Starting phenix.real_space_refine on Sun Feb 18 22:52:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/02_2024/6zv6_11441_updated.pdb" } resolution = 2.9 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1678 5.49 5 Mg 3 5.21 5 S 192 5.16 5 C 41501 2.51 5 N 14009 2.21 5 O 18842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O ARG 149": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "a ARG 87": "NH1" <-> "NH2" Residue "a ARG 89": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 102": "NH1" <-> "NH2" Residue "T ARG 121": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 76226 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 35903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1683, 35903 Inner-chain residues flagged as termini: ['pdbres=" U 2 140 "', 'pdbres=" U 2 287 "', 'pdbres=" G 2 329 "', 'pdbres=" C 2 746 "', 'pdbres=" C 2 791 "', 'pdbres=" G 2 841 "', 'pdbres=" G 21771 "'] Classifications: {'RNA': 1683} Modifications used: {'5*END': 8, 'rna2p': 1, 'rna2p_pur': 131, 'rna2p_pyr': 113, 'rna3p': 1, 'rna3p_pur': 757, 'rna3p_pyr': 680} Link IDs: {'rna2p': 244, 'rna3p': 1438} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "M" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1010 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "R" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "a" Number of atoms: 829 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Conformer: "B" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} bond proxies already assigned to first conformer: 827 Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "e" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 442 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "f" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "h" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1775 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHD:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 7 Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 62536 SG CYS a 23 65.655 168.028 80.270 1.00102.11 S ATOM 62557 SG CYS a 26 68.118 168.009 77.644 1.00103.33 S ATOM 62940 SG CYS a 74 69.612 166.868 80.676 1.00105.23 S ATOM 62959 SG CYS a 77 69.717 170.413 79.768 1.00109.68 S Time building chain proxies: 29.38, per 1000 atoms: 0.39 Number of scatterers: 76226 At special positions: 0 Unit cell: (215.28, 282.88, 184.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 192 16.00 P 1678 15.00 Mg 3 11.99 O 18842 8.00 N 14009 7.00 C 41501 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: 29.20 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " Number of angles added : 6 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 56 sheets defined 29.0% alpha, 14.5% beta 498 base pairs and 886 stacking pairs defined. Time for finding SS restraints: 29.52 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.618A pdb=" N GLN A 84 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 86 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 89 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 92 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 177 removed outlier: 4.681A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.553A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 4.614A pdb=" N SER B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 147 through 160 removed outlier: 3.512A pdb=" N ILE C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.716A pdb=" N LYS C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 247 removed outlier: 4.227A pdb=" N THR C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'D' and resid 7 through 28 Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 248 through 261 Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 108 through 117 Processing helix chain 'F' and resid 143 through 160 Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.669A pdb=" N LYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 153 through 156 Processing helix chain 'G' and resid 184 through 229 removed outlier: 3.620A pdb=" N ALA G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 30 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.953A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 134 removed outlier: 4.248A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 180 removed outlier: 3.812A pdb=" N TYR H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 89 through 92 No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 107 through 116 Processing helix chain 'I' and resid 131 through 137 Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 160 through 168 removed outlier: 4.146A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 205 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 62 removed outlier: 4.145A pdb=" N ARG J 45 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU J 59 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR J 62 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 94 through 97 No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 102 through 106 Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 123 through 131 Processing helix chain 'J' and resid 152 through 155 removed outlier: 4.090A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 155' Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.579A pdb=" N LYS J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 18 removed outlier: 3.567A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU K 15 " --> pdb=" O ILE K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 73 through 80 Processing helix chain 'L' and resid 24 through 27 removed outlier: 3.599A pdb=" N GLU L 27 " --> pdb=" O LEU L 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 24 through 27' Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'M' and resid 14 through 27 removed outlier: 4.101A pdb=" N LEU M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 42 Processing helix chain 'M' and resid 59 through 71 removed outlier: 3.594A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 30 through 43 Processing helix chain 'N' and resid 47 through 56 Processing helix chain 'N' and resid 63 through 66 No H-bonds generated for 'chain 'N' and resid 63 through 66' Processing helix chain 'N' and resid 71 through 78 removed outlier: 3.704A pdb=" N LYS N 78 " --> pdb=" O ILE N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 102 Processing helix chain 'N' and resid 109 through 131 removed outlier: 3.937A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR N 131 " --> pdb=" O ARG N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 4.037A pdb=" N SER N 147 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 71 through 88 Processing helix chain 'O' and resid 110 through 122 removed outlier: 4.243A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 27 Processing helix chain 'P' and resid 31 through 34 No H-bonds generated for 'chain 'P' and resid 31 through 34' Processing helix chain 'P' and resid 39 through 46 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 45 through 63 removed outlier: 4.784A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU Q 53 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Proline residue: Q 54 - end of helix removed outlier: 4.622A pdb=" N GLY Q 59 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LYS Q 60 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU Q 61 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.862A pdb=" N LYS Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 115 removed outlier: 3.804A pdb=" N ILE Q 111 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'R' and resid 7 through 19 removed outlier: 3.713A pdb=" N ILE R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 38 removed outlier: 4.288A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 63 Processing helix chain 'R' and resid 74 through 81 removed outlier: 4.310A pdb=" N GLU R 79 " --> pdb=" O GLU R 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 108 Processing helix chain 'S' and resid 26 through 29 No H-bonds generated for 'chain 'S' and resid 26 through 29' Processing helix chain 'S' and resid 38 through 47 Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 100 through 117 removed outlier: 3.653A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP S 110 " --> pdb=" O LYS S 106 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 127 Processing helix chain 'a' and resid 47 through 53 removed outlier: 4.261A pdb=" N ARG a 51 " --> pdb=" O ALA a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 80 No H-bonds generated for 'chain 'a' and resid 77 through 80' Processing helix chain 'a' and resid 89 through 92 No H-bonds generated for 'chain 'a' and resid 89 through 92' Processing helix chain 'U' and resid 29 through 43 Processing helix chain 'U' and resid 95 through 102 removed outlier: 3.757A pdb=" N LYS U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 62 Processing helix chain 'V' and resid 65 through 75 removed outlier: 3.564A pdb=" N ARG V 71 " --> pdb=" O ASP V 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 32 through 44 Processing helix chain 'W' and resid 85 through 92 removed outlier: 3.667A pdb=" N TRP W 89 " --> pdb=" O LEU W 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN W 92 " --> pdb=" O TRP W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 removed outlier: 3.563A pdb=" N ARG W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 23 removed outlier: 3.895A pdb=" N ASP X 19 " --> pdb=" O SER X 15 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 35 through 38 No H-bonds generated for 'chain 'X' and resid 35 through 38' Processing helix chain 'X' and resid 90 through 93 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 37 through 47 removed outlier: 3.593A pdb=" N GLU Y 42 " --> pdb=" O THR Y 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 84 Processing helix chain 'Y' and resid 88 through 94 removed outlier: 3.772A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 116 removed outlier: 4.103A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 64 No H-bonds generated for 'chain 'Z' and resid 62 through 64' Processing helix chain 'Z' and resid 70 through 76 Processing helix chain 'Z' and resid 81 through 93 removed outlier: 3.913A pdb=" N ARG Z 85 " --> pdb=" O GLY Z 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'd' and resid 40 through 50 removed outlier: 5.312A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 15 Processing helix chain 'e' and resid 30 through 41 removed outlier: 4.022A pdb=" N GLN e 37 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR e 38 " --> pdb=" O ARG e 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 105 No H-bonds generated for 'chain 'f' and resid 102 through 105' Processing helix chain 'T' and resid 12 through 23 Processing helix chain 'T' and resid 52 through 65 Processing helix chain 'T' and resid 73 through 77 removed outlier: 3.856A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 73 through 77' Processing helix chain 'T' and resid 98 through 109 Processing helix chain 'T' and resid 125 through 133 Processing helix chain 'T' and resid 135 through 141 removed outlier: 3.657A pdb=" N ALA T 139 " --> pdb=" O ALA T 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 164 through 176 removed outlier: 3.576A pdb=" N MET h 168 " --> pdb=" O PRO h 164 " (cutoff:3.500A) Processing helix chain 'h' and resid 247 through 259 removed outlier: 3.840A pdb=" N ARG h 252 " --> pdb=" O GLU h 248 " (cutoff:3.500A) Processing helix chain 'h' and resid 290 through 292 No H-bonds generated for 'chain 'h' and resid 290 through 292' Processing helix chain 'h' and resid 297 through 316 Processing helix chain 'h' and resid 327 through 329 No H-bonds generated for 'chain 'h' and resid 327 through 329' Processing helix chain 'h' and resid 353 through 370 Processing helix chain 'h' and resid 378 through 386 Processing helix chain 'h' and resid 394 through 408 removed outlier: 3.608A pdb=" N GLN h 408 " --> pdb=" O GLU h 404 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 415 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 100 removed outlier: 5.836A pdb=" N LEU A 121 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 77 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A 123 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 159 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS A 148 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 161 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.369A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.509A pdb=" N LEU B 86 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 69 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 120 through 128 removed outlier: 6.623A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 136 through 144 removed outlier: 3.547A pdb=" N GLY C 119 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 184 through 187 Processing sheet with id= G, first strand: chain 'D' and resid 84 through 87 removed outlier: 6.700A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 148 through 150 removed outlier: 3.592A pdb=" N GLY D 140 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 70 through 72 removed outlier: 4.218A pdb=" N ASP E 88 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 121 through 125 Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'E' and resid 225 through 227 removed outlier: 6.720A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 123 through 127 Processing sheet with id= N, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.784A pdb=" N LEU G 111 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 113 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= P, first strand: chain 'G' and resid 54 through 57 removed outlier: 3.656A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 92 through 96 removed outlier: 6.646A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 51 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 184 through 189 removed outlier: 4.613A pdb=" N ASP H 184 " --> pdb=" O ARG H 152 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 62 through 67 removed outlier: 3.513A pdb=" N GLY I 63 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 170 through 174 removed outlier: 6.631A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 42 through 47 removed outlier: 6.933A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 135 through 137 Processing sheet with id= W, first strand: chain 'K' and resid 58 through 62 Processing sheet with id= X, first strand: chain 'L' and resid 101 through 112 removed outlier: 6.297A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.765A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.893A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 31 through 33 Processing sheet with id= Z, first strand: chain 'M' and resid 51 through 53 removed outlier: 6.292A pdb=" N ILE M 77 " --> pdb=" O LEU M 52 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.832A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL O 30 " --> pdb=" O THR O 45 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AC, first strand: chain 'Q' and resid 10 through 14 Processing sheet with id= AD, first strand: chain 'R' and resid 96 through 98 Processing sheet with id= AE, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= AF, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AG, first strand: chain 'a' and resid 36 through 40 Processing sheet with id= AH, first strand: chain 'U' and resid 20 through 26 removed outlier: 3.655A pdb=" N HIS U 92 " --> pdb=" O LYS U 49 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS U 49 " --> pdb=" O HIS U 92 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 59 through 66 Processing sheet with id= AJ, first strand: chain 'V' and resid 34 through 37 Processing sheet with id= AK, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AL, first strand: chain 'W' and resid 71 through 74 Processing sheet with id= AM, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.542A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id= AO, first strand: chain 'Z' and resid 98 through 101 removed outlier: 6.762A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'c' and resid 19 through 21 Processing sheet with id= AQ, first strand: chain 'c' and resid 14 through 17 removed outlier: 6.729A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'f' and resid 106 through 109 removed outlier: 4.073A pdb=" N ASP f 109 " --> pdb=" O LYS f 113 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS f 113 " --> pdb=" O ASP f 109 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'f' and resid 132 through 134 removed outlier: 3.545A pdb=" N TYR f 140 " --> pdb=" O ALA f 133 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'g' and resid 4 through 7 Processing sheet with id= AU, first strand: chain 'g' and resid 18 through 22 removed outlier: 6.875A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR g 39 " --> pdb=" O SER g 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG g 57 " --> pdb=" O MET g 42 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 69 through 71 removed outlier: 4.112A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP g 91 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR g 97 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 154 through 156 removed outlier: 3.695A pdb=" N VAL g 174 " --> pdb=" O HIS g 188 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 229 through 231 removed outlier: 5.417A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.793A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 108 through 112 removed outlier: 6.942A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'T' and resid 80 through 83 Processing sheet with id= BB, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= BC, first strand: chain 'h' and resid 195 through 198 Processing sheet with id= BD, first strand: chain 'h' and resid 330 through 333 1214 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1244 hydrogen bonds 1972 hydrogen bond angles 0 basepair planarities 498 basepair parallelities 886 stacking parallelities Total time for adding SS restraints: 60.32 Time building geometry restraints manager: 31.