Q 419 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.5006 (tp) REVERT: M 47 GLU cc_start: -0.1622 (OUTLIER) cc_final: -0.2382 (mt-10) REVERT: A 388 LYS cc_start: 0.6926 (ttmp) cc_final: 0.6438 (mptt) REVERT: A 458 GLN cc_start: 0.7045 (mm110) cc_final: 0.6806 (tm-30) REVERT: A 462 LYS cc_start: 0.5508 (mttt) cc_final: 0.5286 (ttmt) REVERT: A 500 VAL cc_start: 0.7091 (t) cc_final: 0.6878 (p) REVERT: A 514 TYR cc_start: 0.5509 (p90) cc_final: 0.5281 (p90) REVERT: A 615 ARG cc_start: 0.5611 (mmm160) cc_final: 0.5300 (mtt90) REVERT: A 633 MET cc_start: 0.5086 (tmm) cc_final: 0.4573 (ppp) REVERT: A 678 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7748 (t) REVERT: A 759 TYR cc_start: 0.6102 (m-80) cc_final: 0.5748 (m-80) REVERT: A 912 VAL cc_start: 0.4299 (t) cc_final: 0.3940 (t) REVERT: A 930 LEU cc_start: 0.5473 (OUTLIER) cc_final: 0.4509 (tp) REVERT: A 1000 MET cc_start: 0.5449 (tpp) cc_final: 0.5172 (ttt) REVERT: A 1057 ILE cc_start: 0.7740 (mp) cc_final: 0.7479 (mt) REVERT: A 1120 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5197 (t80) REVERT: A 1143 LYS cc_start: 0.6674 (mttt) cc_final: 0.5817 (tttt) REVERT: A 1227 MET cc_start: 0.2233 (mmt) cc_final: 0.1876 (mmm) REVERT: A 1238 MET cc_start: 0.5325 (tpp) cc_final: 0.4787 (tpp) REVERT: A 1269 LYS cc_start: 0.4813 (mtmt) cc_final: 0.4586 (mptt) REVERT: A 1301 GLU cc_start: 0.3521 (OUTLIER) cc_final: 0.3314 (tt0) REVERT: A 1329 ILE cc_start: 0.6869 (mt) cc_final: 0.6497 (pt) REVERT: A 1441 LYS cc_start: 0.5460 (tptp) cc_final: 0.4802 (mmtt) REVERT: A 1501 ILE cc_start: 0.4397 (tp) cc_final: 0.3941 (mm) REVERT: A 1519 LEU cc_start: 0.6115 (mt) cc_final: 0.5845 (mm) REVERT: A 1620 GLN cc_start: 0.7632 (tp40) cc_final: 0.6939 (mp10) REVERT: B 39 GLN cc_start: 0.5148 (mp10) cc_final: 0.4339 (mp10) REVERT: B 168 ASN cc_start: 0.6294 (m110) cc_final: 0.5817 (p0) REVERT: B 268 GLU cc_start: 0.7806 (mp0) cc_final: 0.7604 (mp0) REVERT: B 316 ARG cc_start: 0.5084 (tpt90) cc_final: 0.4444 (ptp-170) REVERT: B 654 ARG cc_start: 0.5381 (OUTLIER) cc_final: 0.5152 (ptm160) REVERT: B 702 ASN cc_start: 0.6884 (t0) cc_final: 0.6476 (t0) REVERT: C 40 PHE cc_start: 0.4368 (t80) cc_final: 0.4100 (t80) REVERT: C 72 ILE cc_start: 0.8159 (mt) cc_final: 0.7908 (mt) REVERT: C 100 ARG cc_start: 0.7132 (mtm180) cc_final: 0.6905 (mtt90) REVERT: C 136 LEU cc_start: 0.5417 (tp) cc_final: 0.5184 (tp) REVERT: C 192 LEU cc_start: 0.8008 (tt) cc_final: 0.7778 (tp) REVERT: C 308 MET cc_start: 0.4969 (tpt) cc_final: 0.4413 (mtt) REVERT: D 37 LEU cc_start: 0.8610 (tt) cc_final: 0.8344 (mt) REVERT: E 8 ASN cc_start: 0.5173 (t160) cc_final: 0.4764 (p0) REVERT: E 58 MET cc_start: 0.6421 (mtm) cc_final: 0.6183 (mtm) REVERT: E 87 SER cc_start: 0.5586 (t) cc_final: 0.5191 (m) REVERT: E 215 MET cc_start: 0.4917 (ptp) cc_final: 0.3914 (mtt) REVERT: F 118 LEU cc_start: 0.5051 (tp) cc_final: 0.4672 (tt) REVERT: G 52 MET cc_start: 0.6621 (tmm) cc_final: 0.6290 (tmm) REVERT: G 238 THR cc_start: 0.3634 (OUTLIER) cc_final: 0.3389 (p) REVERT: G 241 ARG cc_start: 0.4948 (mtm-85) cc_final: 0.3560 (mpt180) REVERT: I 53 ASP cc_start: 0.6846 (p0) cc_final: 0.5883 (t0) REVERT: J 4 PRO cc_start: 0.7360 (Cg_exo) cc_final: 0.7031 (Cg_endo) REVERT: K 74 ASN cc_start: 0.6967 (t0) cc_final: 0.6100 (p0) REVERT: K 110 GLU cc_start: 0.5335 (pt0) cc_final: 0.5040 (tp30) REVERT: N 107 MET cc_start: 0.5325 (mmp) cc_final: 0.4539 (mmt) REVERT: O 182 MET cc_start: 0.0476 (ttt) cc_final: -0.1187 (tmm) REVERT: O 187 MET cc_start: 0.4241 (mmp) cc_final: 0.3614 (mmt) REVERT: O 205 ARG cc_start: 0.4924 (mmm-85) cc_final: 0.4685 (mmm-85) REVERT: O 396 MET cc_start: 0.5659 (mtp) cc_final: 0.5424 (mtp) REVERT: O 467 MET cc_start: 0.4641 (mmp) cc_final: 0.4157 (mmt) REVERT: O 472 HIS cc_start: 0.3264 (OUTLIER) cc_final: 0.2461 (p-80) REVERT: O 608 GLU cc_start: 0.3084 (tm-30) cc_final: 0.2379 (pm20) REVERT: S 305 PHE cc_start: 0.5806 (m-10) cc_final: 0.5429 (t80) REVERT: S 344 ILE cc_start: 0.4012 (mm) cc_final: 0.3726 (pt) REVERT: S 476 ILE cc_start: 0.4413 (tp) cc_final: 0.4115 (mm) REVERT: S 614 GLU cc_start: 0.6123 (mt-10) cc_final: 0.5343 (pp20) REVERT: S 706 GLU cc_start: 0.5552 (tp30) cc_final: 0.4177 (mt-10) REVERT: S 730 GLU cc_start: 0.1849 (tp30) cc_final: 0.1221 (mm-30) REVERT: R 253 ILE cc_start: 0.4707 (OUTLIER) cc_final: 0.4498 (pp) REVERT: R 256 GLU cc_start: 0.5511 (OUTLIER) cc_final: 0.4756 (tm-30) REVERT: R 274 MET cc_start: 0.3790 (tpp) cc_final: 0.3264 (tpp) REVERT: R 297 PHE cc_start: 0.6249 (m-80) cc_final: 0.5707 (m-80) REVERT: R 401 ILE cc_start: 0.4252 (OUTLIER) cc_final: 0.3953 (tt) outliers start: 215 outliers final: 103 residues processed: 953 average time/residue: 0.5945 time to fit residues: 952.1998 Evaluate side-chains 723 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 608 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 419 LEU Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 489 ASN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 169 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 360 TRP Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 644 THR Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 256 GLU Chi-restraints excluded: chain R residue 401 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 491 optimal weight: 0.9990 chunk 335 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 439 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 503 optimal weight: 0.8980 chunk 408 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 0.8980 chunk 530 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 HIS A1525 ASN B 173 ASN B 248 ASN B 282 HIS ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS E 146 HIS ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 GLN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.8694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 52007 Z= 0.266 Angle : 0.714 14.387 70659 Z= 0.366 Chirality : 0.046 0.409 7878 Planarity : 0.005 0.107 8735 Dihedral : 14.204 179.833 7610 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.49 % Allowed : 15.44 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.10), residues: 5986 helix: -1.74 (0.10), residues: 2069 sheet: -1.86 (0.20), residues: 647 loop : -2.09 (0.10), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 314 HIS 0.016 0.002 HIS O 472 PHE 0.031 0.002 PHE B 313 TYR 0.042 0.002 TYR C 327 ARG 0.012 0.001 ARG N 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 724 time to evaluate : 5.295 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: Q 35 MET cc_start: 0.4130 (ttp) cc_final: 0.2140 (mmp) REVERT: Q 190 MET cc_start: 0.7329 (tpt) cc_final: 0.6957 (tpp) REVERT: M 47 GLU cc_start: -0.1423 (OUTLIER) cc_final: -0.2183 (mt-10) REVERT: M 50 GLU cc_start: 0.6022 (mt-10) cc_final: 0.5250 (pt0) REVERT: A 325 ASP cc_start: 0.5506 (t0) cc_final: 0.5236 (p0) REVERT: A 357 MET cc_start: 0.2929 (tpt) cc_final: 0.1595 (ptm) REVERT: A 388 LYS cc_start: 0.6881 (ttmp) cc_final: 0.6416 (mptt) REVERT: A 470 HIS cc_start: 0.5211 (m-70) cc_final: 0.4731 (m-70) REVERT: A 597 LYS cc_start: 0.6085 (ttpt) cc_final: 0.5708 (mptt) REVERT: A 612 LYS cc_start: 0.6778 (mmmt) cc_final: 0.6528 (mptt) REVERT: A 635 MET cc_start: 0.4548 (tmm) cc_final: 0.4225 (tmm) REVERT: A 712 ILE cc_start: 0.6202 (mt) cc_final: 0.5951 (mt) REVERT: A 821 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5725 (pt) REVERT: A 830 MET cc_start: 0.8054 (mmm) cc_final: 0.7839 (mmm) REVERT: A 925 MET cc_start: 0.5837 (mmp) cc_final: 0.5321 (mmp) REVERT: A 930 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5385 (tp) REVERT: A 1120 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.5411 (t80) REVERT: A 1200 MET cc_start: 0.4224 (OUTLIER) cc_final: 0.3897 (ptm) REVERT: A 1227 MET cc_start: 0.3110 (mmt) cc_final: 0.2735 (mmm) REVERT: A 1238 MET cc_start: 0.6203 (tpp) cc_final: 0.5890 (tpp) REVERT: A 1269 LYS cc_start: 0.5589 (mtmt) cc_final: 0.5154 (mptt) REVERT: A 1295 ARG cc_start: 0.5756 (mmm-85) cc_final: 0.5419 (mmm-85) REVERT: A 1329 ILE cc_start: 0.7519 (mt) cc_final: 0.7050 (pt) REVERT: A 1441 LYS cc_start: 0.5209 (tptp) cc_final: 0.4841 (mmmt) REVERT: A 1620 GLN cc_start: 0.7709 (tp40) cc_final: 0.7017 (mp10) REVERT: B 31 ASP cc_start: 0.2666 (OUTLIER) cc_final: 0.2430 (m-30) REVERT: B 200 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 316 ARG cc_start: 0.4960 (tpt90) cc_final: 0.4153 (ptp-170) REVERT: B 408 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6852 (pp) REVERT: B 421 LEU cc_start: 0.7091 (mm) cc_final: 0.6723 (mm) REVERT: B 461 MET cc_start: 0.6446 (tpp) cc_final: 0.6118 (tpp) REVERT: B 680 GLU cc_start: 0.4584 (pt0) cc_final: 0.4219 (pt0) REVERT: B 702 ASN cc_start: 0.7069 (t0) cc_final: 0.6863 (t0) REVERT: B 842 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6792 (mt-10) REVERT: B 882 ILE cc_start: 0.5873 (mp) cc_final: 0.5109 (mp) REVERT: B 886 ASN cc_start: 0.7308 (m-40) cc_final: 0.6060 (p0) REVERT: B 936 MET cc_start: 0.7826 (mmt) cc_final: 0.7384 (mmt) REVERT: B 1053 ASN cc_start: 0.5829 (t0) cc_final: 0.5616 (t0) REVERT: C 33 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6992 (t) REVERT: C 201 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.3876 (mt-10) REVERT: D 37 LEU cc_start: 0.8598 (tt) cc_final: 0.8389 (mt) REVERT: E 22 MET cc_start: 0.4745 (ttp) cc_final: 0.4148 (ttp) REVERT: E 87 SER cc_start: 0.6137 (t) cc_final: 0.5750 (m) REVERT: E 121 MET cc_start: 0.5795 (tpt) cc_final: 0.4263 (mmt) REVERT: E 166 LYS cc_start: 0.8095 (tttt) cc_final: 0.7805 (mmtt) REVERT: E 215 MET cc_start: 0.4934 (ptp) cc_final: 0.4437 (mtt) REVERT: F 128 LYS cc_start: 0.5332 (mmtt) cc_final: 0.4641 (tppt) REVERT: F 137 TYR cc_start: 0.4901 (m-80) cc_final: 0.4550 (m-80) REVERT: F 138 LEU cc_start: 0.6620 (mp) cc_final: 0.6308 (mp) REVERT: G 52 MET cc_start: 0.6805 (tmm) cc_final: 0.6453 (tmm) REVERT: G 158 LYS cc_start: 0.6512 (mptt) cc_final: 0.5847 (mptt) REVERT: G 238 THR cc_start: 0.3701 (OUTLIER) cc_final: 0.3489 (p) REVERT: G 241 ARG cc_start: 0.4786 (mtm-85) cc_final: 0.3650 (mpt180) REVERT: H 52 GLN cc_start: 0.7011 (mm-40) cc_final: 0.6660 (mm-40) REVERT: H 64 ASN cc_start: 0.6820 (t0) cc_final: 0.6345 (t0) REVERT: H 88 SER cc_start: 0.6442 (p) cc_final: 0.6151 (p) REVERT: I 53 ASP cc_start: 0.7030 (p0) cc_final: 0.5909 (t0) REVERT: J 44 TYR cc_start: 0.7435 (p90) cc_final: 0.7186 (p90) REVERT: K 45 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6328 (mt-10) REVERT: K 103 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6833 (tt) REVERT: K 110 GLU cc_start: 0.5693 (pt0) cc_final: 0.5262 (tp30) REVERT: N 90 MET cc_start: 0.4828 (tmm) cc_final: 0.4062 (mmp) REVERT: O 187 MET cc_start: 0.4450 (mmp) cc_final: 0.3743 (mmt) REVERT: O 205 ARG cc_start: 0.5026 (mmm-85) cc_final: 0.4782 (mmm-85) REVERT: O 396 MET cc_start: 0.6117 (mtp) cc_final: 0.5760 (mtp) REVERT: O 467 MET cc_start: 0.4998 (mmp) cc_final: 0.4450 (mmt) REVERT: O 608 GLU cc_start: 0.3108 (tm-30) cc_final: 0.2435 (pm20) REVERT: S 305 PHE cc_start: 0.5557 (m-10) cc_final: 0.5276 (t80) REVERT: S 344 ILE cc_start: 0.4529 (mm) cc_final: 0.4277 (pt) REVERT: S 345 ASP cc_start: 0.4911 (t0) cc_final: 0.4624 (t70) REVERT: S 419 ARG cc_start: 0.6130 (ptt90) cc_final: 0.5705 (ptm160) REVERT: S 614 GLU cc_start: 0.6431 (mt-10) cc_final: 0.5446 (pp20) REVERT: S 706 GLU cc_start: 0.5672 (tp30) cc_final: 0.4268 (mt-10) REVERT: S 730 GLU cc_start: 0.2375 (tp30) cc_final: 0.1856 (mm-30) REVERT: R 175 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6049 (mt) REVERT: R 256 GLU cc_start: 0.5734 (mt-10) cc_final: 0.5471 (tm-30) REVERT: R 274 MET cc_start: 0.5262 (tpp) cc_final: 0.4602 (tpp) REVERT: R 313 LEU cc_start: 0.6875 (mt) cc_final: 0.6455 (mt) outliers start: 191 outliers final: 98 residues processed: 857 average time/residue: 0.6007 time to fit residues: 869.2804 Evaluate side-chains 691 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 580 time to evaluate : 5.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1098 SER Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1200 MET Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1511 GLU Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain A residue 1590 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 360 TRP Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 555 THR Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 644 THR Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 374 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 198 optimal weight: 2.9990 chunk 531 optimal weight: 10.0000 chunk 116 optimal weight: 0.0870 chunk 346 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 591 optimal weight: 0.9990 chunk 490 optimal weight: 9.9990 chunk 273 optimal weight: 0.0770 chunk 49 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 310 optimal weight: 10.