Starting phenix.real_space_refine on Sun Mar 17 18:36:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a2q_3019/03_2024/5a2q_3019.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a2q_3019/03_2024/5a2q_3019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a2q_3019/03_2024/5a2q_3019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a2q_3019/03_2024/5a2q_3019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a2q_3019/03_2024/5a2q_3019.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a2q_3019/03_2024/5a2q_3019.pdb" } resolution = 3.9 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= 0.004 sd= 0.021 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 3 6.06 5 P 1922 5.49 5 Mg 98 5.21 5 S 181 5.16 5 C 43233 2.51 5 N 14825 2.21 5 O 20487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80749 Number of models: 1 Model: "" Number of chains: 45 Chain: "2" Number of atoms: 35552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1665, 35552 Classifications: {'RNA': 1665} Modifications used: {'rna2p_pur': 130, 'rna2p_pyr': 111, 'rna3p_pur': 754, 'rna3p_pyr': 670} Link IDs: {'rna2p': 241, 'rna3p': 1423} Chain breaks: 10 Chain: "3" Number of atoms: 5485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 5485 Classifications: {'RNA': 257} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 29, 'rna3p_pur': 107, 'rna3p_pyr': 97} Link IDs: {'rna2p': 52, 'rna3p': 204} Chain breaks: 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: {'CIS': 1, 'PTRANS': 12, 'TRANS': 204} 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: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1864 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: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} 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: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: "T" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1128 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} 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': 2, 'PTRANS': 1, '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: "a" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 816 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} 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: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} 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: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 585 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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: "h" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 231 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "r" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 118 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "w" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 452 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "2" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Unusual residues: {' MG': 98} Classifications: {'undetermined': 98} Link IDs: {None: 97} 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: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 141 Classifications: {'water': 141} Link IDs: {None: 140} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 74021 SG CYS a 23 84.706 116.963 96.340 1.00 28.46 S ATOM 74042 SG CYS a 26 83.937 116.974 100.657 1.00 31.75 S ATOM 74425 SG CYS a 74 87.430 116.229 99.610 1.00 29.25 S ATOM 74444 SG CYS a 77 83.936 114.363 99.395 1.00 32.86 S ATOM 75944 SG CYS d 21 85.568 58.340 146.542 1.00182.14 S ATOM 75968 SG CYS d 24 85.682 62.224 148.190 1.00202.25 S ATOM 76089 SG CYS d 39 84.178 61.741 144.783 1.00185.05 S ATOM 76115 SG CYS d 42 88.280 61.349 145.019 1.00183.47 S ATOM 77051 SG CYS f 121 71.368 41.475 191.864 1.00297.87 S ATOM 77087 SG CYS f 126 74.946 41.658 190.019 1.00300.61 S ATOM 77205 SG CYS f 141 73.373 45.052 191.506 1.00294.84 S ATOM 77224 SG CYS f 144 71.807 42.756 188.066 1.00295.09 S Time building chain proxies: 32.59, per 1000 atoms: 0.40 Number of scatterers: 80749 At special positions: 0 Unit cell: (225.18, 239.08, 230.74, 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 3 29.99 S 181 16.00 P 1922 15.00 Mg 98 11.99 O 20487 8.00 N 14825 7.00 C 43233 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: 32.84 Conformation dependent library (CDL) restraints added in 6.3 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 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " Number of angles added : 18 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9176 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 59 sheets defined 36.9% alpha, 20.0% beta 584 base pairs and 1003 stacking pairs defined. Time for finding SS restraints: 27.38 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 33 through 36 removed outlier: 4.109A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 33 through 36' Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.674A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.643A pdb=" N TYR A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.717A pdb=" N GLY A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.574A pdb=" N ILE A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.636A pdb=" N SER B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 27' Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.698A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.576A pdb=" N THR B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.954A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.939A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.924A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 218 removed outlier: 3.584A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.414A pdb=" N LYS C 257 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 275 removed outlier: 6.147A pdb=" N ASP C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 54 through 60 removed outlier: 4.063A pdb=" N VAL D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 78 removed outlier: 4.124A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.801A pdb=" N ALA D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'E' and resid 11 through 14 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 261 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 67 through 75 removed outlier: 3.625A pdb=" N SER F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 86 through 104 removed outlier: 3.527A pdb=" N VAL F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F 94 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.567A pdb=" N VAL F 111 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 163 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 204 Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.639A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 152 through 157 removed outlier: 4.129A pdb=" N TYR G 156 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL G 157 " --> pdb=" O VAL G 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 152 through 157' Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.551A pdb=" N ARG G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU G 219 " --> pdb=" O LYS G 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 33 removed outlier: 3.582A pdb=" N GLY H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 43 Processing helix chain 'H' and resid 65 through 88 removed outlier: 3.530A pdb=" N LEU H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER H 71 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.996A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 170 through 181 removed outlier: 3.519A pdb=" N LYS H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' 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 87 through 93 removed outlier: 3.633A pdb=" N VAL I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 153 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 205 removed outlier: 3.686A pdb=" N LEU I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 removed outlier: 3.507A pdb=" N TYR J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 62 removed outlier: 3.820A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 53 " --> pdb=" O THR J 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 94 through 98 Processing helix chain 'J' and resid 102 through 108 removed outlier: 3.931A pdb=" N ARG J 108 " --> pdb=" O ASP J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.621A pdb=" N PHE J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 163 through 168 removed outlier: 3.544A pdb=" N GLY J 168 " --> pdb=" O PRO J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 180 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.953A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 48 Processing helix chain 'K' and resid 48 through 56 removed outlier: 3.808A pdb=" N LEU K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 84 Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.505A pdb=" N ARG K 95 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 28 removed outlier: 3.749A pdb=" N THR L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 52 removed outlier: 3.734A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 28 removed outlier: 4.291A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 43 removed outlier: 4.092A pdb=" N ALA M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 72 removed outlier: 3.643A pdb=" N LYS M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 90 removed outlier: 3.650A pdb=" N LEU M 85 " --> pdb=" O ASP M 81 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY M 90 " --> pdb=" O GLY M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 132 removed outlier: 3.741A pdb=" N LYS M 132 " --> pdb=" O PHE M 