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8952 1.31 - 1.43: 31065 1.43 - 1.56: 37486 1.56 - 1.69: 3358 1.69 - 1.81: 295 Bond restraints: 81156 Sorted by residual: bond pdb=" C3' ADP h 601 " pdb=" C4' ADP h 601 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4' ADP h 601 " pdb=" O4' ADP h 601 " ideal model delta sigma weight residual 1.426 1.611 -0.185 2.00e-02 2.50e+03 8.58e+01 bond pdb=" OD1 PHD h 341 " pdb=" P PHD h 341 " ideal model delta sigma weight residual 1.816 1.650 0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C4 ADP h 601 " pdb=" C5 ADP h 601 " ideal model delta sigma weight residual 1.490 1.331 0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C1' ADP h 601 " pdb=" O4' ADP h 601 " ideal model delta sigma weight residual 1.426 1.302 0.124 2.00e-02 2.50e+03 3.82e+01 ... (remaining 81151 not shown) Histogram of bond angle deviations from ideal: 54.10 - 72.62: 1 72.62 - 91.14: 0 91.14 - 109.66: 28246 109.66 - 128.18: 86621 128.18 - 146.70: 2761 Bond angle restraints: 117629 Sorted by residual: angle pdb=" O3' A 21831 " pdb=" P 6MZ 21832 " pdb=" O1P 6MZ 21832 " ideal model delta sigma weight residual 108.00 54.10 53.90 3.00e+00 1.11e-01 3.23e+02 angle pdb=" O3' A 21831 " pdb=" P 6MZ 21832 " pdb=" O2P 6MZ 21832 " ideal model delta sigma weight residual 108.00 146.70 -38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C1' 6MZ 21832 " pdb=" N9 6MZ 21832 " pdb=" C8 6MZ 21832 " ideal model delta sigma weight residual 91.39 122.98 -31.59 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C1' 6MZ 21832 " pdb=" N9 6MZ 21832 " pdb=" C4 6MZ 21832 " ideal model delta sigma weight residual 154.15 128.34 25.81 3.00e+00 1.11e-01 7.40e+01 angle pdb=" C3' A 21831 " pdb=" O3' A 21831 " pdb=" P 6MZ 21832 " ideal model delta sigma weight residual 120.20 107.79 12.41 1.50e+00 4.44e-01 6.84e+01 ... (remaining 117624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 46887 35.95 - 71.90: 4171 71.90 - 107.85: 508 107.85 - 143.80: 21 143.80 - 179.75: 42 Dihedral angle restraints: 51629 sinusoidal: 37099 harmonic: 14530 Sorted by residual: dihedral pdb=" CA ARG W 28 " pdb=" C ARG W 28 " pdb=" N PRO W 29 " pdb=" CA PRO W 29 " ideal model delta harmonic sigma weight residual -180.00 -119.17 -60.83 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" C4' C 21440 " pdb=" C3' C 21440 " pdb=" C2' C 21440 " pdb=" C1' C 21440 " ideal model delta sinusoidal sigma weight residual -35.00 29.99 -64.99 1 8.00e+00 1.56e-02 8.66e+01 dihedral pdb=" O4' U 21662 " pdb=" C1' U 21662 " pdb=" N1 U 21662 " pdb=" C2 U 21662 " ideal model delta sinusoidal sigma weight residual -160.00 15.35 -175.35 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 51626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 13195 0.089 - 0.178: 1190 0.178 - 0.268: 86 0.268 - 0.357: 22 0.357 - 0.446: 8 Chirality restraints: 14501 Sorted by residual: chirality pdb=" C3' G 21648 " pdb=" C4' G 21648 " pdb=" O3' G 21648 " pdb=" C2' G 21648 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" C3' G 21425 " pdb=" C4' G 21425 " pdb=" O3' G 21425 " pdb=" C2' G 21425 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" C3' U 21649 " pdb=" C4' U 21649 " pdb=" O3' U 21649 " pdb=" C2' U 21649 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 14498 not shown) Planarity restraints: 8687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ 21832 " -0.024 2.00e-02 2.50e+03 5.39e-01 6.54e+03 pdb=" C4' 6MZ 21832 " -0.436 2.00e-02 2.50e+03 pdb=" O4' 6MZ 21832 " -0.564 2.00e-02 2.50e+03 pdb=" C3' 6MZ 21832 " 0.581 2.00e-02 2.50e+03 pdb=" O3' 6MZ 21832 " 0.526 2.00e-02 2.50e+03 pdb=" C2' 6MZ 21832 " 0.226 2.00e-02 2.50e+03 pdb=" O2' 6MZ 21832 " -0.864 2.00e-02 2.50e+03 pdb=" C1' 6MZ 21832 " -0.243 2.00e-02 2.50e+03 pdb=" N9 6MZ 21832 " 0.798 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' UR3 21830 " 0.718 2.00e-02 2.50e+03 5.18e-01 6.04e+03 pdb=" C4' UR3 21830 " -0.250 2.00e-02 2.50e+03 pdb=" O4' UR3 21830 " -0.485 2.00e-02 2.50e+03 pdb=" C3' UR3 21830 " 0.221 2.00e-02 2.50e+03 pdb=" O3' UR3 21830 " -0.875 2.00e-02 2.50e+03 pdb=" C2' UR3 21830 " 0.602 2.00e-02 2.50e+03 pdb=" O2' UR3 21830 " 0.509 2.00e-02 2.50e+03 pdb=" C1' UR3 21830 " -0.406 2.00e-02 2.50e+03 pdb=" N1 UR3 21830 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG W 28 " 0.095 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO W 29 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO W 29 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO W 29 " 0.075 5.00e-02 4.00e+02 ... (remaining 8684 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 3800 2.67 - 3.23: 64474 3.23 - 3.79: 147451 3.79 - 4.34: 189914 4.34 - 4.90: 269060 Nonbonded interactions: 674699 Sorted by model distance: nonbonded pdb="MG MG h 602 " pdb=" O HOH h 701 " model vdw 2.116 2.170 nonbonded pdb=" OH TYR P 37 " pdb=" O ILE P 112 " model vdw 2.191 2.440 nonbonded pdb=" O2A ADP h 601 " pdb="MG MG h 602 " model vdw 2.209 2.170 nonbonded pdb=" OD1 PHD h 341 " pdb="MG MG h 602 " model vdw 2.218 2.170 nonbonded pdb=" O SER g 157 " pdb=" OG SER g 160 " model vdw 2.234 2.440 ... (remaining 674694 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 13.730 Check model and map are aligned: 0.830 Set scattering table: 0.540 Process input model: 214.690 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.227 81156 Z= 0.481 Angle : 1.073 53.904 117629 Z= 0.567 Chirality : 0.054 0.446 14501 Planarity : 0.011 0.539 8687 Dihedral : 21.955 179.748 42255 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 0.48 % Allowed : 3.91 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.23 % 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: -3.48 (0.10), residues: 4976 helix: -2.62 (0.10), residues: 1563 sheet: -2.08 (0.16), residues: 853 loop : -2.13 (0.10), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP g 83 HIS 0.013 0.003 HIS f 135 PHE 0.041 0.004 PHE C 236 TYR 0.042 0.003 TYR P 97 ARG 0.022 0.001 ARG J 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2284 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 2263 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8687 (mt) cc_final: 0.8464 (mt) REVERT: A 9 GLN cc_start: 0.8307 (tp-100) cc_final: 0.8068 (tp-100) REVERT: A 42 LYS cc_start: 0.7549 (pptt) cc_final: 0.7303 (pptt) REVERT: A 44 ASP cc_start: 0.5403 (m-30) cc_final: 0.5104 (m-30) REVERT: A 126 ASP cc_start: 0.8519 (t0) cc_final: 0.8018 (t0) REVERT: A 145 ILE cc_start: 0.8084 (mt) cc_final: 0.7747 (tp) REVERT: A 184 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7258 (ptm160) REVERT: A 186 ARG cc_start: 0.8560 (mtp180) cc_final: 0.8348 (mtp85) REVERT: B 41 ILE cc_start: 0.8809 (mm) cc_final: 0.8416 (mp) REVERT: B 49 VAL cc_start: 0.8717 (t) cc_final: 0.8185 (p) REVERT: B 115 LYS cc_start: 0.9053 (mttt) cc_final: 0.8651 (mttm) REVERT: B 144 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8743 (ttpp) REVERT: B 146 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8377 (mmt90) REVERT: B 159 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8842 (mm-40) REVERT: B 177 GLN cc_start: 0.8679 (pt0) cc_final: 0.8348 (pm20) REVERT: B 223 PHE cc_start: 0.6797 (t80) cc_final: 0.6165 (t80) REVERT: B 229 MET cc_start: 0.8260 (mmt) cc_final: 0.7965 (mmm) REVERT: C 74 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7513 (mmtm) REVERT: C 84 PHE cc_start: 0.8370 (m-80) cc_final: 0.8000 (m-80) REVERT: C 121 ARG cc_start: 0.8148 (ppp80) cc_final: 0.7811 (ppp80) REVERT: C 188 CYS cc_start: 0.8300 (t) cc_final: 0.8021 (t) REVERT: C 211 LYS cc_start: 0.9472 (ttmt) cc_final: 0.9165 (ttmp) REVERT: C 212 LYS cc_start: 0.9375 (mttp) cc_final: 0.8818 (mmmt) REVERT: C 236 PHE cc_start: 0.8634 (t80) cc_final: 0.8382 (t80) REVERT: C 257 LYS cc_start: 0.8937 (pptt) cc_final: 0.8545 (pptt) REVERT: D 14 ASP cc_start: 0.8644 (t0) cc_final: 0.8377 (t0) REVERT: D 27 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8233 (ttm-80) REVERT: D 32 ASP cc_start: 0.7742 (m-30) cc_final: 0.7456 (m-30) REVERT: D 34 TYR cc_start: 0.8411 (t80) cc_final: 0.8137 (t80) REVERT: D 48 ILE cc_start: 0.8626 (mt) cc_final: 0.8324 (mt) REVERT: D 62 LYS cc_start: 0.8617 (mttt) cc_final: 0.8138 (tttt) REVERT: D 68 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7981 (mt-10) REVERT: D 85 GLU cc_start: 0.7666 (tp30) cc_final: 0.6750 (tp30) REVERT: D 86 LEU cc_start: 0.8461 (mt) cc_final: 0.7279 (mt) REVERT: D 106 ARG cc_start: 0.9433 (ttt-90) cc_final: 0.8989 (ttp80) REVERT: D 116 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8593 (ttp-170) REVERT: D 138 VAL cc_start: 0.9207 (t) cc_final: 0.8980 (m) REVERT: D 141 LYS cc_start: 0.9261 (mtmt) cc_final: 0.8730 (mttt) REVERT: D 150 MET cc_start: 0.8453 (ptp) cc_final: 0.7725 (ptp) REVERT: D 152 PHE cc_start: 0.9055 (m-80) cc_final: 0.7852 (m-80) REVERT: D 166 TYR cc_start: 0.8789 (p90) cc_final: 0.8103 (p90) REVERT: D 174 HIS cc_start: 0.8792 (m-70) cc_final: 0.8457 (m90) REVERT: E 79 ASP cc_start: 0.8798 (t70) cc_final: 0.8449 (t0) REVERT: E 149 TYR cc_start: 0.9262 (m-10) cc_final: 0.9046 (m-80) REVERT: E 223 SER cc_start: 0.9445 (m) cc_final: 0.9203 (t) REVERT: E 244 ILE cc_start: 0.8850 (mt) cc_final: 0.8575 (pp) REVERT: E 254 LYS cc_start: 0.9490 (tmmt) cc_final: 0.9247 (ttmm) REVERT: F 27 ASP cc_start: 0.8838 (p0) cc_final: 0.8350 (p0) REVERT: F 47 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8798 (mmtt) REVERT: F 118 ASN cc_start: 0.8833 (m110) cc_final: 0.8564 (m-40) REVERT: F 167 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8134 (mtpt) REVERT: F 171 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8168 (mt-10) REVERT: F 188 TYR cc_start: 0.9062 (t80) cc_final: 0.8714 (t80) REVERT: F 191 LYS cc_start: 0.8775 (mttp) cc_final: 0.7800 (mtmm) REVERT: F 193 LYS cc_start: 0.8458 (tmmt) cc_final: 0.7939 (tttm) REVERT: F 195 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8072 (mm-30) REVERT: G 23 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8715 (mttm) REVERT: G 56 ASN cc_start: 0.7937 (m110) cc_final: 0.7716 (m-40) REVERT: G 100 CYS cc_start: 0.7730 (p) cc_final: 0.7403 (p) REVERT: G 146 ASN cc_start: 0.9218 (m110) cc_final: 0.8888 (m110) REVERT: G 152 ASP cc_start: 0.9295 (t0) cc_final: 0.8990 (t0) REVERT: H 9 VAL cc_start: 0.7744 (p) cc_final: 0.7537 (t) REVERT: H 32 MET cc_start: 0.8120 (mpp) cc_final: 0.7806 (mpp) REVERT: H 82 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6807 (mt-10) REVERT: H 100 ILE cc_start: 0.7037 (mm) cc_final: 0.6667 (tt) REVERT: H 142 LYS cc_start: 0.8569 (mttt) cc_final: 0.8209 (pttp) REVERT: H 145 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.6989 (tmt-80) REVERT: H 160 LYS cc_start: 0.8446 (tppt) cc_final: 0.7611 (ttpt) REVERT: I 80 ASP cc_start: 0.8633 (t70) cc_final: 0.8261 (t0) REVERT: I 148 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8588 (tttt) REVERT: I 149 TYR cc_start: 0.8243 (m-10) cc_final: 0.7913 (m-10) REVERT: I 153 LYS cc_start: 0.9227 (mttp) cc_final: 0.8758 (mptp) REVERT: I 159 SER cc_start: 0.9234 (t) cc_final: 0.8969 (t) REVERT: I 163 GLU cc_start: 0.8377 (tp30) cc_final: 0.8106 (tp30) REVERT: I 167 GLN cc_start: 0.8867 (mm110) cc_final: 0.8654 (mm110) REVERT: I 178 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8207 (mtm180) REVERT: I 193 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8956 (mmpt) REVERT: J 30 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8511 (ttmm) REVERT: J 75 ASN cc_start: 0.8953 (m110) cc_final: 0.8569 (m-40) REVERT: J 104 ASP cc_start: 0.8992 (m-30) cc_final: 0.8557 (m-30) REVERT: K 9 ILE cc_start: 0.9585 (mm) cc_final: 0.8856 (mm) REVERT: K 18 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8392 (mm-30) REVERT: K 21 MET cc_start: 0.8234 (tpp) cc_final: 0.8001 (tpp) REVERT: K 31 LYS cc_start: 0.9316 (mttt) cc_final: 0.8997 (mtpt) REVERT: L 51 ILE cc_start: 0.9173 (pt) cc_final: 0.8779 (pp) REVERT: L 84 ARG cc_start: 0.9004 (mtt90) cc_final: 0.8760 (mtt-85) REVERT: L 85 THR cc_start: 0.9163 (p) cc_final: 0.8870 (p) REVERT: L 104 LYS cc_start: 0.8613 (tptp) cc_final: 0.8394 (tptm) REVERT: L 107 LYS cc_start: 0.9056 (mmtp) cc_final: 0.8848 (mmtp) REVERT: L 132 ARG cc_start: 0.9285 (ptt90) cc_final: 0.9045 (ptm-80) REVERT: M 12 MET cc_start: 0.6445 (mpt) cc_final: 0.6117 (ttt) REVERT: M 76 LEU cc_start: 0.8461 (tp) cc_final: 0.8172 (tt) REVERT: M 78 LYS cc_start: 0.8884 (mppt) cc_final: 0.8527 (mppt) REVERT: M 83 LYS cc_start: 0.8888 (mppt) cc_final: 0.8614 (mppt) REVERT: N 11 LEU cc_start: 0.8017 (tp) cc_final: 0.7764 (tt) REVERT: N 58 HIS cc_start: 0.8810 (m90) cc_final: 0.8032 (m-70) REVERT: N 100 LYS cc_start: 0.9187 (ptmm) cc_final: 0.8887 (ttpt) REVERT: N 145 THR cc_start: 0.9317 (p) cc_final: 0.9076 (p) REVERT: O 31 CYS cc_start: 0.7724 (t) cc_final: 0.6999 (p) REVERT: O 32 HIS cc_start: 0.8380 (m-70) cc_final: 0.7661 (m-70) REVERT: O 39 ASP cc_start: 0.6574 (p0) cc_final: 0.6116 (p0) REVERT: O 83 GLN cc_start: 0.8795 (tp40) cc_final: 0.8580 (tm130) REVERT: O 86 LYS cc_start: 0.8784 (mptm) cc_final: 0.8574 (mmtp) REVERT: O 87 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8021 (mt-10) REVERT: O 137 SER cc_start: 0.7506 (t) cc_final: 0.7080 (p) REVERT: P 24 GLN cc_start: 0.8752 (mt0) cc_final: 0.8415 (mt0) REVERT: P 105 VAL cc_start: 0.9522 (t) cc_final: 0.9275 (p) REVERT: Q 97 GLN cc_start: 0.8790 (tp-100) cc_final: 0.7690 (tp40) REVERT: R 33 ARG cc_start: 0.8770 (mmp-170) cc_final: 0.8549 (mmp80) REVERT: R 40 ILE cc_start: 0.9338 (mt) cc_final: 0.9045 (pp) REVERT: R 46 LEU cc_start: 0.9067 (tp) cc_final: 0.8785 (tm) REVERT: a 54 SER cc_start: 0.9341 (t) cc_final: 0.8600 (p) REVERT: U 32 LEU cc_start: 0.9114 (tp) cc_final: 0.8887 (tp) REVERT: U 51 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8442 (mmmt) REVERT: V 49 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8463 (mp10) REVERT: V 50 PHE cc_start: 0.8904 (p90) cc_final: 0.8463 (p90) REVERT: V 76 ASP cc_start: 0.8806 (m-30) cc_final: 0.7936 (OUTLIER) REVERT: W 86 LEU cc_start: 0.9503 (tp) cc_final: 0.8957 (tt) REVERT: W 90 GLN cc_start: 0.8974 (mt0) cc_final: 0.8666 (mt0) REVERT: W 101 PHE cc_start: 0.8381 (m-80) cc_final: 0.8100 (m-80) REVERT: W 111 MET cc_start: 0.7800 (ptp) cc_final: 0.7451 (ptp) REVERT: X 11 ARG cc_start: 0.9003 (ttm-80) cc_final: 0.8721 (ttm110) REVERT: Y 18 LEU cc_start: 0.9429 (mt) cc_final: 0.9128 (mt) REVERT: Y 39 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8478 (tp30) REVERT: Y 77 ASP cc_start: 0.9008 (m-30) cc_final: 0.8792 (m-30) REVERT: Y 112 ASN cc_start: 0.9118 (m110) cc_final: 0.8854 (m-40) REVERT: b 31 TYR cc_start: 0.7503 (p90) cc_final: 0.7253 (p90) REVERT: b 34 ASP cc_start: 0.8025 (m-30) cc_final: 0.7692 (m-30) REVERT: b 63 LEU cc_start: 0.8373 (mt) cc_final: 0.7932 (mt) REVERT: b 82 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8675 (mmmt) REVERT: c 10 LYS cc_start: 0.9286 (mmtp) cc_final: 0.8892 (mmtt) REVERT: c 35 MET cc_start: 0.4162 (mmp) cc_final: 0.3947 (mmm) REVERT: c 44 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7633 (mmm160) REVERT: f 146 LEU cc_start: 0.8185 (mt) cc_final: 0.7870 (mp) REVERT: g 27 PHE cc_start: 0.9077 (m-80) cc_final: 0.8659 (m-80) REVERT: g 31 ILE cc_start: 0.8616 (mm) cc_final: 0.8029 (tp) REVERT: g 92 LEU cc_start: 0.8882 (mt) cc_final: 0.8520 (mt) REVERT: g 140 TYR cc_start: 0.7859 (t80) cc_final: 0.7154 (t80) REVERT: g 148 SER cc_start: 0.9160 (m) cc_final: 0.8922 (p) REVERT: g 152 SER cc_start: 0.7956 (t) cc_final: 0.7735 (t) REVERT: g 153 CYS cc_start: 0.7732 (t) cc_final: 0.7470 (p) REVERT: g 175 LYS cc_start: 0.8008 (mttt) cc_final: 0.7157 (mptp) REVERT: g 189 ILE cc_start: 0.7647 (mt) cc_final: 0.6798 (mt) REVERT: g 218 LEU cc_start: 0.9472 (mp) cc_final: 0.9244 (mp) REVERT: g 228 TYR cc_start: 0.7664 (m-10) cc_final: 0.7444 (m-80) REVERT: g 259 TRP cc_start: 0.6519 (m100) cc_final: 0.6181 (m100) REVERT: g 285 GLN cc_start: 0.9064 (mm110) cc_final: 0.8719 (mm110) REVERT: T 42 HIS cc_start: 0.7356 (t-90) cc_final: 0.7121 (t-90) REVERT: T 67 ARG cc_start: 0.8415 (ttt180) cc_final: 0.7555 (ttm170) REVERT: T 82 ARG cc_start: 0.9029 (ttp-170) cc_final: 0.8816 (ttp80) REVERT: T 118 ASP cc_start: 0.9064 (t70) cc_final: 0.8713 (t0) REVERT: T 122 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8006 (pttt) REVERT: T 130 ASP cc_start: 0.8515 (t0) cc_final: 0.8257 (t0) REVERT: h 165 ARG cc_start: 0.8841 (ptp-110) cc_final: 0.8479 (ptp-110) REVERT: h 173 MET cc_start: 0.9417 (mmm) cc_final: 0.8956 (mmm) REVERT: h 181 GLU cc_start: 0.8700 (pt0) cc_final: 0.8456 (pt0) REVERT: h 266 GLU cc_start: 0.7570 (pp20) cc_final: 0.6761 (pp20) REVERT: h 330 MET cc_start: 0.7389 (ptp) cc_final: 0.7005 (ptp) REVERT: h 337 VAL cc_start: 0.8777 (t) cc_final: 0.8268 (t) REVERT: h 378 VAL cc_start: 0.8307 (m) cc_final: 0.8073 (m) outliers start: 21 outliers final: 6 residues processed: 2270 average time/residue: 1.6387 time to fit residues: 4875.5502 Evaluate side-chains 1674 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1669 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 205 ARG Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain g residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 0.9990 chunk 500 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 337 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 517 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 385 optimal weight: 0.0980 chunk 599 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 113 GLN A 164 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 145 GLN E 8 HIS E 161 GLN E 188 ASN E 201 HIS E 209 HIS E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 107 ASN F 110 GLN F 114 ASN F 118 ASN ** F 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 56 ASN G 163 ASN G 202 ASN H 73 GLN H 126 HIS H 157 HIS H 163 GLN H 186 ASN I 99 ASN I 138 ASN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN K 7 ASN L 5 GLN L 39 ASN L 65 ASN L 121 GLN M 72 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN Q 80 GLN Q 97 GLN R 26 ASN S 11 HIS S 87 GLN ** S 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN a 72 HIS ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN W 64 ASN W 70 ASN X 20 GLN X 87 ASN Z 45 ASN Z 46 ASN Z 64 ASN Z 103 HIS c 29 GLN c 45 ASN d 3 HIS d 26 ASN d 28 HIS d 45 GLN e 44 ASN f 139 HIS g 14 HIS ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN h 193 ASN ** h 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 81156 Z= 0.258 Angle : 0.713 13.498 117629 Z= 0.372 Chirality : 0.042 0.288 14501 Planarity : 0.006 0.128 8687 Dihedral : 24.091 179.997 31875 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 5.61 % Allowed : 22.32 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.08 % 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: -2.27 (0.11), residues: 4976 helix: -1.18 (0.12), residues: 1554 sheet: -1.64 (0.16), residues: 891 loop : -1.59 (0.11), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 67 HIS 0.009 0.001 HIS T 42 PHE 0.026 0.002 PHE M 128 TYR 0.021 0.002 TYR I 113 