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 54 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1320 GLN A1525 ASN B 45 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 368 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 438 GLN ** S 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 665 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 moved from start: 0.9156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 52007 Z= 0.196 Angle : 0.642 14.163 70659 Z= 0.327 Chirality : 0.044 0.312 7878 Planarity : 0.005 0.077 8735 Dihedral : 14.055 179.973 7610 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.73 % Allowed : 17.32 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.10), residues: 5986 helix: -1.42 (0.11), residues: 2071 sheet: -1.60 (0.21), residues: 617 loop : -1.98 (0.10), residues: 3298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 314 HIS 0.009 0.001 HIS B 399 PHE 0.031 0.002 PHE B 798 TYR 0.025 0.001 TYR C 327 ARG 0.010 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 652 time to evaluate : 5.620 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: Q 35 MET cc_start: 0.3648 (ttp) cc_final: 0.1880 (mmp) REVERT: Q 190 MET cc_start: 0.6916 (tpt) cc_final: 0.6657 (tpp) REVERT: Q 364 SER cc_start: 0.4792 (OUTLIER) cc_final: 0.4581 (m) REVERT: M 47 GLU cc_start: -0.1327 (OUTLIER) cc_final: -0.2047 (mt-10) REVERT: M 50 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5496 (pt0) REVERT: A 325 ASP cc_start: 0.5601 (t0) cc_final: 0.5251 (p0) REVERT: A 357 MET cc_start: 0.2952 (tpt) cc_final: 0.1695 (ptm) REVERT: A 388 LYS cc_start: 0.6881 (ttmp) cc_final: 0.6425 (mptt) REVERT: A 470 HIS cc_start: 0.5361 (m-70) cc_final: 0.5062 (m-70) REVERT: A 597 LYS cc_start: 0.6075 (ttpt) cc_final: 0.5718 (mptt) REVERT: A 635 MET cc_start: 0.4417 (tmm) cc_final: 0.4169 (tmm) REVERT: A 712 ILE cc_start: 0.6404 (mt) cc_final: 0.6160 (mt) REVERT: A 821 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5826 (pt) REVERT: A 925 MET cc_start: 0.5853 (mmp) cc_final: 0.5449 (mmp) REVERT: A 1057 ILE cc_start: 0.7823 (mm) cc_final: 0.7502 (mm) REVERT: A 1120 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.5418 (t80) REVERT: A 1227 MET cc_start: 0.3239 (mmt) cc_final: 0.2914 (mmm) REVERT: A 1269 LYS cc_start: 0.5412 (mtmt) cc_final: 0.5039 (mptt) REVERT: A 1275 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6441 (p) REVERT: A 1329 ILE cc_start: 0.7572 (mt) cc_final: 0.7114 (pt) REVERT: A 1469 TRP cc_start: 0.6781 (p-90) cc_final: 0.6226 (p-90) REVERT: A 1592 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7167 (tp40) REVERT: A 1620 GLN cc_start: 0.7442 (tp40) cc_final: 0.6810 (mp10) REVERT: B 31 ASP cc_start: 0.2667 (OUTLIER) cc_final: 0.2451 (m-30) REVERT: B 200 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: B 282 HIS cc_start: 0.5446 (OUTLIER) cc_final: 0.5163 (m-70) REVERT: B 316 ARG cc_start: 0.5016 (tpt90) cc_final: 0.4240 (ptp-170) REVERT: B 372 ARG cc_start: 0.7456 (mtm110) cc_final: 0.6987 (mtm110) REVERT: B 421 LEU cc_start: 0.6996 (mm) cc_final: 0.6657 (mm) REVERT: B 461 MET cc_start: 0.6514 (tpp) cc_final: 0.6116 (tpp) REVERT: B 654 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.5457 (ptm160) REVERT: B 680 GLU cc_start: 0.4348 (pt0) cc_final: 0.3931 (pt0) REVERT: B 702 ASN cc_start: 0.7214 (t0) cc_final: 0.7009 (t0) REVERT: B 769 PHE cc_start: 0.7145 (p90) cc_final: 0.6827 (p90) REVERT: B 882 ILE cc_start: 0.6028 (mp) cc_final: 0.5290 (mp) REVERT: B 977 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6134 (pt) REVERT: B 1053 ASN cc_start: 0.6196 (t0) cc_final: 0.5892 (t0) REVERT: B 1097 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.5941 (p0) REVERT: B 1192 MET cc_start: 0.4354 (pmm) cc_final: 0.4002 (pmm) REVERT: C 201 GLU cc_start: 0.3965 (OUTLIER) cc_final: 0.3421 (mt-10) REVERT: E 22 MET cc_start: 0.5094 (ttp) cc_final: 0.4422 (ttt) REVERT: E 87 SER cc_start: 0.6142 (t) cc_final: 0.5758 (m) REVERT: E 93 MET cc_start: 0.4424 (OUTLIER) cc_final: 0.3491 (tmm) REVERT: E 105 PHE cc_start: 0.4302 (m-80) cc_final: 0.3767 (m-80) REVERT: E 121 MET cc_start: 0.5528 (tpt) cc_final: 0.4268 (mmt) REVERT: E 166 LYS cc_start: 0.8066 (tttt) cc_final: 0.7761 (mmtt) REVERT: E 192 ARG cc_start: 0.6076 (ttm110) cc_final: 0.5794 (mtm-85) REVERT: E 215 MET cc_start: 0.5057 (ptp) cc_final: 0.4423 (mtt) REVERT: F 60 GLN cc_start: 0.6833 (mm-40) cc_final: 0.5803 (mt0) REVERT: F 128 LYS cc_start: 0.5514 (mmtt) cc_final: 0.4821 (tppt) REVERT: F 137 TYR cc_start: 0.4935 (m-80) cc_final: 0.4705 (m-80) REVERT: F 138 LEU cc_start: 0.6466 (mp) cc_final: 0.6236 (mp) REVERT: F 145 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6378 (m-30) REVERT: G 52 MET cc_start: 0.6250 (tmm) cc_final: 0.5756 (tmm) REVERT: G 119 HIS cc_start: 0.4173 (t-90) cc_final: 0.3701 (t-90) REVERT: G 158 LYS cc_start: 0.6475 (mptt) cc_final: 0.5835 (tptt) REVERT: G 241 ARG cc_start: 0.4738 (mtm-85) cc_final: 0.3628 (mpt180) REVERT: H 64 ASN cc_start: 0.6924 (t0) cc_final: 0.6423 (t0) REVERT: I 53 ASP cc_start: 0.7151 (p0) cc_final: 0.5986 (t0) REVERT: K 45 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6346 (mt-10) REVERT: K 103 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6772 (tt) REVERT: K 110 GLU cc_start: 0.5602 (pt0) cc_final: 0.4933 (tp30) REVERT: N 90 MET cc_start: 0.5180 (tmm) cc_final: 0.4687 (mmp) REVERT: N 107 MET cc_start: 0.5143 (mmp) cc_final: 0.4371 (mmt) REVERT: O 156 MET cc_start: 0.2049 (OUTLIER) cc_final: 0.1458 (mtm) REVERT: O 205 ARG cc_start: 0.4937 (mmm-85) cc_final: 0.4642 (mmm-85) REVERT: O 221 TYR cc_start: 0.4710 (OUTLIER) cc_final: 0.3733 (m-80) REVERT: O 243 GLU cc_start: 0.5572 (mt-10) cc_final: 0.4433 (tp30) REVERT: O 396 MET cc_start: 0.5994 (mtp) cc_final: 0.5682 (mtp) REVERT: O 467 MET cc_start: 0.4873 (mmp) cc_final: 0.4583 (mmt) REVERT: O 608 GLU cc_start: 0.3118 (tm-30) cc_final: 0.2439 (pm20) REVERT: S 323 ASN cc_start: 0.6220 (p0) cc_final: 0.5849 (p0) REVERT: S 344 ILE cc_start: 0.4530 (mm) cc_final: 0.4234 (pt) REVERT: S 345 ASP cc_start: 0.4893 (t0) cc_final: 0.4615 (t70) REVERT: S 405 TYR cc_start: 0.6355 (t80) cc_final: 0.5931 (t80) REVERT: S 614 GLU cc_start: 0.6453 (mt-10) cc_final: 0.5356 (pp20) REVERT: S 706 GLU cc_start: 0.5540 (tp30) cc_final: 0.4135 (mt-10) REVERT: S 730 GLU cc_start: 0.2545 (tp30) cc_final: 0.2016 (mm-30) REVERT: R 175 ILE cc_start: 0.6307 (OUTLIER) cc_final: 0.6033 (mt) REVERT: R 256 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.4961 (tm-30) REVERT: R 274 MET cc_start: 0.5101 (tpp) cc_final: 0.4370 (tpp) REVERT: R 401 ILE cc_start: 0.4232 (OUTLIER) cc_final: 0.3965 (tt) outliers start: 149 outliers final: 82 residues processed: 756 average time/residue: 0.6035 time to fit residues: 778.7810 Evaluate side-chains 662 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 560 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 416 LYS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 232 ASN Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 465 VAL