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 43 Processing helix chain 'N' and resid 46 through 58 Processing helix chain 'N' and resid 62 through 68 removed outlier: 3.613A pdb=" N VAL N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 78 Processing helix chain 'N' and resid 85 through 105 removed outlier: 4.345A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.868A pdb=" N LYS N 112 " --> pdb=" O ASP N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 150 removed outlier: 3.726A pdb=" N VAL N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.626A pdb=" N VAL O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 65 through 69 removed outlier: 4.032A pdb=" N SER O 69 " --> pdb=" O ARG O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 89 removed outlier: 3.643A pdb=" N ALA O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 122 removed outlier: 3.988A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 28 Processing helix chain 'P' and resid 29 through 35 Processing helix chain 'P' and resid 38 through 47 removed outlier: 3.667A pdb=" N ARG P 47 " --> pdb=" O ARG P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 66 removed outlier: 3.818A pdb=" N LEU P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 Processing helix chain 'P' and resid 109 through 114 removed outlier: 3.658A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY P 113 " --> pdb=" O GLU P 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.669A pdb=" N PHE P 119 " --> pdb=" O LEU P 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 42 removed outlier: 3.531A pdb=" N MET Q 41 " --> pdb=" O PRO Q 38 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE Q 42 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 38 through 42' Processing helix chain 'Q' and resid 47 through 52 removed outlier: 3.889A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU Q 52 " --> pdb=" O GLN Q 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 47 through 52' Processing helix chain 'Q' and resid 52 through 59 Processing helix chain 'Q' and resid 76 through 99 removed outlier: 3.624A pdb=" N ILE Q 81 " --> pdb=" O HIS Q 77 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN Q 97 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.561A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN Q 114 " --> pdb=" O ASP Q 110 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.568A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 62 Processing helix chain 'R' and resid 71 through 83 removed outlier: 3.516A pdb=" N ASN R 83 " --> pdb=" O GLU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 109 removed outlier: 3.640A pdb=" N LEU R 109 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 Processing helix chain 'S' and resid 37 through 48 Processing helix chain 'S' and resid 60 through 73 removed outlier: 3.539A pdb=" N ASN S 73 " --> pdb=" O THR S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 removed outlier: 3.657A pdb=" N LEU S 84 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 118 removed outlier: 3.888A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG S 118 " --> pdb=" O LEU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.661A pdb=" N VAL T 9 " --> pdb=" O VAL T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.685A pdb=" N ALA T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 Processing helix chain 'T' and resid 71 through 79 removed outlier: 4.339A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 110 Processing helix chain 'T' and resid 124 through 146 removed outlier: 3.612A pdb=" N SER T 146 " --> pdb=" O ASN T 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 46 removed outlier: 3.519A pdb=" N LEU U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL U 35 " --> pdb=" O SER U 31 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 105 removed outlier: 3.847A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.692A pdb=" N ARG V 60 " --> pdb=" O CYS V 56 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG V 61 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 56 through 62' Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.571A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 4.004A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 23 removed outlier: 3.769A pdb=" N HIS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.150A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 89 through 93 Processing helix chain 'X' and resid 130 through 136 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 4.183A pdb=" N GLU Y 42 " --> pdb=" O THR Y 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR Y 48 " --> pdb=" O LEU Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 95 removed outlier: 3.764A pdb=" N LEU Y 91 " --> pdb=" O PRO Y 87 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 115 removed outlier: 3.637A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 125 removed outlier: 3.661A pdb=" N LYS Y 122 " --> pdb=" O GLY Y 119 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL Y 125 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 69 through 77 Processing helix chain 'Z' and resid 80 through 94 removed outlier: 3.583A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 56 removed outlier: 4.233A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA a 56 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 82 removed outlier: 3.661A pdb=" N ILE a 79 " --> pdb=" O VAL a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 94 removed outlier: 3.626A pdb=" N ASP a 94 " --> pdb=" O ALA a 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'd' and resid 40 through 51 removed outlier: 6.174A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 40 Processing helix chain 'f' and resid 101 through 104 Processing helix chain 'h' and resid 2 through 21 Processing helix chain 'r' and resid 162 through 174 Processing helix chain 'w' and resid 86 through 95 Processing helix chain 'w' and resid 97 through 126 removed outlier: 3.835A pdb=" N ALA w 126 " --> pdb=" O SER w 122 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.736A pdb=" N TYR A 47 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 97 through 100 Processing sheet with id= BA, first strand: chain 'B' and resid 43 through 48 removed outlier: 23.989A pdb=" N TRP B 30 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 21.016A pdb=" N PHE B 100 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 12.940A pdb=" N ASP B 32 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N CYS B 96 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.270A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.051A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 136 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 43 through 48 removed outlier: 23.989A pdb=" N TRP B 30 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 21.016A pdb=" N PHE B 100 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 12.940A pdb=" N ASP B 32 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N CYS B 96 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS B 96 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 91 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR B 98 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'C' and resid 102 through 116 removed outlier: 5.128A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS C 136 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= DA, first strand: chain 'D' and resid 34 through 41 removed outlier: 3.708A pdb=" N ALA D 52 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.992A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'D' and resid 209 through 210 Processing sheet with id= DD, first strand: chain 'D' and resid 223 through 226 removed outlier: 5.816A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU g 173 " --> pdb=" O GLY g 169 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE g 164 " --> pdb=" O PHE g 156 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE g 156 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'E' and resid 42 through 43 Processing sheet with id= EB, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.512A pdb=" N LYS E 75 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP E 88 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id= EC, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.038A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id= ED, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.532A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 230 " --> pdb=" O LYS E 233 " (cutoff:3.500A) Processing sheet with id= FA, first strand: chain 'F' and resid 123 through 128 removed outlier: 25.129A pdb=" N ARG F 136 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 18.957A pdb=" N ILE c 43 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 12.398A pdb=" N ALA F 138 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN c 45 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'G' and resid 12 through 17 removed outlier: 4.282A pdb=" N SER G 107 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP G 57 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU G 109 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY G 55 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU G 111 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER G 53 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE G 113 " --> pdb=" O ARG G 51 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG G 51 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id= GB, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= GC, first strand: chain 'G' and resid 160 through 164 removed outlier: 6.137A pdb=" N LYS G 160 