ARG 0.013 0.001 ARG a 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2083 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1839 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8887 (mttm) cc_final: 0.8585 (mttm) REVERT: A 53 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6415 (mmp80) REVERT: A 57 LYS cc_start: 0.8312 (mmpt) cc_final: 0.7765 (mtpp) REVERT: A 120 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7387 (mmm-85) REVERT: A 126 ASP cc_start: 0.8499 (t0) cc_final: 0.8142 (t0) REVERT: A 155 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.8026 (ttt180) REVERT: A 174 MET cc_start: 0.8761 (tpp) cc_final: 0.8557 (mpp) REVERT: B 113 MET cc_start: 0.8601 (mtm) cc_final: 0.8373 (mtp) REVERT: B 115 LYS cc_start: 0.8995 (mttt) cc_final: 0.8589 (mttm) REVERT: B 144 LYS cc_start: 0.9069 (ttpt) cc_final: 0.8770 (ttpp) REVERT: B 146 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8311 (mmt90) REVERT: B 223 PHE cc_start: 0.6920 (t80) cc_final: 0.6153 (t80) REVERT: C 90 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7325 (tt0) REVERT: C 96 PHE cc_start: 0.8974 (t80) cc_final: 0.8706 (t80) REVERT: C 108 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8603 (ttpp) REVERT: C 121 ARG cc_start: 0.8191 (ppp80) cc_final: 0.7852 (ppp80) REVERT: C 127 PHE cc_start: 0.9109 (m-80) cc_final: 0.8614 (m-80) REVERT: C 183 LYS cc_start: 0.9115 (mttt) cc_final: 0.8586 (mttt) REVERT: C 188 CYS cc_start: 0.8163 (t) cc_final: 0.7829 (t) REVERT: C 200 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7933 (ttp-170) REVERT: D 10 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8655 (tppt) REVERT: D 25 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9176 (mt) REVERT: D 27 ARG cc_start: 0.8996 (tpp80) cc_final: 0.8695 (tpp-160) REVERT: D 32 ASP cc_start: 0.7188 (m-30) cc_final: 0.6932 (m-30) REVERT: D 50 ILE cc_start: 0.7773 (mm) cc_final: 0.7381 (tp) REVERT: D 62 LYS cc_start: 0.8695 (mttt) cc_final: 0.8123 (tttt) REVERT: D 68 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7919 (mt-10) REVERT: D 141 LYS cc_start: 0.9355 (mtmt) cc_final: 0.8869 (mttt) REVERT: D 150 MET cc_start: 0.8080 (ptp) cc_final: 0.7776 (ptp) REVERT: D 152 PHE cc_start: 0.9002 (m-80) cc_final: 0.7794 (m-80) REVERT: D 166 TYR cc_start: 0.8683 (p90) cc_final: 0.7569 (p90) REVERT: D 174 HIS cc_start: 0.8612 (m-70) cc_final: 0.8324 (m90) REVERT: D 217 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6867 (tp) REVERT: E 79 ASP cc_start: 0.8716 (t70) cc_final: 0.8498 (t0) REVERT: E 168 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8804 (mmmt) REVERT: E 223 SER cc_start: 0.9411 (m) cc_final: 0.9180 (t) REVERT: E 254 LYS cc_start: 0.9484 (tmmt) cc_final: 0.9231 (ttmm) REVERT: F 27 ASP cc_start: 0.8796 (p0) cc_final: 0.8439 (p0) REVERT: F 29 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7479 (mm110) REVERT: F 33 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9311 (pp) REVERT: F 36 GLN cc_start: 0.8491 (tp40) cc_final: 0.8070 (tp40) REVERT: F 47 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8816 (mmtt) REVERT: F 118 ASN cc_start: 0.8816 (m-40) cc_final: 0.8570 (m-40) REVERT: F 182 LYS cc_start: 0.9448 (mtmm) cc_final: 0.9243 (mtmm) REVERT: F 188 TYR cc_start: 0.9042 (t80) cc_final: 0.8633 (t80) REVERT: F 193 LYS cc_start: 0.8359 (tmmt) cc_final: 0.8038 (tttm) REVERT: F 195 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8362 (tp30) REVERT: G 23 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8801 (mttm) REVERT: G 146 ASN cc_start: 0.9173 (m110) cc_final: 0.8909 (m110) REVERT: H 58 LYS cc_start: 0.7179 (mmtt) cc_final: 0.6846 (mmpt) REVERT: H 142 LYS cc_start: 0.8614 (mttt) cc_final: 0.8272 (mtmt) REVERT: H 160 LYS cc_start: 0.8108 (tppt) cc_final: 0.7052 (ttpp) REVERT: H 163 GLN cc_start: 0.8155 (tt0) cc_final: 0.7867 (tm-30) REVERT: H 178 LYS cc_start: 0.5942 (tptt) cc_final: 0.5506 (ttpp) REVERT: H 188 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7326 (mm-30) REVERT: I 80 ASP cc_start: 0.8634 (t70) cc_final: 0.8186 (t0) REVERT: I 99 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8850 (t0) REVERT: I 167 GLN cc_start: 0.8994 (mm110) cc_final: 0.8679 (OUTLIER) REVERT: I 168 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8725 (mm-40) REVERT: J 18 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7940 (mmp-170) REVERT: J 30 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8747 (ttmm) REVERT: J 34 GLU cc_start: 0.8836 (tp30) cc_final: 0.8528 (tm-30) REVERT: J 66 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8753 (mmmt) REVERT: J 104 ASP cc_start: 0.8958 (m-30) cc_final: 0.8544 (m-30) REVERT: J 107 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8239 (mm-30) REVERT: K 9 ILE cc_start: 0.9548 (mm) cc_final: 0.8778 (mm) REVERT: K 31 LYS cc_start: 0.9227 (mttt) cc_final: 0.8957 (mtpt) REVERT: K 77 GLN cc_start: 0.8604 (mm110) cc_final: 0.8247 (mm110) REVERT: L 11 GLN cc_start: 0.8830 (mp10) cc_final: 0.8495 (mp10) REVERT: L 56 ILE cc_start: 0.8927 (tp) cc_final: 0.8663 (pp) REVERT: L 83 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: L 141 ASN cc_start: 0.9022 (t0) cc_final: 0.8408 (t0) REVERT: M 76 LEU cc_start: 0.8307 (tp) cc_final: 0.7933 (tt) REVERT: M 78 LYS cc_start: 0.8847 (mppt) cc_final: 0.8426 (mppt) REVERT: M 84 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8310 (mmmt) REVERT: M 116 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6364 (tppp) REVERT: N 36 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: O 31 CYS cc_start: 0.7701 (t) cc_final: 0.6780 (p) REVERT: O 39 ASP cc_start: 0.6417 (p0) cc_final: 0.6171 (p0) REVERT: O 86 LYS cc_start: 0.8742 (mptm) cc_final: 0.8330 (mmtm) REVERT: O 87 GLU cc_start: 0.8978 (mt-10) cc_final: 0.7996 (mt-10) REVERT: O 125 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7643 (mmmt) REVERT: O 137 SER cc_start: 0.6969 (t) cc_final: 0.6491 (p) REVERT: P 58 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8222 (mmmt) REVERT: Q 35 ASN cc_start: 0.9207 (t0) cc_final: 0.8948 (m-40) REVERT: R 40 ILE cc_start: 0.9307 (mt) cc_final: 0.9003 (pp) REVERT: R 46 LEU cc_start: 0.9016 (tp) cc_final: 0.8759 (tm) REVERT: S 23 ARG cc_start: 0.8733 (mpp80) cc_final: 0.8479 (mpp80) REVERT: U 20 ILE cc_start: 0.7797 (mp) cc_final: 0.7505 (mp) REVERT: U 32 LEU cc_start: 0.8886 (tp) cc_final: 0.8683 (tp) REVERT: U 34 LYS cc_start: 0.8895 (tppp) cc_final: 0.8550 (tppp) REVERT: U 51 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8326 (mmmt) REVERT: V 10 ASP cc_start: 0.9057 (m-30) cc_final: 0.8439 (m-30) REVERT: V 70 LEU cc_start: 0.8736 (tp) cc_final: 0.8483 (tp) REVERT: V 72 LEU cc_start: 0.8899 (tp) cc_final: 0.8663 (tp) REVERT: V 76 ASP cc_start: 0.8671 (m-30) cc_final: 0.7990 (OUTLIER) REVERT: W 51 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7671 (mt-10) REVERT: W 86 LEU cc_start: 0.9503 (tp) cc_final: 0.9047 (tt) REVERT: W 90 GLN cc_start: 0.9046 (mt0) cc_final: 0.8806 (mt0) REVERT: W 98 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8420 (mt0) REVERT: Y 10 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8174 (mtm-85) REVERT: Y 18 LEU cc_start: 0.9384 (mt) cc_final: 0.9171 (mt) REVERT: Y 39 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8563 (tp30) REVERT: Y 77 ASP cc_start: 0.8988 (m-30) cc_final: 0.8758 (m-30) REVERT: Y 112 ASN cc_start: 0.9061 (m110) cc_final: 0.8796 (m-40) REVERT: Z 58 LEU cc_start: 0.8045 (tp) cc_final: 0.7734 (mt) REVERT: Z 61 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8853 (mm-30) REVERT: b 51 GLN cc_start: 0.7567 (mt0) cc_final: 0.7313 (mt0) REVERT: c 13 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7355 (ttm110) REVERT: c 35 MET cc_start: 0.4284 (mmp) cc_final: 0.4006 (mpp) REVERT: c 44 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7560 (mmm160) REVERT: c 66 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6612 (ptp-170) REVERT: d 28 HIS cc_start: 0.8456 (m-70) cc_final: 0.8245 (m90) REVERT: d 32 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7829 (mtp180) REVERT: f 113 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8216 (pmtt) REVERT: f 143 LYS cc_start: 0.8172 (tmtp) cc_final: 0.7732 (tttt) REVERT: g 5 MET cc_start: 0.8238 (mmm) cc_final: 0.7295 (mmm) REVERT: g 27 PHE cc_start: 0.8896 (m-80) cc_final: 0.8673 (m-80) REVERT: g 87 LEU cc_start: 0.8977 (mm) cc_final: 0.8721 (mt) REVERT: g 133 ASN cc_start: 0.8194 (t0) cc_final: 0.7722 (p0) REVERT: g 148 SER cc_start: 0.9035 (m) cc_final: 0.8802 (p) REVERT: g 153 CYS cc_start: 0.7483 (t) cc_final: 0.7235 (p) REVERT: g 189 ILE cc_start: 0.7650 (mt) cc_final: 0.7104 (mt) REVERT: g 218 LEU cc_start: 0.9416 (mp) cc_final: 0.9157 (mp) REVERT: g 237 ASN cc_start: 0.8115 (m110) cc_final: 0.7857 (m-40) REVERT: g 285 GLN cc_start: 0.9039 (mm110) cc_final: 0.8573 (mm110) REVERT: T 130 ASP cc_start: 0.8436 (t0) cc_final: 0.8086 (t0) REVERT: h 165 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8639 (ptp-110) REVERT: h 173 MET cc_start: 0.9402 (mmm) cc_final: 0.9163 (mmm) REVERT: h 266 GLU cc_start: 0.8158 (pp20) cc_final: 0.7746 (pp20) REVERT: h 330 MET cc_start: 0.7252 (ptp) cc_final: 0.7015 (ptp) REVERT: h 403 MET cc_start: 0.3931 (OUTLIER) cc_final: 0.3446 (ptm) outliers start: 244 outliers final: 122 residues processed: 1905 average time/residue: 1.5998 time to fit residues: 4045.7043 Evaluate side-chains 1809 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1672 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 205 ARG Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 55 ARG Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 104 ASP Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 134 GLN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 63 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 59 LYS Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 80 LYS Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 244 ASN Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain g residue 314 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 403 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 498 optimal weight: 0.5980 chunk 408 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 600 optimal weight: 5.9990 chunk 648 optimal weight: 5.9990 chunk 534 optimal weight: 0.0050 chunk 595 optimal weight: 0.0470 chunk 204 optimal weight: 3.9990 chunk 481 optimal weight: 0.3980 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 118 GLN B 163 GLN C 172 ASN C 235 ASN D 4 GLN E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN L 5 GLN L 65 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 GLN Q 86 GLN S 11 HIS ** S 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 HIS V 35 ASN W 64 ASN W 70 ASN X 20 GLN X 63 ASN d 26 ASN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 272 GLN T 63 HIS T 83 GLN h 196 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 81156 Z= 0.165 Angle : 0.660 12.434 117629 Z= 0.340 Chirality : 0.038 0.294 14501 Planarity : 0.005 0.121 8687 Dihedral : 23.910 179.729 31875 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 5.08 % Allowed : 25.79 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % 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: -1.67 (0.11), residues: 4976 helix: -0.54 (0.13), residues: 1532 sheet: -1.33 (0.16), residues: 886 loop : -1.32 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP g 177 HIS 0.011 0.001 HIS N 58 PHE 0.038 0.002 PHE C 97 TYR 0.022 0.002 TYR I 113 ARG 0.015 0.001 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2015 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1794 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8228 (tp-100) REVERT: A 46 ILE cc_start: 0.8125 (mt) cc_final: 0.7866 (mp) REVERT: A 52 LYS cc_start: 0.8943 (mttm) cc_final: 0.8675 (mttm) REVERT: A 56 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7479 (tp30) REVERT: A 152 SER cc_start: 0.7442 (m) cc_final: 0.7067 (p) REVERT: A 174 MET cc_start: 0.8705 (tpp) cc_final: 0.8492 (mpp) REVERT: B 36 PRO cc_start: 0.8341 (Cg_exo) cc_final: 0.8102 (Cg_endo) REVERT: B 42 ARG cc_start: 0.8343 (tpp-160) cc_final: 0.8132 (tpp-160) REVERT: B 96 CYS cc_start: 0.6127 (p) cc_final: 0.5705 (p) REVERT: B 115 LYS cc_start: 0.8982 (mttt) cc_final: 0.8603 (mttm) REVERT: B 144 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8742 (ttpp) REVERT: B 146 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8192 (mmt90) REVERT: B 183 GLU cc_start: 0.8495 (mp0) cc_final: 0.8156 (mp0) REVERT: B 218 LEU cc_start: 0.8576 (mm) cc_final: 0.8356 (mp) REVERT: B 223 PHE cc_start: 0.6950 (t80) cc_final: 0.6222 (t80) REVERT: C 60 TRP cc_start: 0.8194 (t60) cc_final: 0.7880 (t60) REVERT: C 90 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7061 (tt0) REVERT: C 108 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: C 121 ARG cc_start: 0.8190 (ppp80) cc_final: 0.7859 (ppp80) REVERT: C 125 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8776 (mtpp) REVERT: C 127 PHE cc_start: 0.9142 (m-80) cc_final: 0.8747 (m-80) REVERT: C 183 LYS cc_start: 0.9077 (mttt) cc_final: 0.8583 (mttt) REVERT: C 200 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7939 (ttp-170) REVERT: D 10 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8650 (tppt) REVERT: D 47 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7126 (tp30) REVERT: D 50 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7193 (tp) REVERT: D 62 LYS cc_start: 0.8625 (mttt) cc_final: 0.7984 (tttt) REVERT: D 68 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 116 ARG cc_start: 0.9132 (ttp-170) cc_final: 0.8692 (tpp-160) REVERT: D 150 MET cc_start: 0.7967 (ptp) cc_final: 0.7525 (ptp) REVERT: D 152 PHE cc_start: 0.9007 (m-80) cc_final: 0.7656 (m-80) REVERT: D 162 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8046 (p0) REVERT: D 166 TYR cc_start: 0.8598 (p90) cc_final: 0.7771 (p90) REVERT: D 174 HIS cc_start: 0.8476 (m-70) cc_final: 0.8167 (m90) REVERT: D 193 ASP cc_start: 0.8364 (p0) cc_final: 0.8025 (p0) REVERT: D 217 ILE cc_start: 0.7254 (mm) cc_final: 0.6936 (tp) REVERT: E 56 LEU cc_start: 0.9357 (mt) cc_final: 0.9142 (mp) REVERT: E 66 MET cc_start: 0.9146 (mmm) cc_final: 0.8907 (mmm) REVERT: E 168 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8750 (mmmt) REVERT: E 199 GLU cc_start: 0.8221 (pm20) cc_final: 0.7795 (pm20) REVERT: E 223 SER cc_start: 0.9374 (m) cc_final: 0.9137 (t) REVERT: E 254 LYS cc_start: 0.9499 (tmmt) cc_final: 0.9252 (ttmm) REVERT: F 27 ASP cc_start: 0.8818 (p0) cc_final: 0.8601 (p0) REVERT: F 29 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7735 (mm110) REVERT: F 36 GLN cc_start: 0.8454 (tp40) cc_final: 0.8090 (tp40) REVERT: F 59 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8390 (mtmt) REVERT: F 62 ARG cc_start: 0.8458 (mtt180) cc_final: 0.7352 (mtt180) REVERT: F 118 ASN cc_start: 0.8739 (m-40) cc_final: 0.8486 (m-40) REVERT: F 197 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8503 (mm-30) REVERT: G 23 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8809 (mmtp) REVERT: G 100 CYS cc_start: 0.7691 (p) cc_final: 0.7486 (p) REVERT: G 105 ASN cc_start: 0.8994 (m-40) cc_final: 0.8554 (m-40) REVERT: G 146 ASN cc_start: 0.9104 (m110) cc_final: 0.8809 (m110) REVERT: G 155 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: H 113 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7584 (tmtt) REVERT: H 115 LYS cc_start: 0.5214 (ptmt) cc_final: 0.4610 (tttt) REVERT: H 142 LYS cc_start: 0.8539 (mttt) cc_final: 0.8322 (mtmt) REVERT: H 160 LYS cc_start: 0.8137 (tppt) cc_final: 0.7130 (tppp) REVERT: H 178 LYS cc_start: 0.5820 (tptt) cc_final: 0.5409 (ttpp) REVERT: H 188 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7609 (mm-30) REVERT: I 80 ASP cc_start: 0.8664 (t70) cc_final: 0.8223 (t0) REVERT: I 99 ASN cc_start: 0.8907 (t0) cc_final: 0.8476 (t0) REVERT: I 132 GLU cc_start: 0.9324 (pm20) cc_final: 0.8992 (pm20) REVERT: I 133 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8737 (mp0) REVERT: I 159 SER cc_start: 0.9201 (t) cc_final: 0.8868 (p) REVERT: I 167 GLN cc_start: 0.9028 (mm110) cc_final: 0.8702 (OUTLIER) REVERT: I 168 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8727 (mm-40) REVERT: J 18 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7884 (mmp-170) REVERT: J 34 GLU cc_start: 0.8807 (tp30) cc_final: 0.8572 (tp30) REVERT: J 65 GLU cc_start: 0.7806 (pp20) cc_final: 0.7121 (tm-30) REVERT: J 104 ASP cc_start: 0.8934 (m-30) cc_final: 0.8587 (m-30) REVERT: J 107 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: K 5 LYS cc_start: 0.9233 (ttpp) cc_final: 0.9008 (ttpp) REVERT: K 9 ILE cc_start: 0.9515 (mm) cc_final: 0.8995 (mm) REVERT: K 17 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8821 (ttmt) REVERT: K 24 LYS cc_start: 0.8295 (tmtm) cc_final: 0.7985 (tptp) REVERT: K 25 LYS cc_start: 0.8745 (tppp) cc_final: 0.8463 (tppp) REVERT: K 31 LYS cc_start: 0.9257 (mttt) cc_final: 0.8967 (mttt) REVERT: K 77 GLN cc_start: 0.8591 (mm110) cc_final: 0.8104 (mm110) REVERT: L 81 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8414 (mmmm) REVERT: L 83 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: M 12 MET cc_start: 0.7351 (ttt) cc_final: 0.6969 (ppp) REVERT: M 78 LYS cc_start: 0.8919 (mppt) cc_final: 0.8649 (mppt) REVERT: M 84 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8295 (mmmt) REVERT: M 116 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6526 (tppp) REVERT: N 99 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8526 (ttm110) REVERT: O 83 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7634 (tp-100) REVERT: O 86 LYS cc_start: 0.8643 (mptm) cc_final: 0.8303 (mmtm) REVERT: O 87 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8444 (mt-10) REVERT: O 125 LYS cc_start: 0.7870 (mmmt) cc_final: 0.7641 (mmmt) REVERT: O 137 SER cc_start: 0.6374 (t) cc_final: 0.6052 (p) REVERT: P 77 LYS cc_start: 0.9226 (mtpp) cc_final: 0.8808 (mtmt) REVERT: P 106 GLU cc_start: 0.8273 (tt0) cc_final: 0.7952 (tt0) REVERT: Q 35 ASN cc_start: 0.9179 (t0) cc_final: 0.8959 (m-40) REVERT: Q 37 ARG cc_start: 0.8315 (mtt90) cc_final: 0.8096 (mtt180) REVERT: Q 80 GLN cc_start: 0.9181 (mt0) cc_final: 0.8882 (mt0) REVERT: Q 117 ARG cc_start: 0.8625 (ptm160) cc_final: 0.8238 (ttt90) REVERT: R 11 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8563 (mmtm) REVERT: R 32 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8591 (pttp) REVERT: R 40 ILE cc_start: 0.9221 (mt) cc_final: 0.8968 (pp) REVERT: S 23 ARG cc_start: 0.8672 (mpp80) cc_final: 0.8462 (mpp80) REVERT: S 109 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7322 (mm-30) REVERT: U 20 ILE cc_start: 