Chi-restraints excluded: chain S residue 480 VAL Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 731 LEU Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 256 GLU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 401 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 569 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 336 optimal weight: 3.9990 chunk 431 optimal weight: 2.9990 chunk 334 optimal weight: 1.9990 chunk 497 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 588 optimal weight: 7.9990 chunk 368 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 chunk 271 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 435 GLN M 16 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A 753 ASN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1250 GLN A1320 GLN A1564 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 462 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 702 ASN B 711 GLN B 745 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS G 170 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 348 HIS S 401 ASN S 665 ASN ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 1.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.149 52007 Z= 0.322 Angle : 0.797 18.332 70659 Z= 0.410 Chirality : 0.049 0.299 7878 Planarity : 0.006 0.087 8735 Dihedral : 14.304 179.509 7610 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.44 % Allowed : 17.41 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.10), residues: 5986 helix: -1.66 (0.10), residues: 2056 sheet: -1.89 (0.20), residues: 649 loop : -2.11 (0.10), residues: 3281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 314 HIS 0.014 0.002 HIS A 596 PHE 0.037 0.003 PHE B 798 TYR 0.041 0.003 TYR A1290 ARG 0.017 0.001 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 710 time to evaluate : 5.492 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: Q 35 MET cc_start: 0.3705 (ttp) cc_final: 0.1827 (mmp) REVERT: Q 118 TRP cc_start: 0.6341 (t60) cc_final: 0.5690 (t60) REVERT: M 30 PHE cc_start: 0.3740 (t80) cc_final: 0.3384 (t80) REVERT: M 47 GLU cc_start: -0.1760 (OUTLIER) cc_final: -0.2213 (mt-10) REVERT: M 50 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6037 (pt0) REVERT: M 80 LEU cc_start: 0.5051 (tp) cc_final: 0.4255 (tp) REVERT: M 103 LYS cc_start: 0.7189 (mtpp) cc_final: 0.6874 (mmtp) REVERT: A 325 ASP cc_start: 0.5653 (t0) cc_final: 0.5408 (p0) REVERT: A 357 MET cc_start: 0.3519 (tpt) cc_final: 0.2253 (ptm) REVERT: A 388 LYS cc_start: 0.7047 (ttmp) cc_final: 0.6578 (mmtt) REVERT: A 472 MET cc_start: 0.3158 (mmt) cc_final: 0.2508 (mmp) REVERT: A 597 LYS cc_start: 0.6732 (ttpt) cc_final: 0.6128 (mptt) REVERT: A 633 MET cc_start: 0.5368 (ppp) cc_final: 0.4929 (ppp) REVERT: A 712 ILE cc_start: 0.6460 (mt) cc_final: 0.6243 (mt) REVERT: A 925 MET cc_start: 0.5959 (mmp) cc_final: 0.5710 (mmp) REVERT: A 952 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7589 (mt) REVERT: A 1044 THR cc_start: 0.6628 (m) cc_final: 0.6281 (p) REVERT: A 1275 THR cc_start: 0.6674 (OUTLIER) cc_final: 0.6391 (p) REVERT: A 1487 ASN cc_start: 0.7294 (t0) cc_final: 0.6701 (p0) REVERT: A 1503 HIS cc_start: 0.7152 (t-90) cc_final: 0.6878 (t-170) REVERT: A 1592 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7495 (mm-40) REVERT: A 1611 MET cc_start: 0.6300 (ptp) cc_final: 0.6076 (mtm) REVERT: A 1615 TYR cc_start: 0.6513 (t80) cc_final: 0.5404 (t80) REVERT: A 1616 GLU cc_start: 0.5996 (pt0) cc_final: 0.5174 (pp20) REVERT: A 1620 GLN cc_start: 0.7321 (tp40) cc_final: 0.6628 (mp10) REVERT: B 200 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: B 205 MET cc_start: 0.6850 (ptt) cc_final: 0.6366 (ptt) REVERT: B 286 ARG cc_start: 0.6996 (tpt90) cc_final: 0.6793 (tpt90) REVERT: B 372 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7272 (mtm110) REVERT: B 408 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7916 (tp) REVERT: B 461 MET cc_start: 0.6892 (tpp) cc_final: 0.6550 (tpp) REVERT: B 623 ASP cc_start: 0.8241 (t70) cc_final: 0.7331 (m-30) REVERT: B 654 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5598 (ptp-170) REVERT: B 680 GLU cc_start: 0.5279 (pt0) cc_final: 0.5036 (pt0) REVERT: B 760 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6494 (t80) REVERT: B 851 TYR cc_start: 0.5493 (t80) cc_final: 0.5034 (t80) REVERT: B 882 ILE cc_start: 0.6867 (mp) cc_final: 0.6204 (mm) REVERT: B 904 LYS cc_start: 0.6553 (ttmm) cc_final: 0.6190 (ttpt) REVERT: B 946 ASP cc_start: 0.7645 (m-30) cc_final: 0.7382 (m-30) REVERT: B 1053 ASN cc_start: 0.6188 (t0) cc_final: 0.5935 (t0) REVERT: B 1111 LEU cc_start: 0.6562 (mt) cc_final: 0.5860 (pp) REVERT: B 1192 MET cc_start: 0.4630 (pmm) cc_final: 0.4103 (pmm) REVERT: C 71 MET cc_start: 0.6729 (mtm) cc_final: 0.6043 (mtt) REVERT: C 166 ASP cc_start: 0.6675 (m-30) cc_final: 0.6351 (m-30) REVERT: C 192 LEU cc_start: 0.8770 (tt) cc_final: 0.8488 (tp) REVERT: E 22 MET cc_start: 0.5668 (ttp) cc_final: 0.5035 (ttt) REVERT: E 93 MET cc_start: 0.4112 (OUTLIER) cc_final: 0.3214 (tmm) REVERT: E 105 PHE cc_start: 0.5254 (m-80) cc_final: 0.5033 (m-80) REVERT: E 106 GLN cc_start: 0.5330 (tt0) cc_final: 0.4120 (tp40) REVERT: E 166 LYS cc_start: 0.8175 (tttt) cc_final: 0.7697 (mmtt) REVERT: F 137 TYR cc_start: 0.5742 (m-80) cc_final: 0.5411 (m-80) REVERT: F 145 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: G 37 CYS cc_start: 0.7073 (p) cc_final: 0.6722 (p) REVERT: G 52 MET cc_start: 0.6681 (tmm) cc_final: 0.6128 (tmm) REVERT: G 241 ARG cc_start: 0.4278 (mtm-85) cc_final: 0.3284 (mpt180) REVERT: H 64 ASN cc_start: 0.7159 (t0) cc_final: 0.6867 (t0) REVERT: I 53 ASP cc_start: 0.7734 (p0) cc_final: 0.6604 (t0) REVERT: J 9 SER cc_start: 0.7836 (m) cc_final: 0.6372 (m) REVERT: K 45 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6525 (mt-10) REVERT: K 98 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.4218 (pt0) REVERT: K 103 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6541 (tt) REVERT: K 110 GLU cc_start: 0.5955 (pt0) cc_final: 0.4835 (tp30) REVERT: K 134 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8098 (tppt) REVERT: O 128 LEU cc_start: 0.3365 (OUTLIER) cc_final: 0.2715 (pt) REVERT: O 156 MET cc_start: 0.1471 (mtt) cc_final: 0.0901 (mtm) REVERT: O 187 MET cc_start: 0.4353 (mmp) cc_final: 0.3331 (mmt) REVERT: O 396 MET cc_start: 0.6212 (mtp) cc_final: 0.5862 (mtp) REVERT: O 608 GLU cc_start: 0.3173 (tm-30) cc_final: 0.2244 (pm20) REVERT: S 345 ASP cc_start: 0.5078 (t0) cc_final: 0.4784 (t70) REVERT: S 477 TYR cc_start: 0.4191 (t80) cc_final: 0.3792 (t80) REVERT: S 614 GLU cc_start: 0.5550 (mt-10) cc_final: 0.4609 (pp20) REVERT: S 730 