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR G 171 " --> pdb=" O LYS G 160 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU G 162 " --> pdb=" O PRO G 169 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS G 164 " --> pdb=" O LYS G 167 " (cutoff:3.500A) Processing sheet with id= HA, first strand: chain 'H' and resid 47 through 53 Processing sheet with id= HB, first strand: chain 'H' and resid 185 through 188 removed outlier: 6.507A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id= IA, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.978A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id= IB, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.308A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id= IC, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.679A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP I 80 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing sheet with id= JA, first strand: chain 'J' and resid 140 through 141 Processing sheet with id= KA, first strand: chain 'K' and resid 20 through 23 Processing sheet with id= LA, first strand: chain 'L' and resid 72 through 82 removed outlier: 7.147A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE L 140 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS L 112 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR L 85 " --> pdb=" O MET L 80 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N MET L 80 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.186A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 18.010A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) Processing sheet with id= MA, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.606A pdb=" N ILE M 77 " --> pdb=" O CYS M 50 " (cutoff:3.500A) Processing sheet with id= OA, first strand: chain 'O' and resid 52 through 57 removed outlier: 5.356A pdb=" N ILE O 95 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE O 129 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU O 97 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP O 131 " --> pdb=" O LEU O 97 " (cutoff:3.500A) Processing sheet with id= PA, first strand: chain 'P' and resid 76 through 78 removed outlier: 3.606A pdb=" N VAL P 76 " --> pdb=" O MET P 93 " (cutoff:3.500A) Processing sheet with id= QA, first strand: chain 'Q' and resid 10 through 16 Processing sheet with id= RA, first strand: chain 'R' and resid 96 through 98 Processing sheet with id= SA, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= TA, first strand: chain 'T' and resid 81 through 84 Processing sheet with id= TB, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= UA, first strand: chain 'U' and resid 49 through 55 removed outlier: 24.623A pdb=" N VAL U 50 " --> pdb=" O ILE U 84 " (cutoff:3.500A) removed outlier: 18.819A pdb=" N LYS U 86 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 12.941A pdb=" N GLY U 52 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU U 88 " --> pdb=" O GLY U 52 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP U 90 " --> pdb=" O VAL U 54 " (cutoff:3.500A) Processing sheet with id= UB, first strand: chain 'U' and resid 59 through 66 Processing sheet with id= UC, first strand: chain 'U' and resid 110 through 116 Processing sheet with id= UD, first strand: chain 'U' and resid 110 through 116 removed outlier: 7.095A pdb=" N LYS U 49 " --> pdb=" O ASP U 90 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LYS U 51 " --> pdb=" O HIS U 92 " (cutoff:3.500A) Processing sheet with id= VA, first strand: chain 'V' and resid 32 through 39 removed outlier: 6.677A pdb=" N ILE V 32 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR V 53 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N MET V 34 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS V 51 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL V 36 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN V 49 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLU V 38 " --> pdb=" O ASN V 47 " (cutoff:3.500A) Processing sheet with id= WA, first strand: chain 'W' and resid 71 through 74 Processing sheet with id= WB, first strand: chain 'W' and resid 80 through 81 removed outlier: 6.557A pdb=" N ILE W 125 " --> pdb=" O VAL W 81 " (cutoff:3.500A) Processing sheet with id= WC, first strand: chain 'W' and resid 110 through 112 removed outlier: 6.630A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) Processing sheet with id= WD, first strand: chain 'W' and resid 110 through 112 removed outlier: 6.630A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) Processing sheet with id= XA, first strand: chain 'X' and resid 46 through 58 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 99 through 104 current: chain 'X' and resid 80 through 84 Processing sheet with id= YA, first strand: chain 'Y' and resid 6 through 15 removed outlier: 5.874A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id= ZA, first strand: chain 'Z' and resid 67 through 68 removed outlier: 7.174A pdb=" N GLN Z 106 " --> pdb=" O LYS Z 102 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS Z 102 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'a' and resid 20 through 22 No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'a' and resid 36 through 43 No H-bonds generated for sheet with id= AQ Processing sheet with id= BP, first strand: chain 'b' and resid 44 through 47 No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'b' and resid 54 through 56 No H-bonds generated for sheet with id= BQ Processing sheet with id= DP, first strand: chain 'd' and resid 30 through 31 No H-bonds generated for sheet with id= DP Processing sheet with id= FQ, first strand: chain 'f' and resid 106 through 108 No H-bonds generated for sheet with id= FQ Processing sheet with id= FR, first strand: chain 'f' and resid 133 through 134 Processing sheet with id= GP, first strand: chain 'g' and resid 3 through 11 No H-bonds generated for sheet with id= GP Processing sheet with id= GQ, first strand: chain 'g' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 18 through 22 current: chain 'g' and resid 40 through 44 removed outlier: 5.998A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id= GR, first strand: chain 'g' and resid 66 through 71 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 66 through 71 current: chain 'g' and resid 86 through 91 removed outlier: 6.852A pdb=" N LEU g 87 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG g 100 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU g 89 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR g 96 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id= GS, first strand: chain 'g' and resid 108 through 113 removed outlier: 7.030A pdb=" N ILE g 129 " --> pdb=" O THR g 141 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR g 141 " --> pdb=" O ILE g 129 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU g 131 " --> pdb=" O LYS g 139 " (cutoff:3.500A) Processing sheet with id= GT, first strand: chain 'g' and resid 195 through 200 removed outlier: 6.556A pdb=" N ALA g 216 " --> pdb=" O THR g 229 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR g 229 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU g 218 " --> pdb=" O LEU g 227 " (cutoff:3.500A) Processing sheet with id= GU, first strand: chain 'g' and resid 236 through 241 removed outlier: 3.532A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) 1569 hydrogen bonds defined for protein. 4476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1472 hydrogen bonds 2420 hydrogen bond angles 0 basepair planarities 584 basepair parallelities 1003 stacking parallelities Total time for adding SS restraints: 67.72 Time building geometry restraints manager: 35.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17353 1.33 - 1.47: 33027 1.47 - 1.60: 33649 1.60 - 1.74: 1702 1.74 - 1.87: 275 Bond restraints: 86006 Sorted by residual: bond pdb=" CA VAL H 66 " pdb=" CB VAL H 66 " ideal model delta sigma weight residual 1.537 1.507 0.030 5.00e-03 4.00e+04 3.52e+01 bond pdb=" CA HIS X 110 " pdb=" C HIS X 110 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.19e-02 7.06e+03 2.24e+01 bond pdb=" CA PHE W 79 " pdb=" C PHE W 79 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.25e-02 6.40e+03 1.98e+01 bond pdb=" CA ILE W 61 " pdb=" CB ILE W 61 " ideal model delta sigma weight residual 1.540 1.490 0.050 1.23e-02 6.61e+03 1.69e+01 bond pdb=" CA ILE J 144 " pdb=" CB ILE J 144 " ideal model delta sigma weight residual 1.538 1.503 0.035 8.80e-03 1.29e+04 1.62e+01 ... (remaining 86001 not shown) Histogram of bond angle deviations from ideal: 97.49 - 105.96: 11250 105.96 - 114.44: 54445 114.44 - 122.91: 45744 122.91 - 131.38: 13353 131.38 - 139.86: 514 Bond angle restraints: 125306 Sorted by residual: angle pdb=" C GLU Q 43 " pdb=" N PRO Q 44 " pdb=" CA PRO Q 44 " ideal model delta sigma weight residual 120.13 107.80 12.33 1.13e+00 7.83e-01 1.19e+02 angle pdb=" C VAL X 85 " pdb=" N PRO X 86 " pdb=" CA PRO X 86 " ideal model delta sigma weight residual 119.24 129.49 -10.25 1.04e+00 9.25e-01 9.72e+01 angle pdb=" N LYS H 111 " pdb=" CA LYS H 111 " pdb=" C LYS H 111 " ideal model delta sigma weight residual 113.38 102.35 11.03 1.23e+00 6.61e-01 8.03e+01 angle pdb=" C GLY G 134 " pdb=" N PRO G 135 " pdb=" CA PRO G 135 " ideal model delta sigma weight residual 119.93 129.29 -9.36 1.07e+00 8.73e-01 7.65e+01 angle pdb=" C ILE A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta sigma weight residual 119.84 130.25 -10.41 1.25e+00 6.40e-01 6.94e+01 ... (remaining 125301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 48312 35.97 - 71.94: 5887 71.94 - 107.90: 665 107.90 - 143.87: 42 143.87 - 179.84: 59 Dihedral angle restraints: 54965 sinusoidal: 40747 harmonic: 