0.7614 (mp) cc_final: 0.7344 (mp) REVERT: U 34 LYS cc_start: 0.8940 (tppp) cc_final: 0.8527 (tppp) REVERT: U 51 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8240 (mtpt) REVERT: V 50 PHE cc_start: 0.8809 (p90) cc_final: 0.8510 (p90) REVERT: V 70 LEU cc_start: 0.8757 (tp) cc_final: 0.8539 (tp) REVERT: V 76 ASP cc_start: 0.8642 (m-30) cc_final: 0.8182 (t0) REVERT: W 20 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7831 (mtp180) REVERT: W 86 LEU cc_start: 0.9456 (tp) cc_final: 0.9047 (tt) REVERT: W 90 GLN cc_start: 0.9026 (mt0) cc_final: 0.8777 (mt0) REVERT: W 98 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: X 18 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8615 (ttp80) REVERT: X 71 ARG cc_start: 0.7859 (ttt90) cc_final: 0.7512 (ttt90) REVERT: Y 10 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8159 (mtm-85) REVERT: Y 18 LEU cc_start: 0.9300 (mt) cc_final: 0.9073 (mt) REVERT: Y 19 GLN cc_start: 0.9003 (mp10) cc_final: 0.8742 (mp10) REVERT: Y 39 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8553 (tp30) REVERT: Y 112 ASN cc_start: 0.9057 (m110) cc_final: 0.8795 (m-40) REVERT: Z 61 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8929 (mm-30) REVERT: b 51 GLN cc_start: 0.7512 (mt0) cc_final: 0.7217 (mt0) REVERT: c 11 LEU cc_start: 0.8637 (mt) cc_final: 0.7874 (tt) REVERT: c 13 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7770 (ttm110) REVERT: c 35 MET cc_start: 0.3995 (mmp) cc_final: 0.3126 (mmt) REVERT: c 44 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7488 (mmm160) REVERT: c 66 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6589 (ptp-170) REVERT: d 32 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7645 (mtp180) REVERT: f 146 LEU cc_start: 0.8662 (mm) cc_final: 0.8301 (mp) REVERT: g 77 PHE cc_start: 0.8426 (m-80) cc_final: 0.8213 (m-80) REVERT: g 83 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: g 87 LEU cc_start: 0.8819 (mm) cc_final: 0.8564 (mt) REVERT: g 133 ASN cc_start: 0.8171 (t0) cc_final: 0.7881 (p0) REVERT: g 148 SER cc_start: 0.9015 (m) cc_final: 0.8792 (p) REVERT: g 217 MET cc_start: 0.8088 (tpp) cc_final: 0.6970 (mpt) REVERT: g 218 LEU cc_start: 0.9433 (mp) cc_final: 0.9188 (mp) REVERT: g 237 ASN cc_start: 0.7991 (m110) cc_final: 0.7739 (m-40) REVERT: g 285 GLN cc_start: 0.8870 (mm110) cc_final: 0.8464 (mm110) REVERT: g 296 GLN cc_start: 0.7610 (pp30) cc_final: 0.7407 (pp30) REVERT: T 51 ASN cc_start: 0.8711 (m-40) cc_final: 0.8213 (m-40) REVERT: T 67 ARG cc_start: 0.8314 (ttt180) cc_final: 0.7073 (ttm170) REVERT: T 114 GLU cc_start: 0.7890 (pp20) cc_final: 0.7076 (pp20) REVERT: T 118 ASP cc_start: 0.8726 (t0) cc_final: 0.8466 (t0) REVERT: T 130 ASP cc_start: 0.8458 (t0) cc_final: 0.8108 (t0) REVERT: T 137 GLN cc_start: 0.8762 (mp10) cc_final: 0.8549 (mp10) REVERT: h 165 ARG cc_start: 0.8881 (ptp-110) cc_final: 0.8672 (ptp-110) REVERT: h 173 MET cc_start: 0.9412 (mmm) cc_final: 0.9165 (mmm) REVERT: h 266 GLU cc_start: 0.8245 (pp20) cc_final: 0.7787 (pp20) REVERT: h 376 MET cc_start: 0.6573 (mtp) cc_final: 0.6284 (ttm) outliers start: 221 outliers final: 89 residues processed: 1859 average time/residue: 1.5622 time to fit residues: 3871.5798 Evaluate side-chains 1760 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1656 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 59 LYS Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 314 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 42 HIS Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 409 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 3.9990 chunk 451 optimal weight: 0.9990 chunk 311 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 286 optimal weight: 0.6980 chunk 403 optimal weight: 10.0000 chunk 602 optimal weight: 6.9990 chunk 637 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 571 optimal weight: 10.0000 chunk 171 optimal weight: 0.0040 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 118 GLN B 163 GLN C 172 ASN D 145 GLN D 165 ASN E 161 GLN E 224 ASN F 29 GLN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 HIS K 39 ASN L 5 GLN L 65 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 GLN Q 29 ASN Q 86 GLN R 26 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN X 20 GLN X 63 ASN b 49 HIS b 51 GLN d 26 ASN e 15 GLN T 83 GLN T 128 GLN h 253 ASN h 363 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 81156 Z= 0.226 Angle : 0.663 12.241 117629 Z= 0.342 Chirality : 0.039 0.270 14501 Planarity : 0.005 0.125 8687 Dihedral : 23.768 179.236 31869 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 6.18 % Allowed : 27.51 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % 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: -1.38 (0.11), residues: 4976 helix: -0.21 (0.13), residues: 1542 sheet: -1.21 (0.16), residues: 886 loop : -1.19 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 176 HIS 0.014 0.001 HIS N 58 PHE 0.041 0.002 PHE M 128 TYR 0.020 0.002 TYR P 123 ARG 0.013 0.001 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1958 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1689 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8273 (tp-100) REVERT: A 52 LYS cc_start: 0.8927 (mttm) cc_final: 0.8722 (mttm) REVERT: A 56 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7495 (tp30) REVERT: A 161 ILE cc_start: 0.7505 (mp) cc_final: 0.7304 (mm) REVERT: A 174 MET cc_start: 0.8664 (tpp) cc_final: 0.8452 (mpp) REVERT: B 115 LYS cc_start: 0.8984 (mttt) cc_final: 0.8552 (mttm) REVERT: B 144 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8746 (ttpp) REVERT: B 223 PHE cc_start: 0.6956 (t80) cc_final: 0.6233 (t80) REVERT: C 60 TRP cc_start: 0.8285 (t60) cc_final: 0.8063 (t60) REVERT: C 68 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8603 (mtm-85) REVERT: C 90 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7231 (tt0) REVERT: C 121 ARG cc_start: 0.8195 (ppp80) cc_final: 0.7867 (ppp80) REVERT: C 127 PHE cc_start: 0.9141 (m-80) cc_final: 0.8710 (m-80) REVERT: C 183 LYS cc_start: 0.9057 (mttt) cc_final: 0.8591 (mttt) REVERT: C 200 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8087 (ttp-170) REVERT: C 215 MET cc_start: 0.9365 (mtt) cc_final: 0.9115 (mtt) REVERT: C 246 LYS cc_start: 0.9071 (mttt) cc_final: 0.8789 (mttt) REVERT: C 269 PHE cc_start: 0.7841 (m-80) cc_final: 0.7598 (m-80) REVERT: D 10 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8642 (tppt) REVERT: D 22 ASN cc_start: 0.9426 (t0) cc_final: 0.9191 (t0) REVERT: D 26 THR cc_start: 0.9527 (m) cc_final: 0.9170 (p) REVERT: D 47 GLU cc_start: 0.7445 (mm-30) cc_final: 0.5656 (tp30) REVERT: D 61 GLU cc_start: 0.8210 (pp20) cc_final: 0.7973 (tm-30) REVERT: D 62 LYS cc_start: 0.8716 (mttt) cc_final: 0.8153 (tttt) REVERT: D 68 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7946 (mt-10) REVERT: D 116 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8758 (tpp-160) REVERT: D 150 MET cc_start: 0.7932 (ptp) cc_final: 0.7459 (ptp) REVERT: D 152 PHE cc_start: 0.9023 (m-80) cc_final: 0.7870 (m-80) REVERT: D 166 TYR cc_start: 0.8617 (p90) cc_final: 0.7231 (p90) REVERT: D 174 HIS cc_start: 0.8492 (m-70) cc_final: 0.8175 (m90) REVERT: D 193 ASP cc_start: 0.8475 (p0) cc_final: 0.8132 (p0) REVERT: D 217 ILE cc_start: 0.7215 (mm) cc_final: 0.6987 (tp) REVERT: E 66 MET cc_start: 0.9167 (mmm) cc_final: 0.8921 (mmm) REVERT: E 223 SER cc_start: 0.9411 (m) cc_final: 0.9077 (t) REVERT: E 254 LYS cc_start: 0.9506 (tmmt) cc_final: 0.9261 (ttmm) REVERT: F 29 GLN cc_start: 0.8120 (mm110) cc_final: 0.7799 (mm110) REVERT: F 32 ASP cc_start: 0.8738 (t0) cc_final: 0.8443 (t0) REVERT: F 36 GLN cc_start: 0.8553 (tp40) cc_final: 0.8002 (tp40) REVERT: F 59 LYS cc_start: 0.8693 (mttm) cc_final: 0.8416 (mtmt) REVERT: F 62 ARG cc_start: 0.8531 (mtt180) cc_final: 0.7504 (mtt180) REVERT: F 118 ASN cc_start: 0.8771 (m-40) cc_final: 0.8453 (m-40) REVERT: F 146 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8783 (ttp80) REVERT: F 188 TYR cc_start: 0.8966 (t80) cc_final: 0.8511 (t80) REVERT: G 23 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8907 (mmtt) REVERT: G 85 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8337 (ttp80) REVERT: G 100 CYS cc_start: 0.7719 (p) cc_final: 0.7414 (p) REVERT: G 103 ASP cc_start: 0.7754 (p0) cc_final: 0.7505 (p0) REVERT: G 105 ASN cc_start: 0.8985 (m-40) cc_final: 0.8559 (m-40) REVERT: G 146 ASN cc_start: 0.9071 (m110) cc_final: 0.8742 (m110) REVERT: G 155 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8357 (mm-40) REVERT: G 186 GLN cc_start: 0.8555 (tt0) cc_final: 0.8344 (tt0) REVERT: H 115 LYS cc_start: 0.5287 (ptmt) cc_final: 0.4689 (tttt) REVERT: H 142 LYS cc_start: 0.8548 (mttt) cc_final: 0.8348 (mtmt) REVERT: H 178 LYS cc_start: 0.5873 (tptt) cc_final: 0.5459 (ttpp) REVERT: H 188 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7673 (mm-30) REVERT: I 80 ASP cc_start: 0.8687 (t70) cc_final: 0.8208 (t0) REVERT: I 88 ASN cc_start: 0.8809 (t0) cc_final: 0.8370 (t0) REVERT: I 99 ASN cc_start: 0.8992 (t0) cc_final: 0.8693 (t0) REVERT: I 167 GLN cc_start: 0.9040 (mm110) cc_final: 0.8730 (mp10) REVERT: I 168 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8786 (mm-40) REVERT: J 18 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7930 (mmp-170) REVERT: J 34 GLU cc_start: 0.8804 (tp30) cc_final: 0.8559 (tp30) REVERT: J 104 ASP cc_start: 0.9012 (m-30) cc_final: 0.8612 (m-30) REVERT: J 107 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: K 9 ILE cc_start: 0.9530 (mm) cc_final: 0.8920 (mm) REVERT: K 25 LYS cc_start: 0.8699 (tppp) cc_final: 0.8406 (tppp) REVERT: K 31 LYS cc_start: 0.9297 (mttt) cc_final: 0.8875 (mttt) REVERT: K 77 GLN cc_start: 0.8630 (mm110) cc_final: 0.8114 (mm110) REVERT: L 83 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: L 84 ARG cc_start: 0.9170 (mtt-85) cc_final: 0.8732 (mtt-85) REVERT: L 121 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8134 (mm110) REVERT: L 124 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8512 (p0) REVERT: M 12 MET cc_start: 0.7583 (ttt) cc_final: 0.7135 (ppp) REVERT: M 78 LYS cc_start: 0.8937 (mppt) cc_final: 0.8581 (mppt) REVERT: M 83 LYS cc_start: 0.8882 (mppt) cc_final: 0.8580 (ttmm) REVERT: M 128 PHE cc_start: 0.8798 (m-80) cc_final: 0.8431 (m-80) REVERT: N 5 HIS cc_start: 0.8257 (m170) cc_final: 0.8054 (m90) REVERT: N 76 LYS cc_start: 0.8820 (pttp) cc_final: 0.8459 (pptt) REVERT: O 41 PHE cc_start: 0.7543 (m-80) cc_final: 0.7195 (m-80) REVERT: O 83 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7680 (tm130) REVERT: O 86 LYS cc_start: 0.8721 (mptm) cc_final: 0.8337 (mmtm) REVERT: O 87 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8293 (mt-10) REVERT: O 95 ILE cc_start: 0.9059 (mm) cc_final: 0.8800 (pp) REVERT: O 125 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7810 (mmmt) REVERT: O 137 SER cc_start: 0.6684 (t) cc_final: 0.6304 (p) REVERT: P 64 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8468 (ttpt) REVERT: P 130 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7895 (mtp85) REVERT: Q 48 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8431 (tp40) REVERT: Q 80 GLN cc_start: 0.9206 (mt0) cc_final: 0.8872 (mt0) REVERT: Q 117 ARG cc_start: 0.8645 (ptm160) cc_final: 0.8215 (ttt-90) REVERT: R 11 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8710 (mmtm) REVERT: R 40 ILE cc_start: 0.9236 (mt) cc_final: 0.8959 (pp) REVERT: S 65 GLU cc_start: 0.8293 (tp30) cc_final: 0.7990 (tp30) REVERT: S 105 ASN cc_start: 0.7951 (m-40) cc_final: 0.7751 (m110) REVERT: U 34 LYS cc_start: 0.8981 (tppp) cc_final: 0.8516 (tppp) REVERT: U 50 VAL cc_start: 0.9559 (t) cc_final: 0.9339 (p) REVERT: U 51 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8297 (mtpt) REVERT: V 76 ASP cc_start: 0.8611 (m-30) cc_final: 0.8248 (t0) REVERT: W 20 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7883 (mmm160) REVERT: W 51 GLU cc_start: 0.7648 (tt0) cc_final: 0.6800 (mt-10) REVERT: W 68 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7455 (ptp90) REVERT: W 86 LEU cc_start: 0.9474 (tp) cc_final: 0.9053 (tt) REVERT: W 90 GLN cc_start: 0.9044 (mt0) cc_final: 0.8798 (mt0) REVERT: W 111 MET cc_start: 0.7494 (ptp) cc_final: 0.7240 (ptm) REVERT: X 14 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8254 (ttp80) REVERT: X 95 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8188 (mm-30) REVERT: Y 10 ARG cc_start: 0.8737 (ttm110) cc_final: 0.8201 (mtm-85) REVERT: Y 18 LEU cc_start: 0.9327 (mt) cc_final: 0.9062 (mt) REVERT: Y 39 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8600 (tp30) REVERT: Y 112 ASN cc_start: 0.9039 (m110) cc_final: 0.8752 (m-40) REVERT: Z 94 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8770 (mmtp) REVERT: b 34 ASP cc_start: 0.8058 (m-30) cc_final: 0.7798 (m-30) REVERT: b 51 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7270 (mt0) REVERT: c 58 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8611 (pp) REVERT: c 66 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6653 (ptp-170) REVERT: d 32 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7845 (mtp180) REVERT: f 143 LYS cc_start: 0.8091 (tmtp) cc_final: 0.7769 (tptp) REVERT: f 146 LEU cc_start: 0.8591 (mm) cc_final: 0.8367 (mm) REVERT: g 27 PHE cc_start: 0.8901 (m-80) cc_final: 0.8645 (m-80) REVERT: g 77 PHE cc_start: 0.8470 (m-80) cc_final: 0.8200 (m-80) REVERT: g 83 TRP cc_start: 0.8007 (OUTLIER) cc_final: 0.7202 (m100) REVERT: g 87 LEU cc_start: 0.8869 (mm) cc_final: 0.8605 (mt) REVERT: g 107 ASP cc_start: 0.7843 (m-30) cc_final: 0.7569 (m-30) REVERT: g 133 ASN cc_start: 0.8195 (t0) cc_final: 0.7878 (p0) REVERT: g 148 SER cc_start: 0.9064 (m) cc_final: 0.8847 (p) REVERT: g 153 CYS cc_start: 0.7622 (t) cc_final: 0.7322 (p) REVERT: g 217 MET cc_start: 0.8089 (tpp) cc_final: 0.7110 (mpt) REVERT: g 218 LEU cc_start: 0.9378 (mp) cc_final: 0.9150 (mp) REVERT: g 237 ASN cc_start: 0.8065 (m110) cc_final: 0.7828 (m-40) REVERT: g 285 GLN cc_start: 0.8880 (mm110) cc_final: 0.8442 (mm110) REVERT: g 296 GLN cc_start: 0.7772 (pp30) cc_final: 0.7519 (pp30) REVERT: T 51 ASN cc_start: 0.8838 (m-40) cc_final: 0.7821 (m110) REVERT: T 114 GLU cc_start: 0.8424 (pp20) cc_final: 0.8210 (pp20) REVERT: T 122 LYS cc_start: 0.8612 (pttt) cc_final: 0.8344 (pttp) REVERT: T 126 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8080 (tp-100) REVERT: T 130 ASP cc_start: 0.8493 (t0) cc_final: 0.8195 (t0) REVERT: T 133 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7087 (mmm160) REVERT: T 137 GLN cc_start: 0.8814 (mt0) cc_final: 0.8562 (mp10) REVERT: h 173 MET cc_start: 0.9434 (mmm) cc_final: 0.9105 (mmm) REVERT: h 266 GLU cc_start: 0.8183 (pp20) cc_final: 0.7726 (pp20) REVERT: h 376 MET cc_start: 0.6545 (mtp) cc_final: 0.6252 (ttm) outliers start: 269 outliers final: 139 residues processed: 1769 average time/residue: 1.5659 time to fit residues: 3692.9906 Evaluate side-chains 1785 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1629 time to evaluate : 4.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 36 GLN Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 64 LYS Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 GLN Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 134 GLN Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 94 LYS Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 51 GLN Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 187 ASN Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 244 ASN Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 179 ILE Chi-restraints excluded: chain h residue 254 LEU Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 277 MET Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 390 ILE Chi-restraints excluded: chain h residue 409 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 3.9990 chunk 362 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 475 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 544 optimal weight: 0.7980 chunk 440 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 572 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 208 HIS C 172 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 HIS ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN K 39 ASN L 5 GLN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN P 103 ASN Q 11 GLN Q 29 ASN Q 86 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS U 18 HIS ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN W 64 ASN X 20 GLN X 63 ASN Y 85 ASN d 26 ASN e 15 GLN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 81156 Z= 0.299 Angle : 0.692 12.293 117629 Z= 0.357 Chirality : 0.041 0.296 14501 Planarity : 0.005 0.129 8687 Dihedral : 23.721 179.465 31867 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.97 % Favored : 93.91 % Rotamer: Outliers : 6.64 % Allowed : 28.87 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % 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: -1.23 (0.12), residues: 4976 helix: -0.02 (0.13), residues: 1531 sheet: -1.11 (0.17), residues: 874 loop : -1.14 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 67 HIS 0.022 0.001 HIS K 28 PHE 0.045 0.002 PHE M 128 TYR 0.029 0.002 TYR D 87 ARG 0.015 0.001 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1965 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1677 time to evaluate : 4.