GLU cc_start: 0.2399 (tp30) cc_final: 0.1449 (mm-30) REVERT: S 744 LEU cc_start: 0.4310 (tt) cc_final: 0.3409 (mp) REVERT: R 175 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5973 (mt) REVERT: R 256 GLU cc_start: 0.6042 (mt-10) cc_final: 0.5246 (tm-30) REVERT: R 274 MET cc_start: 0.5078 (tpp) cc_final: 0.4058 (tpt) REVERT: R 308 PHE cc_start: 0.4574 (p90) cc_final: 0.4056 (p90) outliers start: 188 outliers final: 106 residues processed: 851 average time/residue: 0.6040 time to fit residues: 865.4229 Evaluate side-chains 706 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 587 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 234 CYS Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 366 TYR Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 416 ILE Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 759 ASP Chi-restraints excluded: chain B residue 760 TYR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 348 HIS Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 352 PHE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 480 VAL Chi-restraints excluded: chain S residue 608 GLN Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 731 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 175 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 364 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 115 optimal weight: 0.2980 chunk 114 optimal weight: 0.9980 chunk 374 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 462 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 283 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A 880 GLN A1036 ASN A1141 GLN ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 368 GLN B 702 ASN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 158 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS K 74 ASN ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN S 665 ASN S 720 GLN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 1.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 52007 Z= 0.212 Angle : 0.670 15.409 70659 Z= 0.341 Chirality : 0.045 0.298 7878 Planarity : 0.005 0.084 8735 Dihedral : 14.088 178.574 7610 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.71 % Allowed : 19.50 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.10), residues: 5986 helix: -1.34 (0.11), residues: 2064 sheet: -1.78 (0.20), residues: 639 loop : -1.99 (0.10), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 229 HIS 0.018 0.001 HIS S 348 PHE 0.047 0.002 PHE B 798 TYR 0.030 0.002 TYR B 995 ARG 0.011 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 643 time to evaluate : 6.037 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: Q 35 MET cc_start: 0.3632 (ttp) cc_final: 0.1812 (mmp) REVERT: Q 190 MET cc_start: 0.8042 (tpp) cc_final: 0.7427 (tpp) REVERT: M 47 GLU cc_start: -0.1814 (OUTLIER) cc_final: -0.2219 (mt-10) REVERT: M 50 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6034 (pt0) REVERT: M 80 LEU cc_start: 0.5115 (tp) cc_final: 0.4328 (tp) REVERT: A 357 MET cc_start: 0.3577 (tpt) cc_final: 0.2406 (ptm) REVERT: A 360 LEU cc_start: 0.5934 (mt) cc_final: 0.5681 (mt) REVERT: A 388 LYS cc_start: 0.6883 (ttmp) cc_final: 0.6408 (mptt) REVERT: A 597 LYS cc_start: 0.6666 (ttpt) cc_final: 0.6113 (mptt) REVERT: A 604 LYS cc_start: 0.7459 (tptm) cc_final: 0.7240 (ttpt) REVERT: A 635 MET cc_start: 0.4243 (tmm) cc_final: 0.3812 (ttp) REVERT: A 686 PHE cc_start: 0.8163 (m-80) cc_final: 0.7918 (m-80) REVERT: A 712 ILE cc_start: 0.6254 (mt) cc_final: 0.6042 (mt) REVERT: A 830 MET cc_start: 0.8128 (mmm) cc_final: 0.7740 (tpp) REVERT: A 877 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5999 (tptt) REVERT: A 925 MET cc_start: 0.5997 (mmp) cc_final: 0.5790 (mmp) REVERT: A 1044 THR cc_start: 0.6422 (m) cc_final: 0.6109 (p) REVERT: A 1049 MET cc_start: 0.6784 (tpp) cc_final: 0.6499 (tpp) REVERT: A 1275 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6526 (p) REVERT: A 1441 LYS cc_start: 0.6085 (mmmt) cc_final: 0.5356 (tptp) REVERT: A 1487 ASN cc_start: 0.7341 (t0) cc_final: 0.6762 (p0) REVERT: A 1503 HIS cc_start: 0.7175 (t-90) cc_final: 0.6799 (t-170) REVERT: A 1611 MET cc_start: 0.6958 (ptp) cc_final: 0.6655 (ptt) REVERT: A 1615 TYR cc_start: 0.6484 (t80) cc_final: 0.5419 (t80) REVERT: A 1616 GLU cc_start: 0.6069 (pt0) cc_final: 0.5188 (pp20) REVERT: A 1620 GLN cc_start: 0.7261 (tp40) cc_final: 0.6702 (mp10) REVERT: B 31 ASP cc_start: 0.4366 (OUTLIER) cc_final: 0.4075 (m-30) REVERT: B 205 MET cc_start: 0.6537 (ptt) cc_final: 0.6040 (ptt) REVERT: B 377 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7057 (mmm) REVERT: B 408 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7720 (tp) REVERT: B 451 MET cc_start: 0.6360 (tpp) cc_final: 0.4971 (ptp) REVERT: B 623 ASP cc_start: 0.7894 (t70) cc_final: 0.7371 (m-30) REVERT: B 654 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5433 (ptp-170) REVERT: B 760 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6430 (t80) REVERT: B 882 ILE cc_start: 0.6700 (mp) cc_final: 0.6243 (mp) REVERT: B 904 LYS cc_start: 0.6493 (ttmm) cc_final: 0.6118 (ttmt) REVERT: B 936 MET cc_start: 0.7587 (mmt) cc_final: 0.7275 (mmt) REVERT: B 946 ASP cc_start: 0.7579 (m-30) cc_final: 0.7306 (m-30) REVERT: B 958 MET cc_start: 0.6735 (mtm) cc_final: 0.6431 (mtm) REVERT: B 1053 ASN cc_start: 0.6288 (t0) cc_final: 0.6049 (t0) REVERT: B 1111 LEU cc_start: 0.6527 (mt) cc_final: 0.5845 (pp) REVERT: B 1133 MET cc_start: 0.3163 (mtt) cc_final: 0.2918 (mtt) REVERT: B 1192 MET cc_start: 0.4933 (pmm) cc_final: 0.4451 (pmm) REVERT: E 22 MET cc_start: 0.5725 (ttp) cc_final: 0.5176 (ttt) REVERT: E 93 MET cc_start: 0.4160 (OUTLIER) cc_final: 0.3352 (tmm) REVERT: E 106 GLN cc_start: 0.5013 (tt0) cc_final: 0.3747 (tp40) REVERT: E 121 MET cc_start: 0.5913 (tpt) cc_final: 0.4501 (mmt) REVERT: E 166 LYS cc_start: 0.8177 (tttt) cc_final: 0.7741 (mmtt) REVERT: F 60 GLN cc_start: 0.7013 (mm-40) cc_final: 0.6126 (mt0) REVERT: F 137 TYR cc_start: 0.5599 (m-80) cc_final: 0.5276 (m-80) REVERT: F 145 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: G 37 CYS cc_start: 0.7101 (p) cc_final: 0.6724 (p) REVERT: G 72 LYS cc_start: 0.6625 (mttt) cc_final: 0.6056 (pttp) REVERT: G 136 TYR cc_start: 0.3795 (OUTLIER) cc_final: 0.2962 (m-80) REVERT: G 158 LYS cc_start: 0.6424 (mptt) cc_final: 0.5842 (tptt) REVERT: G 241 ARG cc_start: 0.4233 (mtm-85) cc_final: 0.3304 (mpt180) REVERT: H 64 ASN cc_start: 0.7067 (t0) cc_final: 0.6799 (t0) REVERT: I 53 ASP cc_start: 0.7777 (p0) cc_final: 0.6663 (t0) REVERT: J 9 SER cc_start: 0.7899 (m) cc_final: 0.6914 (m) REVERT: J 60 PHE cc_start: 0.4519 (OUTLIER) cc_final: 