14218 Sorted by residual: dihedral pdb=" CA ASP D 193 " pdb=" C ASP D 193 " pdb=" N PRO D 194 " pdb=" CA PRO D 194 " ideal model delta harmonic sigma weight residual 180.00 -123.97 -56.03 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" C5' C 21558 " pdb=" C4' C 21558 " pdb=" C3' C 21558 " pdb=" O3' C 21558 " ideal model delta sinusoidal sigma weight residual 147.00 78.45 68.55 1 8.00e+00 1.56e-02 9.52e+01 dihedral pdb=" C4' C 21558 " pdb=" C3' C 21558 " pdb=" C2' C 21558 " pdb=" C1' C 21558 " ideal model delta sinusoidal sigma weight residual -35.00 33.42 -68.42 1 8.00e+00 1.56e-02 9.48e+01 ... (remaining 54962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 14373 0.094 - 0.188: 1083 0.188 - 0.281: 89 0.281 - 0.375: 14 0.375 - 0.469: 6 Chirality restraints: 15565 Sorted by residual: chirality pdb=" C3' A 2 604 " pdb=" C4' A 2 604 " pdb=" O3' A 2 604 " pdb=" C2' A 2 604 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" C3' A 21835 " pdb=" C4' A 21835 " pdb=" O3' A 21835 " pdb=" C2' A 21835 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C3' C 21558 " pdb=" C4' C 21558 " pdb=" O3' C 21558 " pdb=" C2' C 21558 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 15562 not shown) Planarity restraints: 8764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 28 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO E 29 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 638 " 0.048 2.00e-02 2.50e+03 2.61e-02 1.53e+01 pdb=" N1 C 2 638 " -0.060 2.00e-02 2.50e+03 pdb=" C2 C 2 638 " -0.006 2.00e-02 2.50e+03 pdb=" O2 C 2 638 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C 2 638 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C 2 638 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C 2 638 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C 2 638 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C 2 638 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 595 " -0.042 2.00e-02 2.50e+03 2.50e-02 1.41e+01 pdb=" N1 U 2 595 " 0.061 2.00e-02 2.50e+03 pdb=" C2 U 2 595 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U 2 595 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U 2 595 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U 2 595 " -0.008 2.00e-02 2.50e+03 pdb=" O4 U 2 595 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U 2 595 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U 2 595 " 0.000 2.00e-02 2.50e+03 ... (remaining 8761 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 532 2.44 - 3.06: 47854 3.06 - 3.67: 138113 3.67 - 4.29: 211591 4.29 - 4.90: 302104 Nonbonded interactions: 700194 Sorted by model distance: nonbonded pdb=" OP1 A 2 672 " pdb="MG MG 21957 " model vdw 1.830 2.170 nonbonded pdb=" OP2 A 21082 " pdb="MG MG 21935 " model vdw 1.909 2.170 nonbonded pdb=" OP2 C 2 472 " pdb="MG MG 21951 " model vdw 1.959 2.170 nonbonded pdb=" OP1 A 2 654 " pdb="MG MG 21928 " model vdw 1.995 2.170 nonbonded pdb=" OP1 U 2 115 " pdb=" O2' C 2 382 " model vdw 2.009 2.440 ... (remaining 700189 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 5.620 Check model and map are aligned: 0.890 Set scattering table: 0.550 Process input model: 237.330 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 250.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 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 0.104 86006 Z= 0.516 Angle : 1.234 15.976 125306 Z= 0.741 Chirality : 0.053 0.469 15565 Planarity : 0.006 0.126 8764 Dihedral : 24.763 179.841 45789 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 12.93 % Allowed : 12.46 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.11 % 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: -3.44 (0.09), residues: 4859 helix: -3.41 (0.08), residues: 1556 sheet: -1.09 (0.15), residues: 928 loop : -1.87 (0.10), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP I 67 HIS 0.016 0.002 HIS C 178 PHE 0.037 0.003 PHE C 97 TYR 0.021 0.002 TYR C 169 ARG 0.008 0.001 ARG J 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1847 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 549 poor density : 1298 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9434 (mmm) cc_final: 0.9228 (tpp) REVERT: A 40 LYS cc_start: 0.9114 (ptmt) cc_final: 0.8894 (ttpp) REVERT: A 44 ASP cc_start: 0.8588 (m-30) cc_final: 0.7912 (t0) REVERT: A 52 LYS cc_start: 0.8785 (tttt) cc_final: 0.8378 (tppt) REVERT: A 73 ASP cc_start: 0.8701 (m-30) cc_final: 0.8443 (m-30) REVERT: A 77 ILE cc_start: 0.9606 (mt) cc_final: 0.9306 (mm) REVERT: A 80 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8376 (ptt90) REVERT: A 89 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8383 (mmtt) REVERT: A 111 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.8890 (pm20) REVERT: A 118 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8515 (mt-10) REVERT: A 130 ASP cc_start: 0.9211 (OUTLIER) cc_final: 0.8452 (p0) REVERT: A 131 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.7382 (p90) REVERT: A 163 CYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 165 ASN cc_start: 0.8976 (p0) cc_final: 0.8687 (p0) REVERT: A 173 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9244 (tm) REVERT: A 177 MET cc_start: 0.8677 (mtt) cc_final: 0.8437 (mtp) REVERT: A 180 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8393 (ttp-170) REVERT: A 206 ASP cc_start: 0.9162 (t70) cc_final: 0.8775 (t0) REVERT: A 209 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7246 (mp0) REVERT: B 27 LYS cc_start: 0.9110 (mttt) cc_final: 0.8885 (mmmt) REVERT: B 29 ASP cc_start: 0.8781 (t0) cc_final: 0.8243 (t0) REVERT: B 31 TYR cc_start: 0.8966 (m-80) cc_final: 0.8361 (m-10) REVERT: B 33 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8995 (m) REVERT: B 59 SER cc_start: 0.9081 (p) cc_final: 0.8703 (m) REVERT: B 60 ASP cc_start: 0.9079 (t0) cc_final: 0.8823 (t0) REVERT: B 68 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8197 (mm-30) REVERT: B 75 GLN cc_start: 0.7931 (tt0) cc_final: 0.7162 (tt0) REVERT: B 78 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 85 LYS cc_start: 0.9109 (mttt) cc_final: 0.8620 (mttp) REVERT: B 96 CYS cc_start: 0.9204 (m) cc_final: 0.8986 (m) REVERT: B 97 LEU cc_start: 0.9262 (mt) cc_final: 0.8937 (mt) REVERT: B 99 ASN cc_start: 0.8764 (t0) cc_final: 0.8497 (t0) REVERT: B 106 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8772 (p) REVERT: B 136 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8917 (tpp80) REVERT: B 154 SER cc_start: 0.9485 (m) cc_final: 0.9164 (t) REVERT: B 201 CYS cc_start: 0.8402 (m) cc_final: 0.8030 (m) REVERT: B 202 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8754 (mm-40) REVERT: B 213 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8576 (tmm160) REVERT: C 73 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8555 (mmm) REVERT: C 82 TYR cc_start: 0.9169 (m-10) cc_final: 0.8812 (m-10) REVERT: C 90 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8649 (mp0) REVERT: C 92 GLU cc_start: 0.8889 (mp0) cc_final: 0.8468 (mp0) REVERT: C 97 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: C 104 ASP cc_start: 0.9258 (p0) cc_final: 0.8930 (p0) REVERT: C 113 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: C 120 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7292 (mt0) REVERT: C 160 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8732 (tt) REVERT: C 165 VAL cc_start: 0.9636 (OUTLIER) cc_final: 0.9410 (m) REVERT: C 167 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8593 (mpp80) REVERT: C 205 VAL cc_start: 0.9604 (OUTLIER) cc_final: 0.9125 (p) REVERT: C 216 MET cc_start: 0.8632 (mtm) cc_final: 0.7897 (mtp) REVERT: C 227 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8573 (ttt90) REVERT: C 249 SER cc_start: 0.9673 (OUTLIER) cc_final: 0.9172 (t) REVERT: D 70 THR cc_start: 0.7319 (OUTLIER) cc_final: 0.6964 (t) REVERT: D 94 ARG cc_start: 0.8729 (ptt180) cc_final: 0.7438 (ptt90) REVERT: D 127 MET cc_start: 0.7943 (tpp) cc_final: 0.7522 (tpp) REVERT: D 141 LYS cc_start: 0.4198 (mttt) cc_final: 0.3626 (ttmm) REVERT: D 157 MET cc_start: 0.8349 (tpp) cc_final: 0.8060 (tpp) REVERT: D 162 ASP cc_start: 0.8580 (t70) cc_final: 0.8203 (t0) REVERT: D 173 ARG cc_start: 0.7469 (mmt180) cc_final: 0.7054 (mpt180) REVERT: E 19 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8169 (mtt) REVERT: E 32 SER cc_start: 0.9117 (m) cc_final: 0.8850 (p) REVERT: E 40 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: E 49 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.9072 (ttp80) REVERT: E 59 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8192 (t70) REVERT: E 60 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8098 (mt-10) REVERT: E 88 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: E 95 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.8979 (p) REVERT: E 129 ILE cc_start: 0.9312 (mt) cc_final: 0.9037 (tt) REVERT: E 140 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.8998 (m) REVERT: E 143 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8757 (m-30) REVERT: E 145 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.9057 (ttm110) REVERT: E 158 ASP cc_start: 0.8974 (m-30) cc_final: 0.8654 (m-30) REVERT: E 181 CYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8308 (p) REVERT: E 198 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8891 (tmm-80) REVERT: E 251 GLU cc_start: 0.8396 (tt0) cc_final: 0.8153 (tp30) REVERT: F 34 SER cc_start: 0.9137 (p) cc_final: 0.8816 (m) REVERT: F 44 LYS cc_start: 0.8826 (pttt) cc_final: 0.8496 (tmtt) REVERT: F 61 PHE cc_start: 0.9152 (m-80) cc_final: 0.8821 (m-10) REVERT: F 63 LYS cc_start: 0.8187 (pttt) cc_final: 0.7601 (pttt) REVERT: F 74 ASN cc_start: 0.9018 (m-40) cc_final: 0.8641 (m-40) REVERT: F 76 MET cc_start: 0.8285 (tpp) cc_final: 