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8463 (tp-100) REVERT: A 49 ILE cc_start: 0.9020 (mt) cc_final: 0.8506 (tt) REVERT: A 52 LYS cc_start: 0.8897 (mttm) cc_final: 0.8645 (mttm) REVERT: A 53 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6783 (mmp80) REVERT: A 174 MET cc_start: 0.8686 (tpp) cc_final: 0.8468 (mpp) REVERT: B 96 CYS cc_start: 0.6370 (p) cc_final: 0.5991 (p) REVERT: B 115 LYS cc_start: 0.8995 (mttt) cc_final: 0.8537 (mttm) REVERT: B 144 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8715 (ttpp) REVERT: B 183 GLU cc_start: 0.8621 (mp0) cc_final: 0.8151 (mp0) REVERT: B 223 PHE cc_start: 0.6956 (t80) cc_final: 0.6216 (t80) REVERT: B 227 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9135 (tptp) REVERT: C 60 TRP cc_start: 0.8325 (t60) cc_final: 0.8124 (t60) REVERT: C 68 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8647 (mtm-85) REVERT: C 80 GLU cc_start: 0.8697 (pm20) cc_final: 0.8478 (pm20) REVERT: C 90 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7106 (tt0) REVERT: C 121 ARG cc_start: 0.8205 (ppp80) cc_final: 0.7883 (ppp80) REVERT: C 127 PHE cc_start: 0.9101 (m-80) cc_final: 0.8643 (m-80) REVERT: C 183 LYS cc_start: 0.9074 (mttt) cc_final: 0.8622 (mttt) REVERT: C 200 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8096 (ttp-170) REVERT: C 238 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8931 (mtmt) REVERT: C 269 PHE cc_start: 0.7861 (m-80) cc_final: 0.7620 (m-80) REVERT: D 10 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8693 (tppt) REVERT: D 26 THR cc_start: 0.9556 (m) cc_final: 0.9196 (p) REVERT: D 47 GLU cc_start: 0.7828 (mm-30) cc_final: 0.6854 (tp30) REVERT: D 61 GLU cc_start: 0.8333 (pp20) cc_final: 0.8055 (tm-30) REVERT: D 62 LYS cc_start: 0.8853 (mttt) cc_final: 0.8298 (tttt) REVERT: D 68 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 116 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8769 (tpp-160) REVERT: D 125 PHE cc_start: 0.8898 (t80) cc_final: 0.8671 (t80) REVERT: D 166 TYR cc_start: 0.8432 (p90) cc_final: 0.8040 (p90) REVERT: D 174 HIS cc_start: 0.8520 (m-70) cc_final: 0.8178 (m90) REVERT: E 118 GLU cc_start: 0.7927 (tp30) cc_final: 0.7712 (tp30) REVERT: E 125 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9054 (tttt) REVERT: E 136 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8793 (mm) REVERT: E 168 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8597 (mmmt) REVERT: E 199 GLU cc_start: 0.8303 (pm20) cc_final: 0.7969 (pm20) REVERT: E 223 SER cc_start: 0.9395 (m) cc_final: 0.9132 (t) REVERT: E 254 LYS cc_start: 0.9509 (tmmt) cc_final: 0.9257 (ttmm) REVERT: F 29 GLN cc_start: 0.8146 (mm110) cc_final: 0.7907 (mm-40) REVERT: F 32 ASP cc_start: 0.8804 (t0) cc_final: 0.8508 (t0) REVERT: F 36 GLN cc_start: 0.8585 (tp40) cc_final: 0.8015 (tp40) REVERT: F 118 ASN cc_start: 0.8820 (m-40) cc_final: 0.8449 (m-40) REVERT: F 146 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8834 (ttp80) REVERT: F 195 GLU cc_start: 0.8377 (tp30) cc_final: 0.7752 (tp30) REVERT: F 197 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8369 (mm-30) REVERT: G 23 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8907 (mmtt) REVERT: G 100 CYS cc_start: 0.7725 (p) cc_final: 0.7400 (p) REVERT: G 105 ASN cc_start: 0.8950 (m-40) cc_final: 0.8463 (m-40) REVERT: G 145 PHE cc_start: 0.9113 (m-10) cc_final: 0.8909 (m-10) REVERT: G 146 ASN cc_start: 0.9016 (m110) cc_final: 0.8694 (m110) REVERT: H 113 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7504 (tmtt) REVERT: H 115 LYS cc_start: 0.5370 (ptmt) cc_final: 0.4759 (tttt) REVERT: H 160 LYS cc_start: 0.7744 (mmmt) cc_final: 0.6757 (mtpt) REVERT: H 167 GLU cc_start: 0.8304 (pm20) cc_final: 0.8090 (pm20) REVERT: H 178 LYS cc_start: 0.6030 (tptt) cc_final: 0.5760 (tttp) REVERT: H 188 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7750 (mm-30) REVERT: I 75 LYS cc_start: 0.9088 (mtpm) cc_final: 0.8660 (ttmm) REVERT: I 80 ASP cc_start: 0.8730 (t70) cc_final: 0.8290 (t0) REVERT: I 88 ASN cc_start: 0.8743 (t0) cc_final: 0.8293 (t0) REVERT: I 99 ASN cc_start: 0.9024 (t0) cc_final: 0.8767 (t0) REVERT: I 167 GLN cc_start: 0.9077 (mm110) cc_final: 0.8740 (mp10) REVERT: J 18 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8009 (mmp-170) REVERT: J 65 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7242 (tm-30) REVERT: J 104 ASP cc_start: 0.9022 (m-30) cc_final: 0.8620 (m-30) REVERT: J 107 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: J 140 GLN cc_start: 0.8355 (tp-100) cc_final: 0.7508 (tm-30) REVERT: J 174 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8607 (tptp) REVERT: K 9 ILE cc_start: 0.9546 (mm) cc_final: 0.9149 (mm) REVERT: K 21 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7528 (ttp) REVERT: K 25 LYS cc_start: 0.8678 (tppp) cc_final: 0.8326 (tppp) REVERT: K 28 HIS cc_start: 0.8184 (t-170) cc_final: 0.7892 (t-170) REVERT: K 31 LYS cc_start: 0.9273 (mttt) cc_final: 0.8896 (mtpp) REVERT: K 77 GLN cc_start: 0.8659 (mm110) cc_final: 0.8154 (mm110) REVERT: L 49 GLU cc_start: 0.8085 (tp30) cc_final: 0.7566 (tp30) REVERT: L 83 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: L 107 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8712 (mmtp) REVERT: L 124 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8440 (p0) REVERT: M 12 MET cc_start: 0.7556 (ttt) cc_final: 0.7318 (ppp) REVERT: M 78 LYS cc_start: 0.8927 (mppt) cc_final: 0.8592 (mppt) REVERT: M 83 LYS cc_start: 0.8882 (mppt) cc_final: 0.8558 (ttmm) REVERT: N 72 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7705 (tm) REVERT: N 76 LYS cc_start: 0.8816 (pttp) cc_final: 0.8447 (pptt) REVERT: O 83 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7428 (tm130) REVERT: O 86 LYS cc_start: 0.8824 (mptm) cc_final: 0.8412 (mmtm) REVERT: O 87 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8357 (mt-10) REVERT: O 95 ILE cc_start: 0.9069 (mm) cc_final: 0.8803 (pp) REVERT: O 117 ARG cc_start: 0.8332 (tpp80) cc_final: 0.7535 (tpp80) REVERT: O 121 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7755 (mtt90) REVERT: O 125 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7914 (mmmt) REVERT: O 137 SER cc_start: 0.6728 (t) cc_final: 0.6292 (p) REVERT: P 53 GLN cc_start: 0.8967 (mp10) cc_final: 0.8663 (mp10) REVERT: Q 48 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8336 (tp40) REVERT: Q 80 GLN cc_start: 0.9242 (mt0) cc_final: 0.8983 (mt0) REVERT: Q 117 ARG cc_start: 0.8638 (ptm160) cc_final: 0.8200 (ttt-90) REVERT: R 58 MET cc_start: 0.9493 (mmm) cc_final: 0.9236 (mmm) REVERT: S 65 GLU cc_start: 0.8380 (tp30) cc_final: 0.8072 (tp30) REVERT: a 52 ASP cc_start: 0.8679 (t0) cc_final: 0.7912 (t0) REVERT: U 34 LYS cc_start: 0.9031 (tppp) cc_final: 0.8629 (tppp) REVERT: U 50 VAL cc_start: 0.9599 (t) cc_final: 0.9375 (p) REVERT: U 51 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8372 (mtpt) REVERT: W 51 GLU cc_start: 0.7561 (tt0) cc_final: 0.6806 (mt-10) REVERT: W 68 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7477 (ptp90) REVERT: W 86 LEU cc_start: 0.9490 (tp) cc_final: 0.8947 (tt) REVERT: W 90 GLN cc_start: 0.9071 (mt0) cc_final: 0.8633 (mt0) REVERT: W 98 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: W 111 MET cc_start: 0.7516 (ptp) cc_final: 0.7164 (ptm) REVERT: X 95 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8206 (mm-30) REVERT: Y 10 ARG cc_start: 0.8814 (ttm110) cc_final: 0.8433 (ttm110) REVERT: Y 39 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8612 (tp30) REVERT: Y 112 ASN cc_start: 0.9067 (m110) cc_final: 0.8743 (m-40) REVERT: Z 56 ASP cc_start: 0.7938 (p0) cc_final: 0.7685 (p0) REVERT: Z 61 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8692 (mp0) REVERT: b 34 ASP cc_start: 0.8259 (m-30) cc_final: 0.7966 (m-30) REVERT: b 74 THR cc_start: 0.8580 (m) cc_final: 0.8315 (t) REVERT: b 80 ARG cc_start: 0.7666 (mpt180) cc_final: 0.7457 (mmt-90) REVERT: c 13 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7695 (ttm110) REVERT: c 58 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8652 (pp) REVERT: c 66 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6389 (ptp-170) REVERT: d 4 GLN cc_start: 0.8336 (pm20) cc_final: 0.7746 (pp30) REVERT: d 8 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.7160 (t-100) REVERT: d 37 ASN cc_start: 0.9199 (m-40) cc_final: 0.8973 (m-40) REVERT: f 143 LYS cc_start: 0.8270 (tmtp) cc_final: 0.7981 (tptp) REVERT: f 146 LEU cc_start: 0.8623 (mm) cc_final: 0.8410 (mm) REVERT: g 87 LEU cc_start: 0.8865 (mm) cc_final: 0.8612 (mt) REVERT: g 107 ASP cc_start: 0.7950 (m-30) cc_final: 0.7670 (m-30) REVERT: g 127 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8569 (mmtp) REVERT: g 133 ASN cc_start: 0.8285 (t0) cc_final: 0.7909 (p0) REVERT: g 148 SER cc_start: 0.9105 (m) cc_final: 0.8831 (p) REVERT: g 187 ASN cc_start: 0.7841 (t0) cc_final: 0.7601 (t0) REVERT: g 217 MET cc_start: 0.8093 (tpp) cc_final: 0.7077 (mpt) REVERT: g 218 LEU cc_start: 0.9325 (mp) cc_final: 0.9106 (mp) REVERT: g 237 ASN cc_start: 0.8241 (m110) cc_final: 0.7957 (m-40) REVERT: g 285 GLN cc_start: 0.8922 (mm110) cc_final: 0.8484 (mm110) REVERT: g 296 GLN cc_start: 0.7822 (pp30) cc_final: 0.7540 (pp30) REVERT: T 50 GLU cc_start: 0.7736 (pp20) cc_final: 0.7385 (pp20) REVERT: T 51 ASN cc_start: 0.8720 (m-40) cc_final: 0.8000 (m110) REVERT: T 114 GLU cc_start: 0.8639 (pp20) cc_final: 0.8390 (pp20) REVERT: T 126 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8334 (tm-30) REVERT: T 130 ASP cc_start: 0.8570 (t0) cc_final: 0.8228 (t0) REVERT: T 133 ARG cc_start: 0.7802 (tpp-160) cc_final: 0.7038 (mmm160) REVERT: T 137 GLN cc_start: 0.8838 (mt0) cc_final: 0.8549 (mp10) REVERT: h 173 MET cc_start: 0.9447 (mmm) cc_final: 0.9124 (mmm) REVERT: h 266 GLU cc_start: 0.8154 (pp20) cc_final: 0.7688 (pp20) REVERT: h 409 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6347 (pmm-80) outliers start: 288 outliers final: 161 residues processed: 1769 average time/residue: 1.5693 time to fit residues: 3707.2540 Evaluate side-chains 1791 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1607 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 48 GLN Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 134 GLN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 49 GLN Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 127 LYS Chi-restraints excluded: chain g residue 129 ILE Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 244 ASN Chi-restraints excluded: chain g residue 270 LEU Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 178 ILE Chi-restraints excluded: chain h residue 179 ILE Chi-restraints excluded: chain h residue 254 LEU Chi-restraints excluded: chain h residue 257 LEU Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 277 MET Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 373 VAL Chi-restraints excluded: chain h residue 390 ILE Chi-restraints excluded: chain h residue 409 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 3.9990 chunk 574 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 374 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 638 optimal weight: 6.9990 chunk 530 optimal weight: 7.9990 chunk 295 optimal weight: 0.0670 chunk 53 optimal weight: 10.0000 chunk 211 optimal weight: 0.8980 chunk 335 optimal weight: 20.0000 overall best weight: 3.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 124 HIS B 157 GLN C 134 ASN E 157 ASN E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 HIS G 163 ASN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN K 61 GLN L 5 GLN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN Q 11 GLN Q 86 GLN Q 97 GLN ** R 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS ** U 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN X 20 GLN X 63 ASN Y 63 HIS Y 94 HIS d 26 ASN T 83 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 81156 Z= 0.371 Angle : 0.735 12.416 117629 Z= 0.378 Chirality : 0.043 0.317 14501 Planarity : 0.006 0.132 8687 Dihedral : 23.718 179.994 31867 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.75 % Rotamer: Outliers : 6.99 % Allowed : 30.06 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % 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: -1.18 (0.12), residues: 4976 helix: -0.00 (0.13), residues: 1539 sheet: -1.10 (0.17), residues: 873 loop : -1.10 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 67 HIS 0.012 0.001 HIS K 28 PHE 0.027 0.002 PHE J 48 TYR 0.024 0.002 TYR L 36 ARG 0.015 0.001 ARG N 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1970 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1667 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.7531 (ptm) cc_final: 0.7190 (pmm) REVERT: A 49 ILE cc_start: 0.8978 (mt) cc_final: 0.8517 (tt) REVERT: A 52 LYS cc_start: 0.8863 (mttm) cc_final: 0.8622 (mttm) REVERT: A 53 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6817 (mmp80) REVERT: A 145 ILE cc_start: 0.8029 (mp) cc_final: 0.7557 (tp) REVERT: A 185 MET cc_start: 0.8085 (tpt) cc_final: 0.7733 (tpt) REVERT: B 144 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8634 (ttpp) REVERT: B 152 LYS cc_start: 0.9035 (tmmt) cc_final: 0.8510 (mptm) REVERT: B 183 GLU cc_start: 0.8634 (mp0) cc_final: 0.8160 (mp0) REVERT: B 223 PHE cc_start: 0.6969 (t80) cc_final: 0.6186 (t80) REVERT: B 227 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9083 (tptp) REVERT: C 68 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8586 (mtm-85) REVERT: C 108 LYS cc_start: 0.8824 (ttpp) cc_final: 0.8617 (tttm) REVERT: C 121 ARG cc_start: 0.8200 (ppp80) cc_final: 0.7887 (ppp80) REVERT: C 127 PHE cc_start: 0.9109 (m-80) cc_final: 0.8642 (m-80) REVERT: C 183 LYS cc_start: 0.9108 (mttt) cc_final: 0.8643 (mttt) REVERT: C 200 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8120 (ttp-170) REVERT: D 10 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8721 (tppt) REVERT: D 47 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7415 (tp30) REVERT: D 56 GLN cc_start: 0.8763 (pt0) cc_final: 0.8236 (pp30) REVERT: D 61 GLU cc_start: 0.8451 (pp20) cc_final: 0.8169 (tm-30) REVERT: D 62 LYS cc_start: 0.8868 (mttt) cc_final: 0.8325 (tttt) REVERT: D 68 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7932 (mt-10) REVERT: D 116 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8887 (tpp-160) REVERT: D 166 TYR cc_start: 0.8519 (p90) cc_final: 0.8104 (p90) REVERT: D 174 HIS cc_start: 0.8589 (m-70) cc_final: 0.8213 (m90) REVERT: D 179 GLN cc_start: 0.8728 (pm20) cc_final: 0.8501 (pm20) REVERT: D 225 GLU cc_start: 0.8333 (pm20) cc_final: 0.8064 (pm20) REVERT: E 136 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8803 (mm) REVERT: E 199 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: E 223 SER cc_start: 0.9403 (m) cc_final: 0.9074 (t) REVERT: E 254 LYS cc_start: 0.9525 (tmmt) cc_final: 0.9275 (ttmm) REVERT: F 36 GLN cc_start: 0.8600 (tp40) cc_final: 0.8025 (tp40) REVERT: F 62 ARG cc_start: 0.8541 (mtt180) cc_final: 0.8273 (mtt180) REVERT: F 118 ASN cc_start: 0.8899 (m-40) cc_final: 0.8467 (m-40) REVERT: F 137 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7682 (tp-100) REVERT: F 146 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8878 (ttp80) REVERT: F 195 GLU cc_start: 0.8425 (tp30) cc_final: 0.7905 (tp30) REVERT: F 197 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8366 (mm-30) REVERT: F 198 ARG cc_start: 0.8628 (ptt90) cc_final: 0.8287 (ttp-110) REVERT: G 16 ILE cc_start: 0.9168 (tt) cc_final: 0.8949 (tp) REVERT: G 23 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8895 (mmtt) REVERT: G 103 ASP cc_start: 0.7798 (p0) cc_final: 0.7557 (p0) REVERT: G 105 ASN cc_start: 0.8948 (m-40) cc_final: 0.8544 (m-40) REVERT: G 115 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8900 (ttmm) REVERT: G 146 ASN cc_start: 0.9055 (m110) cc_final: 0.8685 (m110) REVERT: G 156 TYR cc_start: 0.8969 (m-80) cc_final: 0.8609 (m-80) REVERT: G 202 ASN cc_start: 0.8851 (m-40) cc_final: 0.8438 (m-40) REVERT: H 115 LYS cc_start: 0.5533 (ptmt) cc_final: 0.4886 (tttt) REVERT: H 160 LYS cc_start: 0.7815 (mmmt) cc_final: 0.6872 (ttpp) REVERT: H 167 GLU cc_start: 0.8342 (pm20) cc_final: 0.8118 (pm20) REVERT: H 178 LYS cc_start: 0.6053 (tptt) cc_final: 0.5822 (tttp) REVERT: H 188 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7674 (mm-30) REVERT: I 27 TYR cc_start: 0.8880 (p90) cc_final: 0.8658 (p90) REVERT: I 75 LYS cc_start: 0.9119 (mtpm) cc_final: 0.8862 (ttmt) REVERT: I 80 ASP cc_start: 0.8705 (t70) cc_final: 0.8289 (t0) REVERT: I 88 ASN cc_start: 0.8756 (t0) cc_final: 0.8310 (t0) REVERT: I 99 ASN cc_start: 0.9048 (t0) cc_final: 0.8799 (t0) REVERT: I 111 GLN cc_start: 0.8552 (mt0) cc_final: 0.7829 (mp10) REVERT: I 167 GLN cc_start: 0.9092 (mm110) cc_final: 0.8783 (mp10) REVERT: I 168 GLN cc_start: 0.8895 (mp10) cc_final: 0.8599 (mm-40) REVERT: J 18 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8043 (mmp-170) REVERT: J 34 GLU cc_start: 0.8770 (tp30) cc_final: 0.8508 (tm-30) REVERT: J 104 ASP cc_start: 0.9030 (m-30) cc_final: 0.8652 (m-30) REVERT: J 107 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: J 174 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8584 (tptp) REVERT: K 9 ILE cc_start: 0.9523 (mm) cc_final: 0.8969 (mm) REVERT: K 21 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7572 (ttp) REVERT: K 25 LYS cc_start: 0.8617 (tppp) cc_final: 0.8224 (tppp) REVERT: K 26 ASP cc_start: 0.8608 (t0) cc_final: 0.8191 (t0) REVERT: K 31 LYS cc_start: 0.9297 (mttt) cc_final: 0.8951 (mttt) REVERT: K 77 GLN cc_start: 0.8696 (mm110) cc_final: 0.8170 (mm110) REVERT: L 83 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: L 124 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8444 (p0) REVERT: M 12 MET cc_start: 0.7495 (ttt) cc_final: 0.7238 (ppp) REVERT: M 83 LYS cc_start: 0.8883 (mppt) cc_final: 0.8569 (ttmm) REVERT: M 99 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7499 (pmtt) REVERT: N 27 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7691 (mmtt) REVERT: N 72 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7737 (tm) REVERT: N 76 LYS cc_start: 0.8847 (pttp) cc_final: 0.8481 (pptt) REVERT: N 86 GLU cc_start: 0.8099 (pm20) cc_final: 0.7758 (pm20) REVERT: O 83 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7814 (tm-30) REVERT: O 86 LYS cc_start: 0.8833 (mptm) cc_final: 0.8405 (mmtm) REVERT: O 87 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8210 (mt-10) REVERT: O 95 ILE cc_start: 0.9072 (mm) cc_final: 0.8776 (pp) REVERT: O 125 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8105 (mmmt) REVERT: O 137 SER cc_start: 0.6819 (t) cc_final: 0.6295 (p) REVERT: Q 117 ARG cc_start: 0.8631 (ptm160) cc_final: 0.8139 (ttt-90) REVERT: R 14 ARG cc_start: 0.9229 (mtt90) cc_final: 0.8888 (mtt-85) REVERT: R 58 MET cc_start: 0.9434 (mmm) cc_final: 0.9152 (mmm) REVERT: S 65 GLU cc_start: 0.8451 (tp30) cc_final: 0.8025 (tp30) REVERT: a 38 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8674 (mmmm) REVERT: a 51 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7204 (mmm160) REVERT: a 52 ASP cc_start: 0.8705 (t0) cc_final: 0.8281 (t0) REVERT: U 34 LYS cc_start: 0.9046 (tppp) cc_final: 0.8640 (tppp) REVERT: U 48 LEU cc_start: 0.9450 (mm) cc_final: 0.9236 (mm) REVERT: U 51 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8405 (mtpt) REVERT: U 100 GLN cc_start: 0.9304 (tm-30) cc_final: 0.9019 (pp30) REVERT: V 51 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7840 (mmtp) REVERT: W 28 ARG cc_start: 0.8345 (ptm-80) cc_final: 0.7884 (ttp80) REVERT: W 51 GLU cc_start: 0.7719 (tt0) cc_final: 0.6983 (mt-10) REVERT: W 68 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7595 (ptp90) REVERT: W 86 LEU cc_start: 0.9504 (tp) cc_final: 0.9024 (tt) REVERT: W 90 GLN cc_start: 0.9133 (mt0) cc_final: 0.8791 (mt0) REVERT: W 98 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: W 111 MET cc_start: 0.7632 (ptp) cc_final: 0.7263 (ptm) REVERT: X 95 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7892 (mm-30) REVERT: X 98 ASP cc_start: 0.7671 (m-30) cc_final: 0.7404 (m-30) REVERT: Y 19 GLN cc_start: 0.9210 (mp10) cc_final: 0.8990 (mp10) REVERT: Y 39 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8621 (tp30) REVERT: Y 112 ASN cc_start: 0.9066 (m110) cc_final: 0.8715 (m-40) REVERT: Z 56 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7652 (p0) REVERT: Z 61 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8525 (mp0) REVERT: Z 98 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8306 (ttpp) REVERT: b 34 ASP cc_start: 0.8379 (m-30) cc_final: 0.8039 (m-30) REVERT: b 74 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8257 (t) REVERT: b 80 ARG cc_start: 0.7550 (mpt180) cc_final: 0.7295 (mmt-90) REVERT: c 66 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6308 (ptp-170) REVERT: d 8 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.7264 (t-100) REVERT: d 37 ASN cc_start: 0.9189 (m-40) cc_final: 0.8952 (m-40) REVERT: f 143 LYS cc_start: 0.8405 (tmtp) cc_final: 0.8113 (tptp) REVERT: g 15 ASN cc_start: 0.8591 (t160) cc_final: 0.8053 (t160) REVERT: g 127 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8633 (mmtp) REVERT: g 133 ASN cc_start: 0.8301 (t0) cc_final: 0.7882 (p0) REVERT: g 148 SER cc_start: 0.9180 (m) cc_final: 0.8931 (p) REVERT: g 187 ASN cc_start: 0.7879 (t0) cc_final: 0.7546 (t0) REVERT: g 217 MET cc_start: 0.8024 (tpp) cc_final: 0.7036 (mpt) REVERT: g 218 LEU cc_start: 0.9258 (mp) cc_final: 0.9056 (mp) REVERT: g 228 TYR cc_start: 0.7631 (m-80) cc_final: 0.7411 (m-80) REVERT: g 285 GLN cc_start: 0.8923 (mm110) cc_final: 0.8493 (mm110) REVERT: g 296 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7484 (pp30) REVERT: T 51 ASN cc_start: 0.8761 (m-40) cc_final: 0.8362 (m110) REVERT: T 126 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8308 (tm-30) REVERT: T 130 ASP cc_start: 0.8584 (t0) cc_final: 0.8290 (t0) REVERT: h 173 MET cc_start: 0.9453 (mmm) cc_final: 0.9119 (mmm) REVERT: h 205 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7002 (tpp-160) REVERT: h 261 GLU cc_start: 0.8091 (tp30) cc_final: 0.7884 (tp30) REVERT: h 266 GLU cc_start: 0.8047 (pp20) cc_final: 0.7615 (pp20) outliers start: 303 outliers final: 190 residues processed: 1771 average time/residue: 1.5518 time to fit residues: 3669.8096 Evaluate side-chains 1800 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1586 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 50 LYS Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 134 GLN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 68 ARG Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 125 VAL Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain g residue 20 GLN Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 127 LYS Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 244 ASN Chi-restraints excluded: chain g residue 270 LEU Chi-restraints excluded: chain g residue 296 GLN Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 178 ILE Chi-restraints excluded: chain h residue 179 ILE Chi-restraints excluded: chain h residue 254 LEU Chi-restraints excluded: chain h residue 256 ARG Chi-restraints excluded: chain h residue 257 LEU Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 277 MET Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 340 ILE Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 373 VAL Chi-restraints excluded: chain h residue 390 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 10.0000 chunk 71 optimal weight: 50.0000 chunk 363 optimal weight: 4.9990 chunk 466 optimal weight: 2.9990 chunk 361 optimal weight: 0.6980 chunk 537 optimal weight: 3.9990 chunk 356 optimal weight: 0.9980 chunk 636 optimal weight: 5.9990 chunk 398 optimal weight: 1.9990 chunk 387 optimal weight: 8.9990 chunk 293 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 29 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN C 134 ASN E 157 ASN E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS I 181 GLN K 39 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 GLN Q 80 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN X 20 GLN X 63 ASN c 29 GLN d 26 ASN e 44 ASN g 237 ASN T 83 GLN T 142 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 81156 Z= 0.217 Angle : 0.685 12.425 117629 Z= 0.351 Chirality : 0.039 0.268 14501 Planarity : 0.005 0.125 8687 Dihedral : 23.668 179.810 31867 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 5.63 % Allowed : 32.38 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % 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: -1.08 (0.12), residues: 4976 helix: 0.10 (0.13), residues: 1533 sheet: -1.02 (0.17), residues: 894 loop : -1.06 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 117 HIS 0.008 0.001 HIS K 28 PHE 0.048 0.002 PHE M 128 TYR 0.023 0.002 TYR N 141 ARG 0.017 0.001 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1892 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1648 time to evaluate : 4.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8818 (ptmm) cc_final: 0.8197 (ptpp) REVERT: A 46 ILE cc_start: 0.8415 (mt) cc_final: 0.8165 (mp) REVERT: A 49 ILE cc_start: 0.8877 (mt) cc_final: 0.8445 (tt) REVERT: A 52 LYS cc_start: 0.8840 (mttm) cc_final: 0.8606 (mttm) REVERT: A 53 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6847 (mmp80) REVERT: A 145 ILE cc_start: 0.7987 (mp) cc_final: 0.7721 (tp) REVERT: A 174 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8213 (mpp) REVERT: A 185 MET cc_start: 0.8045 (tpt) cc_final: 0.7685 (tpt) REVERT: B 120 MET cc_start: 0.8967 (ttp) cc_final: 0.8752 (ttp) REVERT: B 144 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8624 (tmmm) REVERT: B 152 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8526 (mmtm) REVERT: B 183 GLU cc_start: 0.8654 (mp0) cc_final: 0.8179 (mp0) REVERT: B 223 PHE cc_start: 0.6921 (t80) cc_final: 0.6214 (t80) REVERT: C 68 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8523 (mtm-85) REVERT: C 121 ARG cc_start: 0.8164 (ppp80) cc_final: 0.7818 (ppp80) REVERT: C 127 PHE cc_start: 0.9105 (m-80) cc_final: 0.8660 (m-80) REVERT: C 183 LYS cc_start: 0.9076 (mttt) cc_final: 0.8633 (mttt) REVERT: C 200 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8120 (ttp-170) REVERT: C 238 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8790 (mtmt) REVERT: D 10 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8670 (tppt) REVERT: D 47 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7287 (tp30) REVERT: D 56 GLN cc_start: 0.8778 (pt0) cc_final: 0.8254 (pm20) REVERT: D 61 GLU cc_start: 0.8391 (pp20) cc_final: 0.8106 (tm-30) REVERT: D 62 LYS cc_start: 0.8828 (mttt) cc_final: 0.8315 (tttt) REVERT: D 68 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 116 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8904 (tpp-160) REVERT: D 166 TYR cc_start: 0.8468 (p90) cc_final: 0.8093 (p90) REVERT: D 174 HIS cc_start: 0.8547 (m-70) cc_final: 0.8190 (m90) REVERT: D 225 GLU cc_start: 0.8350 (pm20) cc_final: 0.8077 (pm20) REVERT: E 59 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7911 (t70) REVERT: E 199 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: E 223 SER cc_start: 0.9382 (m) cc_final: 0.9048 (t) REVERT: E 254 LYS cc_start: 0.9526 (tmmt) cc_final: 0.9277 (ttmm) REVERT: F 36 GLN cc_start: 0.8485 (tp40) cc_final: 0.7878 (tp40) REVERT: F 43 GLU cc_start: 0.8180 (pm20) cc_final: 0.7938 (pm20) REVERT: F 44 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8440 (mmmt) REVERT: F 118 ASN cc_start: 0.8834 (m-40) cc_final: 0.8406 (m-40) REVERT: F 146 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8895 (ttp80) REVERT: F 195 GLU cc_start: 0.8355 (tp30) cc_final: 0.7735 (tp30) REVERT: F 197 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8298 (mm-30) REVERT: G 16 ILE cc_start: 0.9191 (tt) cc_final: 0.8977 (tp) REVERT: G 23 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8860 (mmtt) REVERT: G 103 ASP cc_start: 0.7666 (p0) cc_final: 0.7407 (p0) REVERT: G 105 ASN cc_start: 0.8957 (m-40) cc_final: 0.8535 (m-40) REVERT: G 145 PHE cc_start: 0.9050 (m-10) cc_final: 0.8827 (m-10) REVERT: G 146 ASN cc_start: 0.8982 (m110) cc_final: 0.8632 (m110) REVERT: G 202 ASN cc_start: 0.8730 (m-40) cc_final: 0.8344 (m-40) REVERT: H 9 VAL cc_start: 0.6781 (t) cc_final: 0.6319 (t) REVERT: H 113 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7510 (tmtt) REVERT: H 115 LYS cc_start: 0.5455 (ptmt) cc_final: 0.4927 (tttt) REVERT: H 160 LYS cc_start: 0.7744 (mmmt) cc_final: 0.7027 (ttpp) REVERT: H 167 GLU cc_start: 0.8370 (pm20) cc_final: 0.8163 (pm20) REVERT: H 178 LYS cc_start: 0.6050 (tptt) cc_final: 0.5834 (tttp) REVERT: H 188 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7701 (mm-30) REVERT: I 27 TYR cc_start: 0.8896 (p90) cc_final: 0.8598 (p90) REVERT: I 80 ASP cc_start: 0.8673 (t70) cc_final: 0.8259 (t0) REVERT: I 88 ASN cc_start: 0.8701 (t0) cc_final: 0.8258 (t0) REVERT: I 167 GLN cc_start: 0.9047 (mm110) cc_final: 0.8764 (mp10) REVERT: I 168 GLN cc_start: 0.8889 (mp10) cc_final: 0.8577 (mm-40) REVERT: J 18 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8048 (mmp-170) REVERT: J 34 GLU cc_start: 0.8727 (tp30) cc_final: 0.8471 (tm-30) REVERT: J 65 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7396 (tm-30) REVERT: J 104 ASP cc_start: 0.9029 (m-30) cc_final: 0.8628 (m-30) REVERT: J 107 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: J 140 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7579 (tm-30) REVERT: J 174 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8584 (tptp) REVERT: K 21 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7604 (ttp) REVERT: K 25 LYS cc_start: 0.8629 (tppp) cc_final: 0.8231 (tppp) REVERT: K 26 ASP cc_start: 0.8590 (t0) cc_final: 0.8111 (t70) REVERT: K 28 HIS cc_start: 0.8184 (t-170) cc_final: 0.7921 (t-170) REVERT: K 31 LYS cc_start: 0.9281 (mttt) cc_final: 0.8950 (mttt) REVERT: K 77 GLN cc_start: 0.8644 (mm110) cc_final: 0.8140 (mm110) REVERT: L 49 GLU cc_start: 0.7846 (tp30) cc_final: 0.7521 (tp30) REVERT: L 83 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: M 12 MET cc_start: 0.7567 (ttt) cc_final: 0.7309 (ppp) REVERT: M 83 LYS cc_start: 0.8905 (mppt) cc_final: 0.8571 (ttmm) REVERT: M 99 LYS cc_start: 0.8329 (mmpt) cc_final: 0.7667 (pmtt) REVERT: N 4 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: N 27 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7599 (mmtt) REVERT: N 34 LYS cc_start: 0.9402 (mttt) cc_final: 0.9192 (mttp) REVERT: N 54 LEU cc_start: 0.9351 (mp) cc_final: 0.9146 (tp) REVERT: N 76 LYS cc_start: 0.8827 (pttp) cc_final: 0.8467 (pptt) REVERT: O 83 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7566 (tm-30) REVERT: O 86 LYS cc_start: 0.8828 (mptm) cc_final: 0.8404 (mmtm) REVERT: O 87 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8186 (mt-10) REVERT: O 95 ILE cc_start: 0.9055 (mm) cc_final: 0.8836 (pt) REVERT: O 125 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8043 (mmmt) REVERT: O 137 SER cc_start: 0.6499 (t) cc_final: 0.6068 (p) REVERT: P 24 GLN cc_start: 0.9055 (mt0) cc_final: 0.8632 (mp10) REVERT: P 50 ARG cc_start: 0.8709 (mmp80) cc_final: 0.8350 (mmp80) REVERT: P 53 GLN cc_start: 0.8657 (mp10) cc_final: 0.8292 (mp10) REVERT: Q 97 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8571 (tt0) REVERT: Q 117 ARG cc_start: 0.8581 (ptm160) cc_final: 0.8198 (ttt-90) REVERT: R 40 ILE cc_start: 0.9326 (mt) cc_final: 0.8920 (pp) REVERT: S 65 GLU cc_start: 0.8396 (tp30) cc_final: 0.7977 (tp30) REVERT: a 38 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8641 (mmmm) REVERT: a 51 ARG cc_start: 0.7478 (mmm160) cc_final: 0.7168 (mmm160) REVERT: a 52 ASP cc_start: 0.8701 (t0) cc_final: 0.8177 (t0) REVERT: U 34 LYS cc_start: 0.9040 (tppp) cc_final: 0.8638 (tppp) REVERT: U 48 LEU cc_start: 0.9364 (mm) cc_final: 0.9096 (mm) REVERT: U 50 VAL cc_start: 0.9622 (t) cc_final: 0.9401 (p) REVERT: U 51 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8339 (mtpt) REVERT: U 97 ILE cc_start: 0.9095 (mp) cc_final: 0.8829 (mp) REVERT: W 28 ARG cc_start: 0.8365 (ptm-80) cc_final: 0.8085 (ttp80) REVERT: W 51 GLU cc_start: 0.7674 (tt0) cc_final: 0.6867 (mt-10) REVERT: W 66 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8189 (p) REVERT: W 86 LEU cc_start: 0.9486 (tp) cc_final: 0.8915 (tt) REVERT: W 90 GLN cc_start: 0.9097 (mt0) cc_final: 0.8606 (mt0) REVERT: W 98 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: W 111 MET cc_start: 0.7599 (ptp) cc_final: 0.7236 (ptm) REVERT: X 98 ASP cc_start: 0.7628 (m-30) cc_final: 0.7398 (m-30) REVERT: Y 39 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8631 (tp30) REVERT: Y 112 ASN cc_start: 0.9045 (m110) cc_final: 0.8727 (m-40) REVERT: Z 61 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8731 (mm-30) REVERT: b 34 ASP cc_start: 0.8360 (m-30) cc_final: 0.7970 (m-30) REVERT: b 74 THR cc_start: 0.8468 (m) cc_final: 0.8220 (t) REVERT: b 80 ARG cc_start: 0.7671 (mpt180) cc_final: 0.7353 (mmt-90) REVERT: b 83 GLN cc_start: 0.8558 (tp-100) cc_final: 0.8298 (mm-40) REVERT: c 10 LYS cc_start: 0.9177 (mmtp) cc_final: 0.8681 (mmtp) REVERT: c 29 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8297 (tp40) REVERT: c 66 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6169 (ptp-170) REVERT: d 8 TRP cc_start: 0.7982 (OUTLIER) cc_final: 0.6821 (t-100) REVERT: d 37 ASN cc_start: 0.9157 (m-40) cc_final: 0.8914 (m-40) REVERT: f 113 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8531 (pmtt) REVERT: f 143 LYS cc_start: 0.8328 (tmtp) cc_final: 0.8005 (tptp) REVERT: g 82 SER cc_start: 0.8297 (t) cc_final: 0.8015 (t) REVERT: g 83 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: g 127 LYS cc_start: 0.8762 (mppt) cc_final: 0.8551 (mmtp) REVERT: g 133 ASN cc_start: 0.8357 (t0) cc_final: 0.7858 (p0) REVERT: g 148 SER cc_start: 0.9146 (m) cc_final: 0.8899 (p) REVERT: g 187 ASN cc_start: 0.7790 (t0) cc_final: 0.7409 (t0) REVERT: g 217 MET cc_start: 0.8001 (tpp) cc_final: 0.6917 (mpt) REVERT: g 218 LEU cc_start: 0.9204 (mp) cc_final: 0.8954 (mp) REVERT: g 222 ASN cc_start: 0.8837 (m110) cc_final: 0.8600 (m110) REVERT: g 228 TYR cc_start: 0.7512 (m-80) cc_final: 0.7263 (m-80) REVERT: g 285 GLN cc_start: 0.8856 (mm110) cc_final: 0.8412 (mm110) REVERT: g 308 ARG cc_start: 0.9209 (mtt90) cc_final: 0.8301 (mtt90) REVERT: T 51 ASN cc_start: 0.8630 (m-40) cc_final: 0.8173 (m110) REVERT: T 90 SER cc_start: 0.8942 (p) cc_final: 0.8634 (p) REVERT: T 114 GLU cc_start: 0.8734 (pp20) cc_final: 0.8348 (pp20) REVERT: T 126 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8293 (tm-30) REVERT: T 130 ASP cc_start: 0.8498 (t0) cc_final: 0.8177 (t0) REVERT: h 173 MET cc_start: 0.9452 (mmm) cc_final: 0.9130 (mmm) REVERT: h 205 ARG cc_start: 0.7304 (mmt-90) cc_final: 0.7018 (tpp-160) REVERT: h 266 GLU cc_start: 0.8093 (pp20) cc_final: 0.7669 (pp20) REVERT: h 409 ARG cc_start: 0.5579 (pmm-80) cc_final: 0.5187 (pmm-80) outliers start: 244 outliers final: 148 residues processed: 1734 average time/residue: 1.5600 time to fit residues: 3605.8146 Evaluate side-chains 1749 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1580 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 97 GLN Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 134 GLN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain c residue 29 GLN Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 244 ASN Chi-restraints excluded: chain g residue 270 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 179 ILE Chi-restraints excluded: chain h residue 254 LEU Chi-restraints excluded: chain h residue 257 LEU Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 277 MET Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 373 VAL Chi-restraints excluded: chain h residue 390 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 379 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 500 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 157 GLN C 134 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS I 99 ASN K 39 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** P 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 GLN Q 48 GLN Q 80 GLN Q 86 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN X 20 GLN X 63 ASN b 51 GLN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 26 ASN e 37 GLN T 142 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 81156 Z= 0.261 Angle : 0.708 12.393 117629 Z= 0.360 Chirality : 0.040 0.281 14501 Planarity : 0.005 0.127 8687 Dihedral : 23.609 179.338 31867 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 5.45 % Allowed : 33.14 % Favored : 61.