0.4138 (m-10) REVERT: K 45 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6567 (mt-10) REVERT: K 98 GLU cc_start: 0.5184 (OUTLIER) cc_final: 0.4943 (pt0) REVERT: K 103 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6615 (tt) REVERT: K 110 GLU cc_start: 0.5631 (pt0) cc_final: 0.4625 (tp30) REVERT: N 107 MET cc_start: 0.4880 (mmp) cc_final: 0.4481 (mmt) REVERT: O 156 MET cc_start: 0.1630 (OUTLIER) cc_final: 0.1069 (mtm) REVERT: O 180 LEU cc_start: 0.3939 (pp) cc_final: 0.3401 (mt) REVERT: O 187 MET cc_start: 0.4738 (mmp) cc_final: 0.3885 (mmt) REVERT: O 243 GLU cc_start: 0.5790 (mt-10) cc_final: 0.4610 (tp30) REVERT: O 396 MET cc_start: 0.6172 (mtp) cc_final: 0.5519 (mtp) REVERT: O 438 GLN cc_start: 0.4740 (mt0) cc_final: 0.4310 (tt0) REVERT: O 525 MET cc_start: 0.4654 (tmm) cc_final: 0.3207 (ttm) REVERT: O 602 TYR cc_start: 0.3426 (t80) cc_final: 0.3136 (t80) REVERT: O 608 GLU cc_start: 0.3208 (tm-30) cc_final: 0.2378 (pm20) REVERT: S 477 TYR cc_start: 0.4175 (t80) cc_final: 0.3821 (t80) REVERT: S 614 GLU cc_start: 0.5320 (mt-10) cc_final: 0.4311 (pp20) REVERT: S 730 GLU cc_start: 0.2574 (tp30) cc_final: 0.1953 (mm-30) REVERT: S 744 LEU cc_start: 0.4416 (tt) cc_final: 0.3557 (mp) REVERT: S 777 MET cc_start: 0.2528 (ppp) cc_final: 0.2036 (tmm) REVERT: R 175 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5796 (mt) REVERT: R 196 GLU cc_start: 0.5872 (tp30) cc_final: 0.5064 (tm-30) REVERT: R 256 GLU cc_start: 0.5892 (mt-10) cc_final: 0.5203 (tm-30) REVERT: R 271 LEU cc_start: 0.6326 (mm) cc_final: 0.5946 (mm) outliers start: 148 outliers final: 91 residues processed: 744 average time/residue: 0.5915 time to fit residues: 748.0929 Evaluate side-chains 677 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 571 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 234 CYS Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 416 ILE Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 880 GLN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1290 TYR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 760 TYR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 348 HIS Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain S residue 480 VAL Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 731 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 535 optimal weight: 0.7980 chunk 564 optimal weight: 0.9990 chunk 514 optimal weight: 0.9980 chunk 548 optimal weight: 3.9990 chunk 330 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 430 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 495 optimal weight: 0.7980 chunk 519 optimal weight: 0.0570 chunk 546 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 497 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 462 GLN B 702 ASN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 moved from start: 1.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 52007 Z= 0.188 Angle : 0.646 15.291 70659 Z= 0.328 Chirality : 0.044 0.305 7878 Planarity : 0.005 0.085 8735 Dihedral : 14.003 178.838 7610 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.41 % Allowed : 20.05 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.10), residues: 5986 helix: -1.16 (0.11), residues: 2076 sheet: -1.60 (0.20), residues: 627 loop : -1.93 (0.10), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 229 HIS 0.010 0.001 HIS S 348 PHE 0.050 0.002 PHE B 49 TYR 0.037 0.002 TYR S 469 ARG 0.008 0.000 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 609 time to evaluate : 6.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.3574 (ttp) cc_final: 0.1809 (mmp) REVERT: Q 190 MET cc_start: 0.7969 (tpp) cc_final: 0.7468 (tpp) REVERT: M 47 GLU cc_start: -0.1800 (OUTLIER) cc_final: -0.2183 (mt-10) REVERT: M 50 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6028 (pt0) REVERT: M 80 LEU cc_start: 0.5170 (tp) cc_final: 0.4391 (tp) REVERT: A 357 MET cc_start: 0.3581 (tpt) cc_final: 0.2459 (ptm) REVERT: A 360 LEU cc_start: 0.5886 (mt) cc_final: 0.5606 (mt) REVERT: A 388 LYS cc_start: 0.6862 (ttmp) cc_final: 0.6364 (mptt) REVERT: A 597 LYS cc_start: 0.6766 (ttpt) cc_final: 0.6210 (mptt) REVERT: A 604 LYS cc_start: 0.7468 (tptm) cc_final: 0.7262 (ttmt) REVERT: A 635 MET cc_start: 0.4207 (tmm) cc_final: 0.3823 (ttp) REVERT: A 712 ILE cc_start: 0.6092 (mt) cc_final: 0.5860 (mt) REVERT: A 830 MET cc_start: 0.8132 (mmm) cc_final: 0.7637 (tpp) REVERT: A 925 MET cc_start: 0.5934 (mmp) cc_final: 0.5721 (mmp) REVERT: A 1044 THR cc_start: 0.6212 (m) cc_final: 0.5894 (p) REVERT: A 1049 MET cc_start: 0.6772 (tpp) cc_final: 0.6526 (tpp) REVERT: A 1238 MET cc_start: 0.6953 (mtp) cc_final: 0.6659 (mtm) REVERT: A 1275 THR cc_start: 0.6982 (OUTLIER) cc_final: 0.6443 (p) REVERT: A 1322 ILE cc_start: 0.8036 (mm) cc_final: 0.7753 (mm) REVERT: A 1441 LYS cc_start: 0.5369 (mmmt) cc_final: 0.5159 (tptp) REVERT: A 1487 ASN cc_start: 0.7454 (t0) cc_final: 0.6864 (p0) REVERT: A 1611 MET cc_start: 0.7064 (ptp) cc_final: 0.6857 (ptt) REVERT: A 1615 TYR cc_start: 0.6473 (t80) cc_final: 0.5381 (t80) REVERT: A 1616 GLU cc_start: 0.6099 (pt0) cc_final: 0.5224 (pp20) REVERT: A 1620 GLN cc_start: 0.7192 (tp40) cc_final: 0.6724 (mp10) REVERT: B 31 ASP cc_start: 0.4203 (OUTLIER) cc_final: 0.3984 (m-30) REVERT: B 193 TYR cc_start: 0.8428 (p90) cc_final: 0.7660 (p90) REVERT: B 205 MET cc_start: 0.6528 (ptt) cc_final: 0.6094 (ptt) REVERT: B 372 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7409 (mtm110) REVERT: B 377 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7090 (mmm) REVERT: B 408 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7760 (tp) REVERT: B 451 MET cc_start: 0.6466 (tpp) cc_final: 0.5058 (ptp) REVERT: B 461 MET cc_start: 0.7012 (tpp) cc_final: 0.6571 (tpp) REVERT: B 623 ASP cc_start: 0.7725 (t70) cc_final: 0.7352 (m-30) REVERT: B 760 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6276 (t80) REVERT: B 882 ILE cc_start: 0.6692 (mp) cc_final: 0.6238 (mp) REVERT: B 904 LYS cc_start: 0.6444 (ttmm) cc_final: 0.6128 (ttmt) REVERT: B 936 MET cc_start: 0.7778 (mmt) cc_final: 0.7399 (mmt) REVERT: B 946 ASP cc_start: 0.7706 (m-30) cc_final: 0.7366 (m-30) REVERT: B 1039 MET cc_start: 0.1238 (mtt) cc_final: 0.0750 (ptp) REVERT: B 1053 ASN cc_start: 0.6518 (t0) cc_final: 0.6253 (t0) REVERT: B 1111 LEU cc_start: 0.6498 (mt) cc_final: 0.5854 (pp) REVERT: B 1192 MET cc_start: 0.5204 (pmm) cc_final: 0.4775 (pmm) REVERT: D 89 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.4901 (mp) REVERT: E 22 MET cc_start: 0.5709 (ttp) cc_final: 0.5165 (ttt) REVERT: E 93 MET cc_start: 0.4212 (OUTLIER) cc_final: 0.3326 (tmm) REVERT: E 121 MET cc_start: 0.5943 (tpt) cc_final: 0.4544 (mmt) REVERT: E 166 LYS cc_start: 0.8069 (tttt) cc_final: 0.7678 (mmtt) REVERT: F 60 GLN cc_start: 0.6785 (mm-40) cc_final: 0.5859 (mt0) REVERT: F 137 TYR cc_start: 0.5163 (m-80) cc_final: 0.4793 (m-80) REVERT: F 145 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: G 37 CYS cc_start: 0.7090 (p) cc_final: 0.6705 (p) REVERT: G 72 LYS cc_start: 0.6616 (mttt) cc_final: 0.5963 (ptmt) REVERT: G 136 TYR cc_start: 0.3717 (OUTLIER) cc_final: 0.2852 (m-80) REVERT: H 64 ASN cc_start: 0.7045 (t0) cc_final: 0.6793 (t0) REVERT: H 115 TYR cc_start: 0.7488 (m-80) cc_final: 0.6993 (m-80) REVERT: H 130 ARG cc_start: 0.5299 (ptp-170) cc_final: 0.4219 (ptp-170) REVERT: I 53 ASP cc_start: 0.7811 (p0) cc_final: 0.6714 (t0) REVERT: I 94 MET cc_start: 0.1445 (ttt) cc_final: 0.1041 (ttt) REVERT: J 9 SER cc_start: 0.7886 (m) cc_final: 0.6899 (m) REVERT: J 60 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.4163 (m-10) REVERT: K 45 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6600 (mt-10) REVERT: K 103 ILE cc_start: 0.6964 (OUTLIER) cc_final: 0.6687 (tt) REVERT: K 110 GLU cc_start: 0.5671 (pt0) cc_final: 0.4969 (tm-30) REVERT: L 29 TYR cc_start: 0.5458 (m-80) cc_final: 0.4937 (m-10) REVERT: L 66 GLN cc_start: 0.4298 (tm-30) cc_final: 0.3616 (mp10) REVERT: N 107 MET cc_start: 0.4982 (mmp) cc_final: 0.4465 (mmt) REVERT: O 156 MET cc_start: 0.1941 (OUTLIER) cc_final: 0.1256 (ptp) REVERT: O 180 LEU cc_start: 0.3743 (pp) cc_final: 0.3184 (mt) REVERT: O 187 MET cc_start: 0.4493 (mmp) cc_final: 0.3736 (mmt) REVERT: O 205 ARG cc_start: 0.5459 (mmm-85) cc_final: 0.5167 (mmm-85) REVERT: O 243 GLU cc_start: 0.5706 (mt-10) cc_final: 0.4600 (tp30) REVERT: O 438 GLN cc_start: 0.4604 (mt0) cc_final: 0.4064 (tt0) REVERT: O 525 MET cc_start: 0.4631 (tmm) cc_final: 0.3175 (ttm) REVERT: O 608 GLU cc_start: 0.3208 (tm-30) cc_final: 0.2376 (pm20) REVERT: S 405 TYR cc_start: 0.6756 (t80) cc_final: 0.6481 (t80) REVERT: S 477 TYR cc_start: 0.4220 (t80) cc_final: 0.3851 (t80) REVERT: S 614 GLU cc_start: 0.5295 (mt-10) cc_final: 0.4179 (pp20) REVERT: S 730 GLU cc_start: 0.2438 (tp30) cc_final: 0.1973 (mm-30) REVERT: S 744 LEU cc_start: 0.4210 (tt) cc_final: 0.3312 (mp) REVERT: S 762 ARG cc_start: 0.5738 (mmt180) cc_final: 0.5432 (mmt180) REVERT: S 777 MET cc_start: 0.2480 (ppp) cc_final: 0.2026 (tmm) REVERT: R 175 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5755 (mt) REVERT: R 256 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5690 (tm-30) REVERT: R 271 LEU cc_start: 0.6154 (mm) cc_final: 0.5780 (mm) outliers start: 132 outliers final: 95 residues processed: 700 average time/residue: 0.5792 time to fit residues: 697.6060 Evaluate side-chains 662 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 552 time to evaluate : 5.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 41 PHE Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 416 ILE Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1290 TYR Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 760 TYR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 981 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 352 PHE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 704 LEU Chi-restraints excluded: chain S residue 731 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 256 GLU Chi-restraints excluded: chain R residue 409 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 360 optimal weight: 0.0770 chunk 580 optimal weight: 1.9990 chunk 354 optimal weight: 0.0980 chunk 275 optimal weight: 2.9990 chunk 403 optimal weight: 20.0000 chunk 608 optimal weight: 9.9990 chunk 560 optimal weight: 40.0000 chunk 484 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 overall best weight: 1.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1237 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN B 702 ASN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 770 ASN B 912 GLN B 952 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN S 348 HIS S 368 HIS R 221 HIS R 263 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 1.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 52007 Z= 0.258 Angle : 0.712 14.556 70659 Z= 0.363 Chirality : 0.046 0.313 7878 Planarity : 0.005 0.093 8735 Dihedral : 14.098 179.374 7610 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.49 % Allowed : 20.18 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.10), residues: 5986 helix: -1.24 (0.11), residues: 2082 sheet: -1.62 (0.20), residues: 643 loop : -2.00 (0.10), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 79 HIS 0.011 0.002 HIS S 701 PHE 0.046 0.002 PHE B 798 TYR 0.034 0.002 TYR Q 192 ARG 0.014 0.001 ARG S 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11972 Ramachandran restraints generated. 5986 Oldfield, 0 Emsley, 5986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 633 time to evaluate : 5.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 35 MET cc_start: 0.3652 (ttp) cc_final: 0.1863 (mmp) REVERT: Q 109 GLN cc_start: 0.7797 (pp30) cc_final: 0.6315 (mt0) REVERT: Q 118 TRP cc_start: 0.6985 (t60) cc_final: 0.6676 (t60) REVERT: M 45 LYS cc_start: 0.2771 (pttp) cc_final: 0.2275 (mtmm) REVERT: M 47 GLU cc_start: -0.1984 (OUTLIER) cc_final: -0.2558 (mt-10) REVERT: M 80 LEU cc_start: 0.5460 (tp) cc_final: 0.4807 (tp) REVERT: A 339 PHE cc_start: 0.6728 (m-80) cc_final: 0.6163 (m-80) REVERT: A 357 MET cc_start: 0.3923 (tpt) cc_final: 0.2821 (ptm) REVERT: A 388 LYS cc_start: 0.6979 (ttmp) cc_final: 0.6402 (mptt) REVERT: A 597 LYS cc_start: 0.6731 (ttpt) cc_final: 0.6029 (mptt) REVERT: A 604 LYS cc_start: 0.7618 (tptm) cc_final: 0.7343 (ttmt) REVERT: A 712 ILE cc_start: 0.6521 (mt) cc_final: 0.6308 (mt) REVERT: A 804 GLU cc_start: 0.7673 (pt0) cc_final: 0.6898 (tp30) REVERT: A 1044 THR cc_start: 0.6467 (m) cc_final: 0.6166 (p) REVERT: A 1275 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6218 (p) REVERT: A 1487 ASN cc_start: 0.7482 (t0) cc_final: 0.6756 (p0) REVERT: A 1604 GLU cc_start: 0.4268 (mt-10) cc_final: 0.3251 (tp30) REVERT: A 1611 MET cc_start: 0.7334 (ptp) cc_final: 0.7101 (ptp) REVERT: A 1620 GLN cc_start: 0.7170 (tp40) cc_final: 0.6602 (mp10) REVERT: B 193 TYR cc_start: 0.8495 (p90) cc_final: 0.8125 (p90) REVERT: B 268 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6144 (pt0) REVERT: B 408 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7898 (tp) REVERT: B 502 MET cc_start: 0.7769 (ttp) cc_final: 0.7428 (ttm) REVERT: B 542 LEU cc_start: 0.8701 (tp) cc_final: 0.8363 (tt) REVERT: B 600 GLN cc_start: 0.6950 (tp-100) cc_final: 0.6737 (tp40) REVERT: B 760 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6327 (t80) REVERT: B 882 ILE cc_start: 0.6742 (mp) cc_final: 0.6216 (mp) REVERT: B 904 LYS cc_start: 0.6436 (ttmm) cc_final: 0.6142 (ttmt) REVERT: B 936 MET cc_start: 0.7866 (mmt) cc_final: 0.7605 (mmt) REVERT: B 946 ASP cc_start: 0.7688 (m-30) cc_final: 0.7379 (m-30) REVERT: B 1053 ASN cc_start: 0.6868 (t0) cc_final: 0.6620 (t0) REVERT: B 1111 LEU cc_start: 0.6776 (mt) cc_final: 0.6179 (pp) REVERT: B 1192 MET cc_start: 0.5032 (pmm) cc_final: 0.4545 (pmm) REVERT: C 50 ARG cc_start: 0.7261 (tpp80) cc_final: 0.6887 (tpp80) REVERT: C 201 GLU cc_start: 0.5121 (OUTLIER) cc_final: 0.4232 (mt-10) REVERT: E 22 MET cc_start: 0.5300 (ttp) cc_final: 0.4666 (ttt) REVERT: E 93 MET cc_start: 0.4322 (OUTLIER) cc_final: 0.3593 (tmm) REVERT: E 106 GLN cc_start: 0.5036 (tt0) cc_final: 0.3938 (tp40) REVERT: E 166 LYS cc_start: 0.8088 (tttt) cc_final: 0.7756 (mmtt) REVERT: F 60 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6085 (mt0) REVERT: F 137 TYR cc_start: 0.5691 (m-80) cc_final: 0.5316 (m-80) REVERT: F 145 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: G 37 CYS cc_start: 0.7253 (p) cc_final: 0.6783 (p) REVERT: G 72 LYS cc_start: 0.6794 (mttt) cc_final: 0.6140 (ptmt) REVERT: G 136 TYR cc_start: 0.3841 (OUTLIER) cc_final: 0.3097 (m-80) REVERT: H 64 ASN cc_start: 0.7229 (t0) cc_final: 0.7017 (t0) REVERT: H 130 ARG cc_start: 0.4989 (ptp-170) cc_final: 0.4055 (ptp-170) REVERT: I 53 ASP cc_start: 0.7973 (p0) cc_final: 0.7045 (t0) REVERT: I 81 THR cc_start: 0.4635 (m) cc_final: 0.4405 (t) REVERT: I 94 MET cc_start: 0.1884 (ttt) cc_final: 0.1619 (ttt) REVERT: J 9 SER cc_start: 0.8301 (m) cc_final: 0.6823 (m) REVERT: J 60 PHE cc_start: 0.4714 (OUTLIER) cc_final: 0.4171 (m-10) REVERT: K 45 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6851 (mt-10) REVERT: K 103 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6624 (tt) REVERT: K 110 GLU cc_start: 0.5904 (pt0) cc_final: 0.5025 (tm-30) REVERT: L 66 GLN cc_start: 0.4166 (tm-30) cc_final: 0.3709 (mp10) REVERT: O 180 LEU cc_start: 0.4622 (pp) cc_final: 0.3991 (mt) REVERT: O 187 MET cc_start: 0.4672 (mmp) cc_final: 0.3783 (mmt) REVERT: O 243 GLU cc_start: 0.5708 (mt-10) cc_final: 0.4528 (tp30) REVERT: O 396 MET cc_start: 0.6424 (mtp) cc_final: 0.6211 (mtp) REVERT: O 438 GLN cc_start: 0.5076 (mt0) cc_final: 0.4701 (tt0) REVERT: O 525 MET cc_start: 0.4523 (tmm) cc_final: 0.3153 (ttm) REVERT: O 608 GLU cc_start: 0.3198 (tm-30) cc_final: 0.2338 (pm20) REVERT: S 380 MET cc_start: 0.5493 (ptp) cc_final: 0.4623 (ptm) REVERT: S 421 ILE cc_start: 0.5378 (OUTLIER) cc_final: 0.5170 (mp) REVERT: S 477 TYR cc_start: 0.4875 (t80) cc_final: 0.4615 (t80) REVERT: S 614 GLU cc_start: 0.5362 (mt-10) cc_final: 0.4229 (pp20) REVERT: S 730 GLU cc_start: 0.2561 (tp30) cc_final: 0.1697 (mm-30) REVERT: S 762 ARG cc_start: 0.5834 (mmt180) cc_final: 0.5533 (mmt180) REVERT: S 777 MET cc_start: 0.2650 (ppp) cc_final: 0.2233 (tmm) REVERT: R 175 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5759 (mt) REVERT: R 196 GLU cc_start: 0.5607 (tp30) cc_final: 0.4953 (tm-30) outliers start: 136 outliers final: 97 residues processed: 727 average time/residue: 0.5851 time to fit residues: 733.7235 Evaluate side-chains 674 residues out of total 5483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 565 time to evaluate : 4.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 41 PHE Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain Q residue 433 THR Chi-restraints excluded: chain Q residue 493 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1120 TYR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1290 TYR Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 760 TYR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 981 SER Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1099 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 60 PHE Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 240 ILE Chi-restraints excluded: chain O residue 472 HIS Chi-restraints excluded: chain O residue 486 PHE Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 244 SER Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 348 HIS Chi-restraints excluded: chain S residue 351 ILE Chi-restraints excluded: chain S residue 366 PHE Chi-restraints excluded: chain S residue 421 ILE Chi-restraints excluded: chain S residue 424 VAL Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain S residue 692 THR Chi-restraints excluded: chain S residue 704 LEU Chi-restraints excluded: chain S residue 731 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 409 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 611 random chunks: chunk 385 optimal weight: 9.9990 chunk 516 optimal weight: 0.0770 chunk 148 optimal weight: 3.9990 chunk 446 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 485 optimal weight: 5.9990 chunk 203 optimal weight: 0.0270 chunk 498 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A1503 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN ** B 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 332 ASN S 348 HIS S 665 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.216368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.192679 restraints weight = 77481.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.192149 restraints weight = 101969.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.193225 restraints weight = 95403.248| |-----------------------------------------------------------------------------| r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4721 r_free = 0.4721 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 666 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4721 r_free = 0.4721 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 667 | |-----------------------------------------------------------------------------| r_final: 0.4721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 1.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 52007 Z= 0.236 Angle : 0.697 16.912 70659 Z= 0.353 Chirality : 0.045 0.305 7878 Planarity : 0.005 0.074 8735 Dihedral : 14.057 178.812 7610 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.27 % Allowed : 21.02 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.10), residues: 5986 helix: -1.19 (0.11), residues: 2088 sheet: -1.47 (0.21), residues: 630 loop : -1.96 (0.10), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 79 HIS 0.056 0.002 HIS S 348 PHE 0.044 0.002 PHE B 798 TYR 0.026 0.002 TYR S 405 ARG 0.009 0.001 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13627.50 seconds wall clock time: 244 minutes 58.01 seconds (14698.01 seconds total)