0.8080 (mmt) REVERT: F 125 SER cc_start: 0.8932 (m) cc_final: 0.8241 (p) REVERT: F 130 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6793 (pmt170) REVERT: F 160 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7409 (pp20) REVERT: F 168 THR cc_start: 0.8040 (m) cc_final: 0.7625 (p) REVERT: G 28 TYR cc_start: 0.9000 (m-10) cc_final: 0.8373 (m-10) REVERT: G 63 MET cc_start: 0.8862 (mtp) cc_final: 0.8411 (mtm) REVERT: G 92 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8417 (ptp-170) REVERT: G 105 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8469 (t0) REVERT: G 136 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8013 (tttp) REVERT: G 155 GLN cc_start: 0.9129 (tt0) cc_final: 0.8482 (tm-30) REVERT: G 181 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8501 (m) REVERT: H 84 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8485 (mm-30) REVERT: H 87 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8114 (t80) REVERT: H 105 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8244 (p) REVERT: H 159 ASP cc_start: 0.8903 (t0) cc_final: 0.8535 (t70) REVERT: I 28 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8548 (mt-10) REVERT: I 35 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8858 (m110) REVERT: I 52 ASN cc_start: 0.8972 (m110) cc_final: 0.8695 (m-40) REVERT: I 70 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8307 (mm-30) REVERT: I 84 ASN cc_start: 0.9286 (t0) cc_final: 0.8979 (t0) REVERT: I 95 THR cc_start: 0.9636 (OUTLIER) cc_final: 0.9348 (p) REVERT: I 121 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8835 (mt) REVERT: I 130 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.7611 (p) REVERT: I 147 LYS cc_start: 0.8936 (tttt) cc_final: 0.8345 (tttt) REVERT: I 165 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8360 (mp10) REVERT: I 168 GLN cc_start: 0.8454 (tt0) cc_final: 0.8197 (mt0) REVERT: I 184 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8841 (mtt180) REVERT: I 194 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.9124 (pt0) REVERT: J 64 ASP cc_start: 0.7582 (t0) cc_final: 0.6920 (p0) REVERT: J 65 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8125 (tm-30) REVERT: J 67 ASP cc_start: 0.9479 (t70) cc_final: 0.9090 (t0) REVERT: J 88 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8191 (p0) REVERT: J 104 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: J 150 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8604 (mtt180) REVERT: J 158 ASP cc_start: 0.8721 (m-30) cc_final: 0.8367 (m-30) REVERT: K 21 MET cc_start: 0.0823 (tpp) cc_final: 0.0538 (mmm) REVERT: K 29 MET cc_start: 0.3060 (tpp) cc_final: 0.2673 (ttt) REVERT: K 64 TRP cc_start: 0.7119 (m100) cc_final: 0.6863 (m100) REVERT: L 5 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.8893 (mm-40) REVERT: L 13 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.9026 (tt0) REVERT: L 35 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8464 (mmt90) REVERT: L 37 TYR cc_start: 0.9241 (p90) cc_final: 0.8957 (p90) REVERT: L 39 ASN cc_start: 0.9205 (t0) cc_final: 0.8878 (t0) REVERT: L 49 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: L 58 LYS cc_start: 0.8872 (pttt) cc_final: 0.8311 (ptmt) REVERT: L 97 ARG cc_start: 0.8413 (ttt180) cc_final: 0.8203 (ttp-170) REVERT: L 101 ARG cc_start: 0.9489 (OUTLIER) cc_final: 0.8988 (mtt-85) REVERT: L 103 GLU cc_start: 0.8735 (pt0) cc_final: 0.8310 (pt0) REVERT: L 104 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8604 (mttt) REVERT: L 120 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8657 (p) REVERT: L 121 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7735 (mm-40) REVERT: L 124 ASP cc_start: 0.9229 (p0) cc_final: 0.8992 (p0) REVERT: L 130 GLU cc_start: 0.8853 (tt0) cc_final: 0.8491 (tm-30) REVERT: L 131 CYS cc_start: 0.8840 (t) cc_final: 0.8298 (t) REVERT: L 132 ARG cc_start: 0.9498 (OUTLIER) cc_final: 0.8807 (ptt90) REVERT: L 144 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.9001 (ptmm) REVERT: M 60 MET cc_start: 0.7229 (tpp) cc_final: 0.6907 (ttt) REVERT: M 88 TRP cc_start: 0.2753 (m100) cc_final: 0.2131 (m100) REVERT: N 12 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7938 (p) REVERT: N 14 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9134 (p) REVERT: N 36 GLN cc_start: 0.9283 (tp40) cc_final: 0.9032 (mm-40) REVERT: N 62 GLN cc_start: 0.9039 (mm110) cc_final: 0.8717 (mt0) REVERT: N 101 HIS cc_start: 0.9406 (OUTLIER) cc_final: 0.8700 (t70) REVERT: N 125 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8853 (mt) REVERT: N 140 LYS cc_start: 0.9271 (tttt) cc_final: 0.8800 (tttp) REVERT: N 144 SER cc_start: 0.9381 (p) cc_final: 0.8878 (t) REVERT: N 145 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8337 (p) REVERT: O 52 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9173 (p) REVERT: O 61 LYS cc_start: 0.8893 (mmpt) cc_final: 0.8620 (mmtt) REVERT: O 63 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7230 (mmmt) REVERT: O 96 LYS cc_start: 0.8962 (mttt) cc_final: 0.8754 (mtpp) REVERT: O 105 THR cc_start: 0.9681 (OUTLIER) cc_final: 0.9332 (p) REVERT: O 129 ILE cc_start: 0.9321 (mm) cc_final: 0.9106 (mt) REVERT: O 147 ARG cc_start: 0.9583 (OUTLIER) cc_final: 0.9252 (mtm-85) REVERT: O 150 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8619 (ptt-90) REVERT: P 40 ARG cc_start: 0.4917 (tpt170) cc_final: 0.2435 (ptp-170) REVERT: P 102 PHE cc_start: 0.3597 (m-80) cc_final: 0.3247 (m-10) REVERT: Q 43 GLU cc_start: 0.4339 (OUTLIER) cc_final: 0.2507 (mm-30) REVERT: Q 132 PHE cc_start: 0.8831 (p90) cc_final: 0.8491 (p90) REVERT: R 5 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8032 (mtt-85) REVERT: R 7 LYS cc_start: 0.7499 (mttt) cc_final: 0.6707 (mttm) REVERT: R 18 GLU cc_start: 0.8670 (tt0) cc_final: 0.7587 (tp30) REVERT: R 41 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7797 (mp) REVERT: R 63 ARG cc_start: 0.6790 (mtt180) cc_final: 0.6452 (ttm110) REVERT: R 81 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6482 (ttp-110) REVERT: R 88 VAL cc_start: 0.8515 (t) cc_final: 0.8301 (p) REVERT: R 95 ILE cc_start: 0.8752 (mt) cc_final: 0.8100 (tp) REVERT: R 101 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.8985 (m-30) REVERT: S 11 HIS cc_start: 0.6678 (t70) cc_final: 0.5980 (t70) REVERT: S 14 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8121 (mmm160) REVERT: S 83 PHE cc_start: 0.6178 (m-80) cc_final: 0.5791 (m-80) REVERT: S 98 VAL cc_start: 0.5086 (OUTLIER) cc_final: 0.4645 (t) REVERT: S 117 ILE cc_start: 0.6344 (mt) cc_final: 0.6138 (tp) REVERT: T 35 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.7977 (p0) REVERT: T 36 THR cc_start: 0.5871 (OUTLIER) cc_final: 0.4769 (p) REVERT: T 56 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6285 (ttt180) REVERT: T 67 ARG cc_start: 0.2883 (OUTLIER) cc_final: 0.2030 (tpp-160) REVERT: T 78 ILE cc_start: 0.5005 (OUTLIER) cc_final: 0.4705 (mt) REVERT: T 83 GLN cc_start: 0.7581 (tp40) cc_final: 0.7046 (pt0) REVERT: T 112 MET cc_start: 0.5543 (mtp) cc_final: 0.4701 (mtp) REVERT: T 126 GLN cc_start: 0.8189 (tt0) cc_final: 0.7652 (tm-30) REVERT: U 20 ILE cc_start: 0.7130 (mt) cc_final: 0.6925 (mp) REVERT: U 22 ILE cc_start: 0.9033 (mt) cc_final: 0.8827 (mp) REVERT: U 23 THR cc_start: 0.7485 (m) cc_final: 0.7235 (p) REVERT: U 28 ASN cc_start: 0.8720 (p0) cc_final: 0.8455 (p0) REVERT: U 35 VAL cc_start: 0.7361 (t) cc_final: 0.7011 (t) REVERT: U 61 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6334 (mp) REVERT: U 62 ARG cc_start: 0.7516 (mtt180) cc_final: 0.6916 (mtm180) REVERT: U 75 LYS cc_start: 0.6303 (mttm) cc_final: 0.5796 (mttt) REVERT: U 76 THR cc_start: 0.9337 (m) cc_final: 0.9087 (p) REVERT: U 78 ASP cc_start: 0.7441 (m-30) cc_final: 0.7033 (m-30) REVERT: U 91 LEU cc_start: 0.8428 (mt) cc_final: 0.8135 (tp) REVERT: U 101 ILE cc_start: 0.6579 (mt) cc_final: 0.6332 (tt) REVERT: U 107 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: V 24 ILE cc_start: 0.9281 (mt) cc_final: 0.9073 (mt) REVERT: V 27 LYS cc_start: 0.9361 (mtpt) cc_final: 0.9091 (mtpp) REVERT: V 43 THR cc_start: 0.9390 (OUTLIER) cc_final: 0.9093 (p) REVERT: V 72 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8524 (mt) REVERT: V 76 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8913 (t0) REVERT: W 5 ASN cc_start: 0.9234 (t0) cc_final: 0.8785 (t0) REVERT: W 9 ASP cc_start: 0.8236 (m-30) cc_final: 0.7932 (m-30) REVERT: W 56 HIS cc_start: 0.9296 (OUTLIER) cc_final: 0.8824 (m-70) REVERT: W 85 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8540 (t0) REVERT: W 97 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8612 (ttm110) REVERT: W 111 MET cc_start: 0.9348 (ptp) cc_final: 0.8912 (ptt) REVERT: X 5 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8539 (mtm-85) REVERT: X 32 LEU cc_start: 0.9388 (tp) cc_final: 0.9112 (tp) REVERT: X 39 ASN cc_start: 0.9454 (t0) cc_final: 0.8951 (t0) REVERT: X 55 VAL cc_start: 0.9225 (t) cc_final: 0.8986 (p) REVERT: X 64 SER cc_start: 0.9381 (m) cc_final: 0.8869 (p) REVERT: X 77 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8351 (p0) REVERT: X 90 CYS cc_start: 0.9197 (m) cc_final: 0.8629 (m) REVERT: X 100 VAL cc_start: 0.9534 (OUTLIER) cc_final: 0.9145 (m) REVERT: X 107 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8546 (mtm180) REVERT: X 134 TYR cc_start: 0.9199 (t80) cc_final: 0.8963 (t80) REVERT: Y 23 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8516 (ptt) REVERT: Y 86 GLU cc_start: 0.9277 (tp30) cc_final: 0.8715 (tp30) REVERT: Y 102 THR cc_start: 0.9036 (p) cc_final: 0.8797 (p) REVERT: Y 112 ASN cc_start: 0.9332 (m-40) cc_final: 0.9104 (m-40) REVERT: Y 115 LYS cc_start: 0.9266 (ttmt) cc_final: 0.8899 (tppt) REVERT: Z 45 ASN cc_start: 0.8684 (m-40) cc_final: 0.8337 (m-40) REVERT: Z 47 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.4905 (tp) REVERT: Z 54 THR cc_start: 0.8312 (m) cc_final: 0.8059 (t) REVERT: Z 88 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6759 (mt) REVERT: a 30 VAL cc_start: 0.9716 (OUTLIER) cc_final: 0.9511 (m) REVERT: a 52 ASP cc_start: 0.8625 (m-30) cc_final: 0.8412 (m-30) REVERT: a 67 LEU cc_start: 0.9223 (tp) cc_final: 0.8809 (tt) REVERT: a 69 VAL cc_start: 0.9621 (t) cc_final: 0.9266 (m) REVERT: a 70 LYS cc_start: 0.9460 (tttm) cc_final: 0.9252 (tttm) REVERT: a 72 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8420 (m90) REVERT: b 11 SER cc_start: 0.9067 (p) cc_final: 0.8862 (p) REVERT: b 17 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (ttt-90) REVERT: b 20 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8648 (pttm) REVERT: b 34 ASP cc_start: 0.8906 (t0) cc_final: 0.8462 (t0) REVERT: b 43 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8440 (mp) REVERT: c 55 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8370 (p) REVERT: c 57 THR cc_start: 0.8075 (m) cc_final: 0.7381 (p) REVERT: c 67 ARG cc_start: 0.8578 (ttt180) cc_final: 0.7613 (tmm-80) REVERT: c 68 LEU cc_start: 0.6645 (mt) cc_final: 0.6412 (mt) REVERT: d 8 TRP cc_start: 0.4799 (t-100) cc_final: 0.4197 (t-100) REVERT: d 27 ARG cc_start: 0.5458 (mtt180) cc_final: 0.4798 (mtt90) REVERT: d 37 ASN cc_start: 0.8423 (m-40) cc_final: 0.8209 (m-40) REVERT: e 11 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8270 (ttmt) REVERT: e 24 LYS cc_start: 0.8400 (pttt) cc_final: 0.8114 (ptpp) REVERT: e 29 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8728 (p) REVERT: e 34 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8939 (tpp-160) REVERT: e 36 MET cc_start: 0.8104 (ttp) cc_final: 0.7820 (tmm) REVERT: f 91 ASN cc_start: 0.5906 (m110) cc_final: 0.5683 (m-40) REVERT: f 93 HIS cc_start: 0.3814 (t70) cc_final: 0.3353 (p-80) REVERT: f 132 MET cc_start: 0.5691 (mtp) cc_final: 0.5421 (mpp) REVERT: g 4 GLN cc_start: 0.7984 (mm-40) cc_final: 0.6916 (tt0) REVERT: g 20 GLN cc_start: 0.5209 (mm-40) cc_final: 0.4658 (mm-40) REVERT: g 41 ILE cc_start: 0.2615 (OUTLIER) cc_final: 0.2166 (mt) REVERT: g 90 TRP cc_start: 0.6880 (m100) cc_final: 0.5447 (m100) REVERT: g 97 THR cc_start: 0.4277 (OUTLIER) cc_final: 0.4031 (m) REVERT: g 106 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8552 (mtpt) REVERT: g 150 TRP cc_start: 0.7284 (m-10) cc_final: 0.5978 (m-10) REVERT: g 217 MET cc_start: 0.7809 (mmt) cc_final: 0.7420 (mmm) REVERT: g 230 LEU cc_start: 0.7266 (mt) cc_final: 0.6551 (mt) REVERT: g 246 TYR cc_start: 0.6201 (t80) cc_final: 0.5494 (t80) REVERT: g 271 LYS cc_start: 0.7612 (pttt) cc_final: 0.7235 (tptm) REVERT: h 9 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8272 (ttp80) REVERT: h 10 MET cc_start: 0.8950 (tpp) cc_final: 0.8604 (tpp) REVERT: h 14 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8745 (ttpt) REVERT: h 18 ARG cc_start: 0.8638 (ttm170) cc_final: 0.8325 (ttm170) REVERT: h 21 ARG cc_start: 0.8706 (ttt180) cc_final: 0.8482 (ptm-80) REVERT: r 168 GLU cc_start: 0.9129 (pt0) cc_final: 0.8837 (pt0) REVERT: r 170 ARG cc_start: 0.8334 (ttm170) cc_final: 0.7950 (ttm110) REVERT: w 91 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7953 (mmp) outliers start: 549 outliers final: 178 residues processed: 1664 average time/residue: 0.8831 time to fit residues: 2364.7805 Evaluate side-chains 1111 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 822 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 181 CYS Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 130 ARG Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 178 ARG Chi-restraints excluded: chain I residue 184 ARG Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain I residue 194 GLU Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 21 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 18 GLN Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 49 GLU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 74 SER 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 85 THR Chi-restraints excluded: chain L residue 101 ARG Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 144 LYS Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 101 HIS Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 127 ARG Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 98 ARG Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 137 SER Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 147 ARG Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 75 VAL Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 125 ARG Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 56 ARG Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 78 ILE Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain U residue 36 CYS Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 56 HIS Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 97 ARG Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 5 ARG Chi-restraints excluded: chain X residue 9 THR Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 107 ARG Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 23 MET Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 7 ASN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 72 HIS Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain b residue 17 ARG Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain e residue 11 LYS Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 41 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 3.9990 chunk 504 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 172 optimal weight: 40.0000 chunk 340 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 522 optimal weight: 0.0060 chunk 202 optimal weight: 9.9990 chunk 317 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 604 optimal weight: 9.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 141 ASN A 193 HIS B 159 GLN D 56 GLN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN E 8 HIS E 50 ASN E 179 ASN E 209 HIS E 214 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 ASN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 186 GLN H 91 HIS ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 HIS H 157 HIS I 84 ASN I 87 ASN I 168 GLN J 125 HIS L 11 GLN L 65 ASN N 58 HIS N 105 ASN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 GLN P 79 HIS P 114 HIS ** Q 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 HIS S 11 HIS T 142 ASN X 31 HIS X 39 ASN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 91 ASN f 111 ASN ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 296 GLN h 22 GLN w 96 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 86006 Z= 0.191 Angle : 0.719 10.465 125306 Z= 0.368 Chirality : 0.041 0.356 15565 Planarity : 0.005 0.095 8764 Dihedral : 25.366 179.625 36158 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 8.12 % Allowed : 19.03 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 4859 helix: -0.74 (0.12), residues: 1601 sheet: -0.46 (0.15), residues: 978 loop : -1.11 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 33 HIS 0.010 0.001 HIS H 157 PHE 0.021 0.002 PHE D 24 TYR 0.023 0.002 TYR K 68 ARG 0.018 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 994 time to evaluate : 4.474 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: A 34 MET cc_start: 0.9298 (mmm) cc_final: 0.9061 (tpp) REVERT: A 43 SER cc_start: 0.9140 (t) cc_final: 0.8849 (m) REVERT: A 44 ASP cc_start: 0.7697 (m-30) cc_final: 0.7227 (t0) REVERT: A 47 TYR cc_start: 0.9166 (m-80) cc_final: 0.8926 (m-10) REVERT: A 52 LYS cc_start: 0.8673 (tttt) cc_final: 0.8464 (tppt) REVERT: A 73 ASP cc_start: 0.8580 (m-30) cc_final: 0.8199 (m-30) REVERT: A 80 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8072 (ptp90) REVERT: A 111 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8817 (pm20) REVERT: A 130 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8479 (p0) REVERT: A 165 ASN cc_start: 0.8853 (p0) cc_final: 0.8487 (p0) REVERT: A 177 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8315 (mtp) REVERT: A 200 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 31 TYR cc_start: 0.8922 (m-80) cc_final: 0.8457 (m-10) REVERT: B 48 LEU cc_start: 0.9042 (tp) cc_final: 0.8295 (tp) REVERT: B 59 SER cc_start: 0.9183 (p) cc_final: 0.8853 (m) REVERT: B 60 ASP cc_start: 0.8845 (t0) cc_final: 0.8501 (t0) REVERT: B 68 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: B 83 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8658 (mtpp) REVERT: B 85 LYS cc_start: 0.9036 (mttt) cc_final: 0.8722 (mtpp) REVERT: B 97 LEU cc_start: 0.9166 (mt) cc_final: 0.8747 (mt) REVERT: B 137 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9301 (mt) REVERT: B 139 CYS cc_start: 0.8573 (t) cc_final: 0.7866 (t) REVERT: B 213 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8475 (tmm160) REVERT: C 73 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8555 (mmm) REVERT: C 80 GLU cc_start: 0.7746 (tp30) cc_final: 0.7492 (tp30) REVERT: C 82 TYR cc_start: 0.8922 (m-10) cc_final: 0.8636 (m-10) REVERT: C 92 GLU cc_start: 0.8695 (mp0) cc_final: 0.8163 (mp0) REVERT: C 104 ASP cc_start: 0.9151 (p0) cc_final: 0.8779 (p0) REVERT: C 113 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: C 120 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: C 125 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8456 (mtpt) REVERT: C 139 LEU cc_start: 0.9579 (tp) cc_final: 0.9315 (tt) REVERT: C 160 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8768 (tt) REVERT: C 211 LYS cc_start: 0.9213 (tttt) cc_final: 0.8867 (ttmm) REVERT: C 216 MET cc_start: 0.8660 (mtm) cc_final: 0.7783 (mtp) REVERT: C 227 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8463 (ttt90) REVERT: D 46 THR cc_start: 0.6506 (m) cc_final: 0.6051 (t) REVERT: D 94 ARG cc_start: 0.8794 (ptt180) cc_final: 0.7732 (ptt90) REVERT: D 162 ASP cc_start: 0.8266 (t70) cc_final: 0.7998 (t0) REVERT: D 193 ASP cc_start: 0.7034 (t0) cc_final: 0.6753 (t0) REVERT: E 19 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8088 (mmm) REVERT: E 66 MET cc_start: 0.9021 (mmm) cc_final: 0.8679 (mmm) REVERT: E 88 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: E 129 ILE cc_start: 0.9389 (mt) cc_final: 0.8998 (tt) REVERT: E 139 LEU cc_start: 0.8402 (mt) cc_final: 0.8037 (mt) REVERT: E 145 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8875 (ttm110) REVERT: E 160 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8970 (pt) REVERT: E 225 ILE cc_start: 0.9078 (tt) cc_final: 0.8672 (tt) REVERT: E 237 SER cc_start: 0.9031 (t) cc_final: 0.8778 (p) REVERT: E 253 ASP cc_start: 0.9380 (t0) cc_final: 0.9156 (t70) REVERT: F 44 LYS cc_start: 0.8840 (pttt) cc_final: 0.8522 (tmtt) REVERT: F 76 MET cc_start: 0.8350 (tpp) cc_final: 0.8068 (mmt) REVERT: F 77 MET cc_start: 0.7261 (ptp) cc_final: 0.6851 (ptp) REVERT: F 82 ASN cc_start: 0.6631 (OUTLIER) cc_final: 0.5237 (p0) REVERT: F 137 GLN cc_start: 0.7691 (tt0) cc_final: 0.7483 (tt0) REVERT: F 160 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7295 (tt0) REVERT: F 168 THR cc_start: 0.8384 (m) cc_final: 0.8104 (p) REVERT: F 176 GLU cc_start: 0.9055 (tp30) cc_final: 0.8775 (tt0) REVERT: F 179 ASN cc_start: 0.9060 (m-40) cc_final: 0.8676 (m110) REVERT: G 28 TYR cc_start: 0.8855 (m-10) cc_final: 0.8137 (m-10) REVERT: G 58 LYS cc_start: 0.9189 (mttt) cc_final: 0.8867 (mtmm) REVERT: G 92 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7994 (ptp-170) REVERT: G 105 ASN cc_start: 0.8768 (m110) cc_final: 0.8436 (m110) REVERT: G 120 ASP cc_start: 0.7907 (t0) cc_final: 0.7573 (t0) REVERT: G 152 ASP cc_start: 0.8306 (t0) cc_final: 0.7410 (p0) REVERT: G 155 GLN cc_start: 0.9143 (tt0) cc_final: 0.8883 (tt0) REVERT: G 181 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8705 (m) REVERT: H 32 MET cc_start: 0.8926 (mmp) cc_final: 0.8537 (ptt) REVERT: H 64 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8036 (t) REVERT: H 68 GLN cc_start: 0.8390 (mt0) cc_final: 0.8156 (mt0) REVERT: H 87 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7551 (t80) REVERT: H 159 ASP cc_start: 0.8937 (t0) cc_final: 0.8566 (t70) REVERT: H 180 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8358 (mt) REVERT: I 36 THR cc_start: 0.9633 (m) cc_final: 0.9392 (m) REVERT: I 62 VAL cc_start: 0.9069 (p) cc_final: 0.8760 (m) REVERT: I 95 THR cc_start: 0.9571 (m) cc_final: 0.9311 (p) REVERT: I 130 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.6928 (p) REVERT: I 134 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: I 161 LEU cc_start: 0.7637 (mt) cc_final: 0.7194 (mt) REVERT: I 165 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8049 (mp10) REVERT: I 184 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8861 (mtt-85) REVERT: I 196 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: J 64 ASP cc_start: 0.7503 (t0) cc_final: 0.7206 (p0) REVERT: J 102 ILE cc_start: 0.9410 (mm) cc_final: 0.9145 (tp) REVERT: J 103 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8319 (mm-30) REVERT: J 104 ASP cc_start: 0.9321 (OUTLIER) cc_final: 0.9089 (m-30) REVERT: J 108 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.7856 (mmp-170) REVERT: J 143 ASN cc_start: 0.9073 (t0) cc_final: 0.8194 (t0) REVERT: J 150 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8450 (mtt180) REVERT: K 61 GLN cc_start: 0.5724 (tp40) cc_final: 0.5471 (mm-40) REVERT: K 64 TRP cc_start: 0.7106 (m100) cc_final: 0.6040 (m100) REVERT: K 67 PHE cc_start: 0.5556 (m-80) cc_final: 0.4894 (m-80) REVERT: L 5 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.8977 (mm-40) REVERT: L 39 ASN cc_start: 0.9019 (t0) cc_final: 0.8106 (p0) REVERT: L 49 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7831 (tp30) REVERT: L 56 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8989 (mt) REVERT: L 58 LYS cc_start: 0.8865 (pttt) cc_final: 0.8164 (ptmt) REVERT: L 65 ASN cc_start: 0.8766 (t0) cc_final: 0.7990 (p0) REVERT: L 101 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.8109 (mtt180) REVERT: N 16 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8628 (mt) REVERT: N 31 ASP cc_start: 0.9118 (m-30) cc_final: 0.8850 (m-30) REVERT: N 119 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8519 (mm-30) REVERT: N 127 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8143 (ttp-110) REVERT: N 140 LYS cc_start: 0.9153 (tttt) cc_final: 0.8865 (tttp) REVERT: N 145 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8459 (p) REVERT: O 52 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9016 (p) REVERT: O 61 LYS cc_start: 0.8704 (mmpt) cc_final: 0.8407 (mmtt) REVERT: O 72 TYR cc_start: 0.8536 (t80) cc_final: 0.7522 (t80) REVERT: O 124 MET cc_start: 0.8047 (tpp) cc_final: 0.7710 (tpp) REVERT: O 135 ILE cc_start: 0.8849 (tt) cc_final: 0.8580 (pt) REVERT: O 150 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8983 (mtm180) REVERT: P 17 TYR cc_start: 0.4727 (t80) cc_final: 0.4134 (t80) REVERT: P 40 ARG cc_start: 0.4796 (tpt170) cc_final: 0.2119 (ptp-170) REVERT: P 72 LYS cc_start: 0.6004 (ttmt) cc_final: 0.5473 (tttt) REVERT: P 84 ILE cc_start: 0.4056 (OUTLIER) cc_final: 0.3544 (tp) REVERT: Q 41 MET cc_start: 0.0876 (tpp) cc_final: 0.0596 (tpt) REVERT: Q 43 GLU cc_start: 0.3219 (OUTLIER) cc_final: 0.1970 (mm-30) REVERT: Q 49 TYR cc_start: 0.7461 (m-80) cc_final: 0.7251 (m-80) REVERT: Q 132 PHE cc_start: 0.8896 (p90) cc_final: 0.8476 (p90) REVERT: R 5 ARG cc_start: 0.8290 (mmt180) cc_final: 0.7585 (mmt90) REVERT: R 18 GLU cc_start: 0.8742 (tt0) cc_final: 0.7659 (tp30) REVERT: R 33 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7557 (mmt-90) REVERT: R 41 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7858 (mp) REVERT: R 92 ASP cc_start: 0.7300 (t0) cc_final: 0.7079 (t0) REVERT: R 101 ASP cc_start: 0.8857 (m-30) cc_final: 0.8405 (m-30) REVERT: S 17 ASN cc_start: 0.6506 (t0) cc_final: 0.6110 (t0) REVERT: T 9 VAL cc_start: 0.4680 (t) cc_final: 0.4073 (m) REVERT: T 35 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.7756 (p0) REVERT: T 36 THR cc_start: 0.4789 (OUTLIER) cc_final: 0.4024 (p) REVERT: T 83 GLN cc_start: 0.7693 (tp40) cc_final: 0.7083 (pt0) REVERT: T 128 GLN cc_start: 0.7569 (tt0) cc_final: 0.7285 (tp-100) REVERT: U 23 THR cc_start: 0.7426 (m) cc_final: 0.7194 (p) REVERT: U 24 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7819 (mm) REVERT: U 67 LYS cc_start: 0.8577 (mttt) cc_final: 0.7915 (mtpp) REVERT: U 75 LYS cc_start: 0.6251 (mttm) cc_final: 0.5921 (mttt) REVERT: U 76 THR cc_start: 0.9295 (m) cc_final: 0.9018 (p) REVERT: U 78 ASP cc_start: 0.6472 (m-30) cc_final: 0.6253 (m-30) REVERT: U 91 LEU cc_start: 0.8209 (mt) cc_final: 0.7751 (tp) REVERT: U 107 GLU cc_start: 0.7303 (tp30) cc_final: 0.6363 (mp0) REVERT: V 9 VAL cc_start: 0.9415 (m) cc_final: 0.9128 (p) REVERT: V 72 LEU cc_start: 0.8830 (mt) cc_final: 0.8457 (mt) REVERT: V 76 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8636 (t0) REVERT: W 9 ASP cc_start: 0.7666 (m-30) cc_final: 0.7461 (m-30) REVERT: W 49 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: W 56 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8296 (m-70) REVERT: W 111 MET cc_start: 0.8972 (ptp) cc_final: 0.8764 (ptt) REVERT: X 25 LYS cc_start: 0.8173 (tttt) cc_final: 0.7900 (ptmt) REVERT: X 26 GLN cc_start: 0.8346 (tp40) cc_final: 0.8116 (mt0) REVERT: X 32 LEU cc_start: 0.9237 (tp) cc_final: 0.8814 (tp) REVERT: X 39 ASN cc_start: 0.9360 (t0) cc_final: 0.8860 (t0) REVERT: X 64 SER cc_start: 0.9280 (m) cc_final: 0.8804 (p) REVERT: X 90 CYS cc_start: 0.9194 (m) cc_final: 0.8296 (m) REVERT: X 100 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.9142 (m) REVERT: X 105 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8868 (t80) REVERT: X 134 TYR cc_start: 0.9006 (t80) cc_final: 0.8607 (t80) REVERT: Y 22 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8770 (pt0) REVERT: Y 23 MET cc_start: 0.8800 (ptp) cc_final: 0.8339 (ptt) REVERT: Y 109 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8530 (mm-30) REVERT: Y 112 ASN cc_start: 0.9266 (m-40) cc_final: 0.9048 (m-40) REVERT: Y 115 LYS cc_start: 0.9299 (ttmt) cc_final: 0.8789 (tppt) REVERT: Z 47 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4558 (tp) REVERT: Z 54 THR cc_start: 0.8434 (m) cc_final: 0.8154 (t) REVERT: b 6 ASP cc_start: 0.8108 (p0) cc_final: 0.7847 (p0) REVERT: b 20 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8626 (pttt) REVERT: c 13 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7991 (mtp85) REVERT: c 43 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6697 (mt) REVERT: c 57 THR cc_start: 0.7679 (m) cc_final: 0.7061 (p) REVERT: c 67 ARG cc_start: 0.8427 (ttt180) cc_final: 0.7693 (tmm-80) REVERT: d 40 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.4269 (ptt180) REVERT: d 55 LEU cc_start: 0.7751 (mm) cc_final: 0.7509 (mm) REVERT: e 29 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8364 (p) REVERT: e 34 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.7220 (mpt-90) REVERT: e 36 MET cc_start: 0.7983 (ttp) cc_final: 0.7551 (tmm) REVERT: e 40 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8309 (ttm-80) REVERT: e 53 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8206 (mmmt) REVERT: f 90 LYS cc_start: 0.5404 (mmtt) cc_final: 0.4771 (tptm) REVERT: f 116 ARG cc_start: 0.4362 (OUTLIER) cc_final: 0.4136 (mmm160) REVERT: g 17 TRP cc_start: 0.6647 (m-10) cc_final: 0.6370 (m-10) REVERT: g 41 ILE cc_start: 0.2063 (OUTLIER) cc_final: 0.1855 (mt) REVERT: g 64 