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % 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: -1.02 (0.12), residues: 4976 helix: 0.19 (0.13), residues: 1511 sheet: -1.03 (0.17), residues: 905 loop : -1.02 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 117 HIS 0.017 0.001 HIS J 124 PHE 0.029 0.002 PHE C 269 TYR 0.022 0.002 TYR P 123 ARG 0.018 0.001 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1850 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1614 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8328 (mm110) cc_final: 0.7492 (mm110) REVERT: A 10 MET cc_start: 0.7435 (pmm) cc_final: 0.6570 (ttp) REVERT: A 46 ILE cc_start: 0.8347 (mt) cc_final: 0.8098 (mp) REVERT: A 49 ILE cc_start: 0.8928 (mt) cc_final: 0.8508 (tt) REVERT: A 52 LYS cc_start: 0.8904 (mttm) cc_final: 0.8550 (mttm) REVERT: A 53 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6903 (mmp80) REVERT: A 174 MET cc_start: 0.8486 (mpp) cc_final: 0.8228 (mpp) REVERT: A 185 MET cc_start: 0.8059 (tpt) cc_final: 0.7722 (tpt) REVERT: B 76 ASN cc_start: 0.8743 (p0) cc_final: 0.8210 (p0) REVERT: B 144 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8623 (tmmm) REVERT: B 152 LYS cc_start: 0.8963 (tmmt) cc_final: 0.8523 (mptm) REVERT: B 183 GLU cc_start: 0.8663 (mp0) cc_final: 0.8249 (mp0) REVERT: B 223 PHE cc_start: 0.6949 (t80) cc_final: 0.6235 (t80) REVERT: C 68 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8628 (mtm-85) REVERT: C 90 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7390 (tt0) REVERT: C 121 ARG cc_start: 0.8189 (ppp80) cc_final: 0.7838 (ppp80) REVERT: C 127 PHE cc_start: 0.9109 (m-80) cc_final: 0.8666 (m-80) REVERT: C 183 LYS cc_start: 0.9089 (mttt) cc_final: 0.8650 (mttt) REVERT: C 200 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8117 (ttp-170) REVERT: C 238 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8766 (mtmt) REVERT: D 10 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8683 (tppt) REVERT: D 26 THR cc_start: 0.9583 (m) cc_final: 0.9214 (p) REVERT: D 47 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7711 (tp30) REVERT: D 56 GLN cc_start: 0.8818 (pt0) cc_final: 0.8269 (pm20) REVERT: D 61 GLU cc_start: 0.8454 (pp20) cc_final: 0.8153 (tm-30) REVERT: D 62 LYS cc_start: 0.8871 (mttt) cc_final: 0.8365 (tttt) REVERT: D 68 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7963 (mt-10) REVERT: D 85 GLU cc_start: 0.7763 (pm20) cc_final: 0.7515 (pm20) REVERT: D 116 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8913 (tpp-160) REVERT: D 125 PHE cc_start: 0.8893 (t80) cc_final: 0.8684 (t80) REVERT: D 166 TYR cc_start: 0.8483 (p90) cc_final: 0.8088 (p90) REVERT: D 174 HIS cc_start: 0.8570 (m-70) cc_final: 0.8217 (m90) REVERT: E 66 MET cc_start: 0.9200 (mmm) cc_final: 0.8989 (mmm) REVERT: E 136 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8851 (mm) REVERT: E 168 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8595 (mmmt) REVERT: E 199 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 36 GLN cc_start: 0.8519 (tp40) cc_final: 0.7918 (tp40) REVERT: F 44 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8539 (mmmt) REVERT: F 118 ASN cc_start: 0.8830 (m-40) cc_final: 0.8422 (m-40) REVERT: F 146 ARG cc_start: 0.9167 (ttp80) cc_final: 0.8906 (ttp80) REVERT: F 195 GLU cc_start: 0.8307 (tp30) cc_final: 0.7836 (tp30) REVERT: F 197 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8338 (mm-30) REVERT: G 16 ILE cc_start: 0.9202 (tt) cc_final: 0.8984 (tp) REVERT: G 23 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8862 (mmtt) REVERT: G 103 ASP cc_start: 0.7676 (p0) cc_final: 0.7471 (p0) REVERT: G 105 ASN cc_start: 0.8939 (m-40) cc_final: 0.8480 (m-40) REVERT: G 115 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8849 (ttpp) REVERT: G 145 PHE cc_start: 0.9097 (m-10) cc_final: 0.8810 (m-10) REVERT: G 146 ASN cc_start: 0.9032 (m110) cc_final: 0.8631 (m110) REVERT: G 202 ASN cc_start: 0.8797 (m-40) cc_final: 0.8421 (m-40) REVERT: H 28 LEU cc_start: 0.8695 (mt) cc_final: 0.8407 (pt) REVERT: H 113 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7536 (tmtt) REVERT: H 115 LYS cc_start: 0.5514 (ptmt) cc_final: 0.4983 (tttt) REVERT: H 138 GLU cc_start: 0.6161 (mt-10) cc_final: 0.5512 (tt0) REVERT: H 160 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7105 (ttpt) REVERT: H 188 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7712 (mm-30) REVERT: I 80 ASP cc_start: 0.8683 (t70) cc_final: 0.8262 (t0) REVERT: I 88 ASN cc_start: 0.8692 (t0) cc_final: 0.8297 (t0) REVERT: I 111 GLN cc_start: 0.8573 (mt0) cc_final: 0.7965 (mp10) REVERT: I 167 GLN cc_start: 0.9044 (mm110) cc_final: 0.8771 (mp10) REVERT: I 168 GLN cc_start: 0.8895 (mp10) cc_final: 0.8628 (mp10) REVERT: I 196 GLU cc_start: 0.8508 (pm20) cc_final: 0.8246 (pm20) REVERT: J 18 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8084 (mmp-170) REVERT: J 34 GLU cc_start: 0.8757 (tp30) cc_final: 0.8489 (tm-30) REVERT: J 104 ASP cc_start: 0.9039 (m-30) cc_final: 0.8647 (m-30) REVERT: J 107 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: J 140 GLN cc_start: 0.8420 (tp-100) cc_final: 0.7592 (tm-30) REVERT: J 174 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8603 (tptp) REVERT: K 21 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7498 (ttp) REVERT: K 25 LYS cc_start: 0.8626 (tppp) cc_final: 0.8223 (tppp) REVERT: K 26 ASP cc_start: 0.8617 (t0) cc_final: 0.8117 (t0) REVERT: K 31 LYS cc_start: 0.9295 (mttt) cc_final: 0.8957 (mttt) REVERT: K 77 GLN cc_start: 0.8689 (mm110) cc_final: 0.8183 (mm110) REVERT: L 49 GLU cc_start: 0.7859 (tp30) cc_final: 0.7562 (tp30) REVERT: L 83 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: L 84 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8628 (mtp180) REVERT: M 12 MET cc_start: 0.7557 (ttt) cc_final: 0.7311 (ppp) REVERT: M 83 LYS cc_start: 0.8896 (mppt) cc_final: 0.8560 (ttmm) REVERT: M 99 LYS cc_start: 0.8358 (mmpt) cc_final: 0.7725 (pmtt) REVERT: N 4 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8251 (ttp) REVERT: N 27 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7571 (mmtt) REVERT: N 34 LYS cc_start: 0.9390 (mttt) cc_final: 0.9173 (mttp) REVERT: N 54 LEU cc_start: 0.9351 (mp) cc_final: 0.9142 (tp) REVERT: N 62 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8285 (mm110) REVERT: N 72 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7707 (tm) REVERT: N 76 LYS cc_start: 0.8838 (pttp) cc_final: 0.8459 (pptt) REVERT: N 127 ARG cc_start: 0.8598 (mtm110) cc_final: 0.8344 (ttp-110) REVERT: O 83 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7554 (tm130) REVERT: O 86 LYS cc_start: 0.8815 (mptm) cc_final: 0.8376 (mmtm) REVERT: O 87 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8067 (mt-10) REVERT: O 95 ILE cc_start: 0.9083 (mm) cc_final: 0.8851 (pt) REVERT: O 125 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8132 (mmmt) REVERT: O 137 SER cc_start: 0.6607 (t) cc_final: 0.6127 (p) REVERT: P 24 GLN cc_start: 0.8996 (mt0) cc_final: 0.8537 (mp10) REVERT: P 32 GLN cc_start: 0.8857 (mp10) cc_final: 0.8530 (mp10) REVERT: P 50 ARG cc_start: 0.8715 (mmp80) cc_final: 0.8318 (mmp80) REVERT: P 53 GLN cc_start: 0.8668 (mp10) cc_final: 0.8266 (mp10) REVERT: P 62 LYS cc_start: 0.9331 (tmtp) cc_final: 0.9008 (tmtt) REVERT: Q 97 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: Q 117 ARG cc_start: 0.8577 (ptm160) cc_final: 0.8285 (ttt-90) REVERT: R 40 ILE cc_start: 0.9336 (mt) cc_final: 0.8924 (pp) REVERT: S 65 GLU cc_start: 0.8413 (tp30) cc_final: 0.7928 (tp30) REVERT: a 51 ARG cc_start: 0.7487 (mmm160) cc_final: 0.7167 (mmm160) REVERT: a 52 ASP cc_start: 0.8735 (t0) cc_final: 0.8148 (t0) REVERT: U 34 LYS cc_start: 0.9049 (tppp) cc_final: 0.8646 (tppp) REVERT: U 50 VAL cc_start: 0.9578 (t) cc_final: 0.9332 (p) REVERT: U 51 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8353 (mtpt) REVERT: U 91 LEU cc_start: 0.9083 (mm) cc_final: 0.8576 (mm) REVERT: W 28 ARG cc_start: 0.8383 (ptm-80) cc_final: 0.8082 (ttp80) REVERT: W 51 GLU cc_start: 0.7685 (tt0) cc_final: 0.6896 (mt-10) REVERT: W 86 LEU cc_start: 0.9480 (tp) cc_final: 0.8895 (tt) REVERT: W 90 GLN cc_start: 0.9131 (mt0) cc_final: 0.8643 (mt0) REVERT: W 111 MET cc_start: 0.7371 (ptp) cc_final: 0.6934 (ptm) REVERT: X 95 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7901 (mm-30) REVERT: X 98 ASP cc_start: 0.7648 (m-30) cc_final: 0.7391 (m-30) REVERT: Y 23 MET cc_start: 0.8557 (pmm) cc_final: 0.8283 (pmm) REVERT: Y 39 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8636 (tp30) REVERT: Y 112 ASN cc_start: 0.9053 (m110) cc_final: 0.8731 (m-40) REVERT: Z 61 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8753 (mm-30) REVERT: b 34 ASP cc_start: 0.8431 (m-30) cc_final: 0.8112 (m-30) REVERT: b 74 THR cc_start: 0.8306 (m) cc_final: 0.8075 (t) REVERT: b 80 ARG cc_start: 0.7754 (mpt180) cc_final: 0.7443 (mmt-90) REVERT: b 82 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8439 (mmmm) REVERT: c 10 LYS cc_start: 0.9218 (mmtp) cc_final: 0.8674 (mmtp) REVERT: c 66 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6179 (ptp-170) REVERT: d 4 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7870 (pp30) REVERT: d 8 TRP cc_start: 0.8106 (OUTLIER) cc_final: 0.7084 (t-100) REVERT: d 37 ASN cc_start: 0.9180 (m-40) cc_final: 0.8978 (m-40) REVERT: f 111 ASN cc_start: 0.8628 (t0) cc_final: 0.8373 (t0) REVERT: f 132 MET cc_start: 0.7064 (tpp) cc_final: 0.6688 (tpp) REVERT: f 143 LYS cc_start: 0.8312 (tmtp) cc_final: 0.7980 (tptp) REVERT: g 60 ARG cc_start: 0.9204 (ptp90) cc_final: 0.8959 (ptp90) REVERT: g 83 TRP cc_start: 0.8166 (OUTLIER) cc_final: 0.7837 (m-10) REVERT: g 87 LEU cc_start: 0.8911 (mm) cc_final: 0.8548 (mt) REVERT: g 127 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8568 (mmtp) REVERT: g 133 ASN cc_start: 0.8348 (t0) cc_final: 0.7818 (p0) REVERT: g 148 SER cc_start: 0.9139 (m) cc_final: 0.8890 (p) REVERT: g 187 ASN cc_start: 0.7984 (t0) cc_final: 0.7555 (t0) REVERT: g 213 ASP cc_start: 0.7782 (p0) cc_final: 0.7544 (p0) REVERT: g 217 MET cc_start: 0.7999 (tpp) cc_final: 0.6911 (mpt) REVERT: g 222 ASN cc_start: 0.8751 (m110) cc_final: 0.8493 (m110) REVERT: g 228 TYR cc_start: 0.7589 (m-80) cc_final: 0.7333 (m-80) REVERT: g 285 GLN cc_start: 0.8906 (mm110) cc_final: 0.8465 (mm110) REVERT: T 51 ASN cc_start: 0.8556 (m-40) cc_final: 0.8326 (m110) REVERT: T 67 ARG cc_start: 0.8756 (ttt180) cc_final: 0.8320 (ttm170) REVERT: T 90 SER cc_start: 0.8863 (p) cc_final: 0.8626 (p) REVERT: T 114 GLU cc_start: 0.8726 (pp20) cc_final: 0.8314 (pp20) REVERT: T 126 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8334 (tm-30) REVERT: T 137 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: h 173 MET cc_start: 0.9456 (mmm) cc_final: 0.9146 (mmm) REVERT: h 205 ARG cc_start: 0.7391 (mmt-90) cc_final: 0.7106 (tpp-160) REVERT: h 266 GLU cc_start: 0.7932 (pp20) cc_final: 0.7595 (pp20) outliers start: 236 outliers final: 155 residues processed: 1696 average time/residue: 1.5944 time to fit residues: 3619.5286 Evaluate side-chains 1748 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1571 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 113 ASP Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 121 ARG Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 97 GLN Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 134 GLN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 71 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 87 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 127 LYS Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 270 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 178 ILE Chi-restraints excluded: chain h residue 179 ILE Chi-restraints excluded: chain h residue 254 LEU Chi-restraints excluded: chain h residue 257 LEU Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 373 VAL Chi-restraints excluded: chain h residue 390 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 6.9990 chunk 609 optimal weight: 5.9990 chunk 556 optimal weight: 10.0000 chunk 592 optimal weight: 10.0000 chunk 356 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 465 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 535 optimal weight: 0.9980 chunk 560 optimal weight: 0.9980 chunk 590 optimal weight: 0.0020 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 118 GLN B 157 GLN C 134 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS K 39 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 HIS Q 11 GLN Q 48 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS ** U 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN W 64 ASN X 20 GLN Z 89 GLN c 29 GLN d 26 ASN g 237 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 81156 Z= 0.265 Angle : 0.710 12.856 117629 Z= 0.362 Chirality : 0.040 0.279 14501 Planarity : 0.005 0.127 8687 Dihedral : 23.581 179.506 31867 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 5.31 % Allowed : 34.04 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % 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: -1.01 (0.12), residues: 4976 helix: 0.18 (0.13), residues: 1510 sheet: -1.00 (0.17), residues: 906 loop : -1.00 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 117 HIS 0.015 0.001 HIS J 124 PHE 0.048 0.002 PHE M 128 TYR 0.028 0.002 TYR T 79 ARG 0.016 0.001 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1831 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1601 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8400 (mm110) cc_final: 0.7548 (mm110) REVERT: A 10 MET cc_start: 0.7371 (pmm) cc_final: 0.6620 (ttp) REVERT: A 40 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8256 (ptpp) REVERT: A 46 ILE cc_start: 0.8345 (mt) cc_final: 0.8100 (mp) REVERT: A 49 ILE cc_start: 0.8872 (mt) cc_final: 0.8422 (tt) REVERT: A 52 LYS cc_start: 0.8929 (mttm) cc_final: 0.8582 (mttm) REVERT: A 145 ILE cc_start: 0.8063 (mp) cc_final: 0.7736 (tp) REVERT: A 174 MET cc_start: 0.8519 (mpp) cc_final: 0.8255 (mpp) REVERT: A 185 MET cc_start: 0.8057 (tpt) cc_final: 0.7728 (tpt) REVERT: B 76 ASN cc_start: 0.8673 (p0) cc_final: 0.8300 (p0) REVERT: B 118 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8431 (pp30) REVERT: B 144 LYS cc_start: 0.9037 (ttpt) cc_final: 0.8625 (tmmm) REVERT: B 152 LYS cc_start: 0.8902 (tmmt) cc_final: 0.8511 (mmtm) REVERT: B 183 GLU cc_start: 0.8664 (mp0) cc_final: 0.8239 (mp0) REVERT: B 223 PHE cc_start: 0.6982 (t80) cc_final: 0.6260 (t80) REVERT: C 68 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8584 (mtm-85) REVERT: C 90 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7359 (tt0) REVERT: C 108 LYS cc_start: 0.8766 (tttm) cc_final: 0.8390 (ttmm) REVERT: C 127 PHE cc_start: 0.9112 (m-80) cc_final: 0.8632 (m-80) REVERT: C 183 LYS cc_start: 0.9086 (mttt) cc_final: 0.8648 (mttt) REVERT: C 200 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8130 (ttp-170) REVERT: C 212 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9221 (mtpt) REVERT: C 238 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8778 (mtmt) REVERT: D 10 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8683 (tppt) REVERT: D 26 THR cc_start: 0.9578 (m) cc_final: 0.9197 (p) REVERT: D 40 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7337 (ptp90) REVERT: D 61 GLU cc_start: 0.8462 (pp20) cc_final: 0.8157 (tm-30) REVERT: D 62 LYS cc_start: 0.8821 (mttt) cc_final: 0.8278 (tmtt) REVERT: D 68 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7941 (mt-10) REVERT: D 85 GLU cc_start: 0.7790 (pm20) cc_final: 0.7539 (pm20) REVERT: D 116 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8885 (tpp-160) REVERT: D 125 PHE cc_start: 0.8903 (t80) cc_final: 0.8699 (t80) REVERT: D 166 TYR cc_start: 0.8498 (p90) cc_final: 0.8180 (p90) REVERT: D 174 HIS cc_start: 0.8582 (m-70) cc_final: 0.8222 (m90) REVERT: D 225 GLU cc_start: 0.8476 (pm20) cc_final: 0.8094 (pm20) REVERT: E 66 MET cc_start: 0.9205 (mmm) cc_final: 0.8991 (mmm) REVERT: E 136 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8857 (mm) REVERT: E 168 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8585 (mmmt) REVERT: E 199 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 36 GLN cc_start: 0.8519 (tp40) cc_final: 0.7922 (tp40) REVERT: F 118 ASN cc_start: 0.8847 (m-40) cc_final: 0.8439 (m-40) REVERT: F 137 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7595 (tp-100) REVERT: F 195 GLU cc_start: 0.8285 (tp30) cc_final: 0.7921 (tp30) REVERT: F 197 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8368 (mm-30) REVERT: G 16 ILE cc_start: 0.9189 (tt) cc_final: 0.8980 (tp) REVERT: G 23 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8855 (mmtt) REVERT: G 103 ASP cc_start: 0.7530 (p0) cc_final: 0.7323 (p0) REVERT: G 105 ASN cc_start: 0.8934 (m-40) cc_final: 0.8455 (m-40) REVERT: G 115 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8847 (ttpp) REVERT: G 145 PHE cc_start: 0.9055 (m-10) cc_final: 0.8849 (m-10) REVERT: G 146 ASN cc_start: 0.8961 (m110) cc_final: 0.8570 (m110) REVERT: G 202 ASN cc_start: 0.8800 (m-40) cc_final: 0.8424 (m-40) REVERT: H 9 VAL cc_start: 0.6673 (t) cc_final: 0.5962 (t) REVERT: H 28 LEU cc_start: 0.8673 (mt) cc_final: 0.8396 (pt) REVERT: H 113 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7578 (tmtt) REVERT: H 115 LYS cc_start: 0.5472 (ptmt) cc_final: 0.4968 (tttt) REVERT: H 138 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5479 (tt0) REVERT: H 160 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7149 (ttpt) REVERT: I 80 ASP cc_start: 0.8688 (t70) cc_final: 0.8284 (t0) REVERT: I 88 ASN cc_start: 0.8716 (t0) cc_final: 0.8266 (t0) REVERT: I 111 GLN cc_start: 0.8597 (mt0) cc_final: 0.7993 (mp10) REVERT: I 167 GLN cc_start: 0.9023 (mm110) cc_final: 0.8779 (mp10) REVERT: I 168 GLN cc_start: 0.8859 (mp10) cc_final: 0.8564 (mm-40) REVERT: I 196 GLU cc_start: 0.8514 (pm20) cc_final: 0.8216 (pm20) REVERT: J 34 GLU cc_start: 0.8762 (tp30) cc_final: 0.8541 (tm-30) REVERT: J 79 ARG cc_start: 0.8301 (tpp-160) cc_final: 0.8010 (mmt-90) REVERT: J 104 ASP cc_start: 0.9046 (m-30) cc_final: 0.8654 (m-30) REVERT: J 107 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8245 (mm-30) REVERT: J 140 GLN cc_start: 0.8448 (tp-100) cc_final: 0.7608 (tm-30) REVERT: J 174 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8605 (tptp) REVERT: K 25 LYS cc_start: 0.8638 (tppp) cc_final: 0.8234 (tppp) REVERT: K 26 ASP cc_start: 0.8602 (t0) cc_final: 0.8069 (t70) REVERT: K 31 LYS cc_start: 0.9284 (mttt) cc_final: 0.8916 (mtpp) REVERT: K 77 GLN cc_start: 0.8675 (mm110) cc_final: 0.8173 (mm110) REVERT: L 49 GLU cc_start: 0.7864 (tp30) cc_final: 0.7556 (tp30) REVERT: L 83 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: M 12 MET cc_start: 0.7472 (ttt) cc_final: 0.7178 (ppp) REVERT: M 78 LYS cc_start: 0.8777 (mppt) cc_final: 0.8435 (mmpt) REVERT: M 83 LYS cc_start: 0.8941 (mppt) cc_final: 0.8613 (ttmm) REVERT: M 99 LYS cc_start: 0.8435 (mmpt) cc_final: 0.7797 (pmtt) REVERT: N 4 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8293 (ttp) REVERT: N 27 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7545 (mmtt) REVERT: N 34 LYS cc_start: 0.9387 (mttt) cc_final: 0.9175 (mttp) REVERT: N 54 LEU cc_start: 0.9348 (mp) cc_final: 0.9147 (tp) REVERT: N 62 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8361 (mm110) REVERT: N 76 LYS cc_start: 0.8873 (pttp) cc_final: 0.8518 (pptt) REVERT: O 46 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7034 (m-30) REVERT: O 83 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7878 (tm130) REVERT: O 86 LYS cc_start: 0.8813 (mptm) cc_final: 0.8386 (mmtm) REVERT: O 87 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8200 (mt-10) REVERT: O 95 ILE cc_start: 0.9080 (mm) cc_final: 0.8841 (pt) REVERT: O 125 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8198 (mmmt) REVERT: O 137 SER cc_start: 0.6714 (t) cc_final: 0.6214 (p) REVERT: P 24 GLN cc_start: 0.8997 (mt0) cc_final: 0.8564 (mp10) REVERT: P 32 GLN cc_start: 0.8882 (mp10) cc_final: 0.8579 (mp10) REVERT: P 50 ARG cc_start: 0.8730 (mmp80) cc_final: 0.8290 (mmp80) REVERT: P 53 GLN cc_start: 0.8657 (mp10) cc_final: 0.8233 (mp10) REVERT: P 89 MET cc_start: 0.8878 (mmm) cc_final: 0.8575 (mtt) REVERT: P 115 TYR cc_start: 0.8864 (m-80) cc_final: 0.7982 (m-10) REVERT: Q 117 ARG cc_start: 0.8561 (ptm160) cc_final: 0.8268 (ttt-90) REVERT: R 33 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8141 (mmm160) REVERT: S 65 GLU cc_start: 0.8398 (tp30) cc_final: 0.7896 (tp30) REVERT: a 38 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8625 (mmmm) REVERT: a 51 ARG cc_start: 0.7525 (mmm160) cc_final: 0.7194 (mmm160) REVERT: a 52 ASP cc_start: 0.8785 (t0) cc_final: 0.8281 (t0) REVERT: U 34 LYS cc_start: 0.9050 (tppp) cc_final: 0.8644 (tppp) REVERT: U 41 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8177 (ttp80) REVERT: U 51 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8278 (mttt) REVERT: V 49 GLN cc_start: 0.8822 (pt0) cc_final: 0.8565 (pm20) REVERT: W 23 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7800 (mmm160) REVERT: W 28 ARG cc_start: 0.8350 (ptm-80) cc_final: 0.7939 (ttp-170) REVERT: W 51 GLU cc_start: 0.7604 (tt0) cc_final: 0.6875 (mm-30) REVERT: W 86 LEU cc_start: 0.9477 (tp) cc_final: 0.9034 (tt) REVERT: W 90 GLN cc_start: 0.9134 (mt0) cc_final: 0.8825 (mt0) REVERT: W 98 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: W 111 MET cc_start: 0.7193 (ptp) cc_final: 0.6886 (ptm) REVERT: X 71 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7632 (ttt90) REVERT: X 98 ASP cc_start: 0.7759 (m-30) cc_final: 0.7440 (m-30) REVERT: Y 8 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5197 (mmt180) REVERT: Y 23 MET cc_start: 0.8569 (pmm) cc_final: 0.8233 (pmm) REVERT: Y 39 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8631 (tp30) REVERT: Y 112 ASN cc_start: 0.9047 (m110) cc_final: 0.8722 (m-40) REVERT: Z 61 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8717 (mm-30) REVERT: b 21 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7961 (mttt) REVERT: b 34 ASP cc_start: 0.8441 (m-30) cc_final: 0.8049 (m-30) REVERT: b 80 ARG cc_start: 0.7701 (mpt180) cc_final: 0.7384 (mmt-90) REVERT: b 82 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8602 (mmmm) REVERT: c 10 LYS cc_start: 0.9227 (mmtp) cc_final: 0.8696 (mmtp) REVERT: c 29 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8356 (tp40) REVERT: c 58 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8871 (pt) REVERT: c 66 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6216 (ptp-170) REVERT: d 4 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: d 8 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.6949 (t60) REVERT: f 111 ASN cc_start: 0.8612 (t0) cc_final: 0.8332 (t0) REVERT: f 132 MET cc_start: 0.7185 (tpp) cc_final: 0.6848 (tpp) REVERT: f 143 LYS cc_start: 0.8251 (tmtp) cc_final: 0.8045 (tppp) REVERT: f 146 LEU cc_start: 0.8527 (mm) cc_final: 0.8272 (mp) REVERT: g 87 LEU cc_start: 0.8859 (mm) cc_final: 0.8565 (mt) REVERT: g 127 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8566 (mmtp) REVERT: g 133 ASN cc_start: 0.8312 (t0) cc_final: 0.7761 (p0) REVERT: g 148 SER cc_start: 0.9166 (m) cc_final: 0.8925 (p) REVERT: g 187 ASN cc_start: 0.7984 (t0) cc_final: 0.7641 (t0) REVERT: g 217 MET cc_start: 0.8022 (tpp) cc_final: 0.6806 (mpp) REVERT: g 222 ASN cc_start: 0.8743 (m110) cc_final: 0.8491 (m110) REVERT: g 285 GLN cc_start: 0.8775 (mm110) cc_final: 0.8334 (mm110) REVERT: T 114 GLU cc_start: 0.8801 (pp20) cc_final: 0.8371 (pp20) REVERT: T 126 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8363 (tm-30) REVERT: T 133 ARG cc_start: 0.7658 (tpp-160) cc_final: 0.6732 (tpp-160) REVERT: T 137 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: h 173 MET cc_start: 0.9441 (mmm) cc_final: 0.9124 (mmm) REVERT: h 205 ARG cc_start: 0.7474 (mmt-90) cc_final: 0.7187 (tpp-160) REVERT: h 266 GLU cc_start: 0.8050 (pp20) cc_final: 0.7606 (pp20) REVERT: h 373 VAL cc_start: 0.6421 (OUTLIER) cc_final: 0.5865 (p) outliers start: 230 outliers final: 158 residues processed: 1682 average time/residue: 1.5391 time to fit residues: 3471.6698 Evaluate side-chains 1751 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1567 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 182 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 21 LYS Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 111 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 127 CYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain S residue 134 GLN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 87 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 110 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 21 LYS Chi-restraints excluded: chain c residue 29 GLN Chi-restraints excluded: chain c residue 38 THR Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain d residue 9 SER Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 127 LYS Chi-restraints excluded: chain g residue 131 LEU Chi-restraints excluded: chain g residue 153 CYS Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 134 ILE Chi-restraints excluded: chain T residue 137 GLN Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 178 ILE Chi-restraints excluded: chain h residue 179 ILE Chi-restraints excluded: chain h residue 254 LEU Chi-restraints excluded: chain h residue 257 LEU Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 358 ARG Chi-restraints excluded: chain h residue 373 VAL Chi-restraints excluded: chain h residue 390 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 0.0050 chunk 626 optimal weight: 0.4980 chunk 382 optimal weight: 0.9980 chunk 297 optimal weight: 0.0270 chunk 435 optimal weight: 8.9990 chunk 657 optimal weight: 0.9990 chunk 605 optimal weight: 8.9990 chunk 523 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 404 optimal weight: 0.0670 chunk 321 optimal weight: 20.0000 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 157 GLN C 172 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS I 111 GLN J 140 GLN K 39 ASN L 65 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 GLN Q 48 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS U 85 HIS ** U 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN W 56 HIS W 64 ASN X 20 GLN X 63 ASN Z 89 GLN c 29 GLN d 26 ASN d 37 ASN h 253 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 81156 Z= 0.171 Angle : 0.702 13.418 117629 Z= 0.355 Chirality : 0.038 0.314 14501 Planarity : 0.005 0.120 8687 Dihedral : 23.513 179.827 31867 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 3.15 % Allowed : 36.75 % Favored : 60.10 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.12), residues: 4976 helix: 0.20 (0.13), residues: 1505 sheet: -0.93 (0.17), residues: 884 loop : -0.98 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 117 HIS 0.019 0.001 HIS C 136 PHE 0.034 0.002 PHE b 79 TYR 0.029 0.002 TYR K 78 ARG 0.019 0.001 ARG N 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1802 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1666 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8437 (mm110) cc_final: 0.7622 (mm110) REVERT: A 10 MET cc_start: 0.7101 (pmm) cc_final: 0.6589 (ttp) REVERT: A 52 LYS cc_start: 0.8901 (mttm) cc_final: 0.8542 (mttm) REVERT: A 174 MET cc_start: 0.8488 (mpp) cc_final: 0.8214 (mpp) REVERT: A 185 MET cc_start: 0.8010 (tpt) cc_final: 0.7700 (tpt) REVERT: B 83 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8533 (mtpt) REVERT: B 144 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8605 (tmmm) REVERT: B 152 LYS cc_start: 0.8865 (tmmt) cc_final: 0.8456 (mmtt) REVERT: B 175 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8281 (mp0) REVERT: B 183 GLU cc_start: 0.8619 (mp0) cc_final: 0.8166 (mp0) REVERT: B 223 PHE cc_start: 0.6903 (t80) cc_final: 0.6259 (t80) REVERT: C 68 ARG cc_start: 0.8848 (mtm-85) cc_final: 0.8579 (mtm-85) REVERT: C 121 ARG cc_start: 0.8222 (ppp80) cc_final: 0.7829 (ppp80) REVERT: C 127 PHE cc_start: 0.9117 (m-80) cc_final: 0.8698 (m-80) REVERT: C 183 LYS cc_start: 0.8945 (mttt) cc_final: 0.8551 (mttt) REVERT: C 238 LYS cc_start: 0.9067 (mtpt) cc_final: 0.8754 (mtmt) REVERT: C 246 LYS cc_start: 0.9085 (mttt) cc_final: 0.8786 (mttt) REVERT: D 10 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8686 (tppt) REVERT: D 61 GLU cc_start: 0.8342 (pp20) cc_final: 0.8037 (tm-30) REVERT: D 62 LYS cc_start: 0.8717 (mttt) cc_final: 0.8095 (tmtt) REVERT: D 68 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 116 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8862 (tpp-160) REVERT: D 125 PHE cc_start: 0.8890 (t80) cc_final: 0.8688 (t80) REVERT: D 151 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8617 (ttpt) REVERT: D 166 TYR cc_start: 0.8343 (p90) cc_final: 0.8044 (p90) REVERT: D 174 HIS cc_start: 0.8505 (m-70) cc_final: 0.8154 (m90) REVERT: D 225 GLU cc_start: 0.8445 (pm20) cc_final: 0.8147 (pm20) REVERT: E 66 MET cc_start: 0.9137 (mmm) cc_final: 0.8921 (mmm) REVERT: E 168 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8503 (mmmt) REVERT: E 199 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: F 36 GLN cc_start: 0.8429 (tp40) cc_final: 0.7878 (tp40) REVERT: F 118 ASN cc_start: 0.8784 (m-40) cc_final: 0.8449 (m-40) REVERT: F 195 GLU cc_start: 0.8170 (tp30) cc_final: 0.7830 (tp30) REVERT: F 197 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8337 (mm-30) REVERT: G 23 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8788 (mmmt) REVERT: G 105 ASN cc_start: 0.8876 (m-40) cc_final: 0.8395 (m-40) REVERT: G 146 ASN cc_start: 0.8999 (m110) cc_final: 0.8596 (m110) REVERT: G 202 ASN cc_start: 0.8691 (m-40) cc_final: 0.8360 (m110) REVERT: G 217 MET cc_start: 0.7822 (mmm) cc_final: 0.7398 (mmm) REVERT: H 9 VAL cc_start: 0.6551 (t) cc_final: 0.5775 (t) REVERT: H 28 LEU cc_start: 0.8567 (mt) cc_final: 0.8243 (pt) REVERT: H 58 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7443 (mmpt) REVERT: H 113 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7633 (tmtt) REVERT: H 115 LYS cc_start: 0.5367 (ptmt) cc_final: 0.4879 (tttt) REVERT: H 138 GLU cc_start: 0.5831 (mt-10) cc_final: 0.5242 (tt0) REVERT: H 145 ARG cc_start: 0.6648 (tmt-80) cc_final: 0.6349 (tpp-160) REVERT: H 160 LYS cc_start: 0.7713 (mmmt) cc_final: 0.7045 (ttpt) REVERT: I 80 ASP cc_start: 0.8670 (t70) cc_final: 0.8251 (t0) REVERT: I 88 ASN cc_start: 0.8699 (t0) cc_final: 0.8309 (t0) REVERT: I 163 GLU cc_start: 0.8486 (mp0) cc_final: 0.8123 (mp0) REVERT: I 167 GLN cc_start: 0.8981 (mm110) cc_final: 0.8727 (mp10) REVERT: I 168 GLN cc_start: 0.8878 (mp10) cc_final: 0.8590 (mm-40) REVERT: I 196 GLU cc_start: 0.8490 (pm20) cc_final: 0.8162 (pm20) REVERT: J 34 GLU cc_start: 0.8774 (tp30) cc_final: 0.8561 (tm-30) REVERT: J 79 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.7980 (mmt-90) REVERT: J 104 ASP cc_start: 0.9022 (m-30) cc_final: 0.8623 (m-30) REVERT: J 107 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8306 (mm-30) REVERT: J 140 GLN cc_start: 0.8209 (tp40) cc_final: 0.7546 (tm-30) REVERT: J 174 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8608 (tptp) REVERT: K 25 LYS cc_start: 0.8593 (tppp) cc_final: 0.8215 (tppp) REVERT: K 26 ASP cc_start: 0.8545 (t0) cc_final: 0.7963 (t70) REVERT: K 31 LYS cc_start: 0.9248 (mttt) cc_final: 0.8950 (mttt) REVERT: K 77 GLN cc_start: 0.8591 (mm110) cc_final: 0.8061 (mm110) REVERT: K 80 ARG cc_start: 0.7567 (mtt-85) cc_final: 0.7117 (mtt-85) REVERT: L 49 GLU cc_start: 0.7720 (tp30) cc_final: 0.7397 (tp30) REVERT: M 12 MET cc_start: 0.7467 (ttt) cc_final: 0.7162 (ppp) REVERT: M 83 LYS cc_start: 0.8962 (mppt) cc_final: 0.8633 (ttmm) REVERT: M 99 LYS cc_start: 0.8463 (mmpt) cc_final: 0.7868 (pmtt) REVERT: N 4 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8069 (ttp) REVERT: N 27 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7506 (mmtt) REVERT: N 62 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8389 (mm110) REVERT: N 76 LYS cc_start: 0.8786 (pttp) cc_final: 0.8441 (pptt) REVERT: N 133 ARG cc_start: 0.8155 (mmm160) cc_final: 0.7839 (mmp-170) REVERT: O 83 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8200 (tm130) REVERT: O 86 LYS cc_start: 0.8758 (mptm) cc_final: 0.8332 (mmtm) REVERT: O 117 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7954 (tpp80) REVERT: O 125 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8159 (mmmt) REVERT: O 137 SER cc_start: 0.6461 (t) cc_final: 0.5973 (m) REVERT: P 24 GLN cc_start: 0.8914 (mt0) cc_final: 0.8468 (mp10) REVERT: P 32 GLN cc_start: 0.8873 (mp10) cc_final: 0.8574 (mp10) REVERT: P 50 ARG cc_start: 0.8705 (mmp80) cc_final: 0.8325 (mmp80) REVERT: P 53 GLN cc_start: 0.8611 (mp10) cc_final: 0.8305 (mp10) REVERT: P 62 LYS cc_start: 0.9327 (tmtp) cc_final: 0.8743 (tptp) REVERT: P 66 GLU cc_start: 0.8537 (pt0) cc_final: 0.7474 (pt0) REVERT: Q 102 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7790 (mm-30) REVERT: Q 117 ARG cc_start: 0.8501 (ptm160) cc_final: 0.8176 (ttt-90) REVERT: R 40 ILE cc_start: 0.9325 (mt) cc_final: 0.8931 (pp) REVERT: S 65 GLU cc_start: 0.8342 (tp30) cc_final: 0.7861 (tp30) REVERT: a 51 ARG cc_start: 0.7421 (mmm160) cc_final: 0.7055 (mmm160) REVERT: a 52 ASP cc_start: 0.8718 (t0) cc_final: 0.8323 (t0) REVERT: U 34 LYS cc_start: 0.9033 (tppp) cc_final: 0.8627 (tppp) REVERT: U 41 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8175 (ttp80) REVERT: U 51 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8302 (mtpt) REVERT: U 91 LEU cc_start: 0.8982 (mm) cc_final: 0.8521 (mm) REVERT: V 2 GLN cc_start: 0.8762 (pt0) cc_final: 0.8353 (tt0) REVERT: W 20 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7477 (mmm160) REVERT: W 23 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7726 (mmm160) REVERT: W 28 ARG cc_start: 0.8179 (ptm-80) cc_final: 0.7847 (ttp80) REVERT: W 51 GLU cc_start: 0.7482 (tt0) cc_final: 0.6387 (mt-10) REVERT: W 83 LEU cc_start: 0.9621 (tp) cc_final: 0.9341 (mp) REVERT: W 86 LEU cc_start: 0.9467 (tp) cc_final: 0.8961 (tt) REVERT: W 90 GLN cc_start: 0.9096 (mt0) cc_final: 0.8634 (mt0) REVERT: W 98 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: X 71 ARG cc_start: 0.7864 (ttt90) cc_final: 0.7515 (ttt90) REVERT: X 95 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7704 (mm-30) REVERT: X 98 ASP cc_start: 0.7735 (m-30) cc_final: 0.7412 (m-30) REVERT: Y 23 MET cc_start: 0.8373 (pmm) cc_final: 0.8144 (pmm) REVERT: Y 99 LYS cc_start: 0.8884 (ptmt) cc_final: 0.8669 (ttpp) REVERT: Y 112 ASN cc_start: 0.9037 (m110) cc_final: 0.8740 (m-40) REVERT: Z 61 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8579 (mm-30) REVERT: b 34 ASP cc_start: 0.8343 (m-30) cc_final: 0.7994 (m-30) REVERT: b 51 GLN cc_start: 0.7737 (mp10) cc_final: 0.7150 (mt0) REVERT: b 80 ARG cc_start: 0.7747 (mpt180) cc_final: 0.7461 (mmt-90) REVERT: b 82 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8450 (mmmm) REVERT: c 10 LYS cc_start: 0.9278 (mmtp) cc_final: 0.8782 (mmtp) REVERT: c 11 LEU cc_start: 0.9299 (mm) cc_final: 0.8434 (tt) REVERT: c 54 ASP cc_start: 0.7838 (m-30) cc_final: 0.7629 (m-30) REVERT: c 58 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8891 (pt) REVERT: c 66 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.6051 (ptp-170) REVERT: d 8 TRP cc_start: 0.7519 (OUTLIER) cc_final: 0.6381 (t60) REVERT: f 111 ASN cc_start: 0.8518 (t0) cc_final: 0.8217 (t0) REVERT: f 132 MET cc_start: 0.6954 (tpp) cc_final: 0.6587 (tpp) REVERT: g 26 GLN cc_start: 0.8752 (mt0) cc_final: 0.8293 (mt0) REVERT: g 42 MET cc_start: 0.7960 (mtm) cc_final: 0.7691 (mmm) REVERT: g 87 LEU cc_start: 0.8824 (mm) cc_final: 0.8466 (mt) REVERT: g 133 ASN cc_start: 0.8174 (t0) cc_final: 0.7656 (p0) REVERT: g 148 SER cc_start: 0.9155 (m) cc_final: 0.8899 (p) REVERT: g 187 ASN cc_start: 0.7928 (t0) cc_final: 0.7678 (t0) REVERT: g 217 MET cc_start: 0.7968 (tpp) cc_final: 0.6721 (mpp) REVERT: g 285 GLN cc_start: 0.8671 (mm110) cc_final: 0.8222 (mm110) REVERT: T 114 GLU cc_start: 0.8695 (pp20) cc_final: 0.8314 (pp20) REVERT: T 126 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8175 (tp-100) REVERT: T 130 ASP cc_start: 0.8455 (t0) cc_final: 0.8164 (t0) REVERT: h 173 MET cc_start: 0.9445 (mmm) cc_final: 0.9177 (mmm) REVERT: h 204 SER cc_start: 0.7822 (m) cc_final: 0.7348 (t) REVERT: h 266 GLU cc_start: 0.8093 (pp20) cc_final: 0.7617 (pp20) outliers start: 136 outliers final: 91 residues processed: 1714 average time/residue: 1.5286 time to fit residues: 3505.4976 Evaluate side-chains 1679 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1577 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 103 GLU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain P residue 52 LYS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 123 TYR Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 33 ARG Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 129 LEU Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 72 CYS Chi-restraints excluded: chain W residue 98 GLN Chi-restraints excluded: chain X residue 87 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 66 ARG Chi-restraints excluded: chain d residue 8 TRP Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain g residue 153 CYS Chi-restraints excluded: chain g residue 174 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 45 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain h residue 176 ARG Chi-restraints excluded: chain h residue 178 ILE Chi-restraints excluded: chain h residue 179 ILE Chi-restraints excluded: chain h residue 254 LEU Chi-restraints excluded: chain h residue 262 ILE Chi-restraints excluded: chain h residue 274 VAL Chi-restraints excluded: chain h residue 303 LEU Chi-restraints excluded: chain h residue 314 MET Chi-restraints excluded: chain h residue 373 VAL Chi-restraints excluded: chain h residue 390 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 3.9990 chunk 557 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 482 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 524 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 538 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN C 134 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS H 73 GLN I 165 GLN J 132 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 11 GLN Q 97 GLN ** R 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS U 18 HIS ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN X 63 ASN c 29 GLN d 26 ASN e 22 GLN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN T 105 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100061 restraints weight = 173776.361| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.32 r_work: 0.3162 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 81156 Z= 0.255 Angle : 0.714 16.689 117629 Z= 0.362 Chirality : 0.040 0.282 14501 Planarity : 0.006 0.125 8687 Dihedral : 23.444 179.667 31867 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 3.22 % Allowed : 38.01 % Favored : 58.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 4976 helix: 0.20 (0.13), residues: 1507 sheet: -0.90 (0.17), residues: 882 loop : -0.91 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 60 HIS 0.014 0.001 HIS J 124 PHE 0.049 0.002 PHE M 128 TYR 0.117 0.002 TYR P 123 ARG 0.019 0.001 ARG C 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46812.53 seconds wall clock time: 806 minutes 9.97 seconds (48369.97 seconds total)