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5721 (t-170) REVERT: g 90 TRP cc_start: 0.6850 (m100) cc_final: 0.5950 (m100) REVERT: g 110 SER cc_start: 0.4944 (OUTLIER) cc_final: 0.4545 (p) REVERT: g 217 MET cc_start: 0.7574 (mmt) cc_final: 0.7155 (mmm) REVERT: g 235 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7499 (mm) REVERT: g 246 TYR cc_start: 0.6182 (t80) cc_final: 0.5585 (t80) REVERT: g 271 LYS cc_start: 0.7596 (pttt) cc_final: 0.7365 (tptm) REVERT: h 9 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8600 (ttp80) REVERT: h 18 ARG cc_start: 0.8897 (ttm170) cc_final: 0.8691 (ttm170) REVERT: r 168 GLU cc_start: 0.9099 (pt0) cc_final: 0.7942 (mm-30) REVERT: r 170 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8012 (ttm110) REVERT: w 91 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7742 (mmp) outliers start: 345 outliers final: 149 residues processed: 1227 average time/residue: 0.8072 time to fit residues: 1653.3343 Evaluate side-chains 1017 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 804 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 232 ASN Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 22 HIS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 ARG Chi-restraints excluded: chain I residue 196 GLU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 101 ARG Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 127 ARG Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 114 HIS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 76 ASP Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 56 HIS Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 7 ASN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 53 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain f residue 116 ARG Chi-restraints excluded: chain g residue 41 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 40.0000 chunk 187 optimal weight: 10.0000 chunk 503 optimal weight: 30.0000 chunk 411 optimal weight: 8.9990 chunk 166 optimal weight: 50.0000 chunk 605 optimal weight: 8.9990 chunk 654 optimal weight: 0.3980 chunk 539 optimal weight: 7.9990 chunk 600 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 486 optimal weight: 9.9990 overall best weight: 7.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN E 112 HIS F 110 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN L 121 GLN O 32 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 24 HIS R 127 ASN S 17 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN X 26 GLN X 46 HIS Y 63 HIS Y 106 GLN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS e 37 GLN ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 HIS ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 222 ASN ** g 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 95 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 86006 Z= 0.384 Angle : 0.790 11.351 125306 Z= 0.399 Chirality : 0.044 0.380 15565 Planarity : 0.006 0.089 8764 Dihedral : 25.199 179.907 35843 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.99 % Favored : 95.82 % Rotamer: Outliers : 7.94 % Allowed : 21.12 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.11), residues: 4859 helix: -0.21 (0.12), residues: 1615 sheet: -0.49 (0.16), residues: 952 loop : -1.05 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP g 132 HIS 0.016 0.002 HIS P 114 PHE 0.024 0.002 PHE C 84 TYR 0.027 0.002 TYR L 37 ARG 0.012 0.001 ARG S 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 831 time to evaluate : 4.433 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: A 44 ASP cc_start: 0.7808 (m-30) cc_final: 0.7466 (t0) REVERT: A 73 ASP cc_start: 0.8591 (m-30) cc_final: 0.8256 (m-30) REVERT: A 130 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.8294 (p0) REVERT: A 131 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7215 (p90) REVERT: A 132 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8693 (tp40) REVERT: A 138 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8984 (m) REVERT: A 165 ASN cc_start: 0.9073 (p0) cc_final: 0.8729 (p0) REVERT: A 177 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8322 (mtp) REVERT: A 186 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8733 (mtt90) REVERT: A 200 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8416 (t0) REVERT: B 31 TYR cc_start: 0.8897 (m-80) cc_final: 0.8694 (m-10) REVERT: B 68 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: B 76 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7820 (p0) REVERT: B 78 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 97 LEU cc_start: 0.9220 (mt) cc_final: 0.8829 (mt) REVERT: B 137 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9308 (mt) REVERT: B 168 MET cc_start: 0.8198 (mtp) cc_final: 0.7522 (mtp) REVERT: B 180 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7593 (p0) REVERT: C 73 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8547 (mmm) REVERT: C 80 GLU cc_start: 0.8132 (tp30) cc_final: 0.7730 (tp30) REVERT: C 104 ASP cc_start: 0.9095 (p0) cc_final: 0.8413 (p0) REVERT: C 121 ARG cc_start: 0.8377 (tmt170) cc_final: 0.8137 (ttt-90) REVERT: C 123 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8147 (mtp180) REVERT: C 160 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8905 (tt) REVERT: C 215 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8363 (ttp) REVERT: C 216 MET cc_start: 0.8771 (mtm) cc_final: 0.8100 (mtp) REVERT: C 227 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8570 (ttt90) REVERT: C 255 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9170 (mt) REVERT: D 31 GLU cc_start: 0.6445 (mm-30) cc_final: 0.6132 (pm20) REVERT: D 46 THR cc_start: 0.6116 (m) cc_final: 0.5718 (t) REVERT: D 66 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6663 (mm) REVERT: D 94 ARG cc_start: 0.8796 (ptt180) cc_final: 0.7670 (ptm160) REVERT: D 150 MET cc_start: 0.4713 (mtt) cc_final: 0.4012 (mmt) REVERT: D 162 ASP cc_start: 0.8357 (t70) cc_final: 0.8123 (t0) REVERT: D 182 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5145 (mm) REVERT: D 193 ASP cc_start: 0.7195 (t0) cc_final: 0.6970 (t0) REVERT: E 19 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: E 60 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8019 (mt-10) REVERT: E 66 MET cc_start: 0.9087 (mmm) cc_final: 0.8794 (mmm) REVERT: E 129 ILE cc_start: 0.9365 (mt) cc_final: 0.9155 (pt) REVERT: E 133 THR cc_start: 0.8610 (m) cc_final: 0.8104 (p) REVERT: E 145 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8835 (ttm110) REVERT: F 44 LYS cc_start: 0.8972 (pttt) cc_final: 0.8562 (tmtt) REVERT: F 48 TYR cc_start: 0.8611 (m-10) cc_final: 0.8197 (m-10) REVERT: F 77 MET cc_start: 0.7585 (ptp) cc_final: 0.6990 (ptp) REVERT: F 82 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.5710 (p0) REVERT: F 160 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7470 (tt0) REVERT: F 179 ASN cc_start: 0.9026 (m-40) cc_final: 0.8642 (m110) REVERT: G 21 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: G 28 TYR cc_start: 0.8890 (m-10) cc_final: 0.8241 (m-10) REVERT: G 152 ASP cc_start: 0.8432 (t0) cc_final: 0.8227 (t0) REVERT: G 156 TYR cc_start: 0.8542 (m-80) cc_final: 0.8236 (m-80) REVERT: H 41 ARG cc_start: 0.8582 (ttm110) cc_final: 0.8280 (ptp-110) REVERT: H 87 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.7653 (t80) REVERT: H 159 ASP cc_start: 0.9029 (t0) cc_final: 0.8809 (t70) REVERT: I 22 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.8830 (p-80) REVERT: I 36 THR cc_start: 0.9561 (m) cc_final: 0.9173 (p) REVERT: I 130 THR cc_start: 0.7293 (p) cc_final: 0.6365 (p) REVERT: I 134 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: I 165 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8700 (mt0) REVERT: I 184 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8874 (mtt180) REVERT: J 64 ASP cc_start: 0.7930 (t0) cc_final: 0.6870 (p0) REVERT: J 65 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7865 (tm-30) REVERT: J 70 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8700 (ttt-90) REVERT: J 102 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9244 (tp) REVERT: J 103 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8287 (mm-30) REVERT: J 108 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.7680 (mmp-170) REVERT: J 150 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8478 (mtt180) REVERT: K 61 GLN cc_start: 0.5494 (tp40) cc_final: 0.5268 (mm-40) REVERT: L 5 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9016 (mm-40) REVERT: L 37 TYR cc_start: 0.8959 (p90) cc_final: 0.8681 (p90) REVERT: L 39 ASN cc_start: 0.8762 (t0) cc_final: 0.8250 (t0) REVERT: L 40 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8341 (mm) REVERT: L 56 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9083 (mt) REVERT: L 101 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8971 (mtt180) REVERT: N 86 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7677 (pp20) REVERT: N 107 LYS cc_start: 0.8530 (tptt) cc_final: 0.8146 (tptt) REVERT: N 140 LYS cc_start: 0.9382 (tttt) cc_final: 0.8910 (tttp) REVERT: N 142 GLU cc_start: 0.8215 (pm20) cc_final: 0.7881 (pm20) REVERT: O 44 VAL cc_start: 0.9456 (t) cc_final: 0.9044 (p) REVERT: O 52 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9246 (p) REVERT: O 61 LYS cc_start: 0.8732 (mmpt) cc_final: 0.8270 (mmtt) REVERT: O 135 ILE cc_start: 0.9153 (tt) cc_final: 0.8839 (pt) REVERT: P 17 TYR cc_start: 0.4785 (t80) cc_final: 0.4430 (t80) REVERT: P 40 ARG cc_start: 0.5036 (tpt170) cc_final: 0.1984 (ptp-170) REVERT: P 108 LYS cc_start: 0.4644 (mmtp) cc_final: 0.4400 (mmtt) REVERT: Q 41 MET cc_start: 0.1387 (tpp) cc_final: 0.0919 (tpt) REVERT: Q 43 GLU cc_start: 0.3210 (OUTLIER) cc_final: 0.1756 (mm-30) REVERT: Q 132 PHE cc_start: 0.8826 (p90) cc_final: 0.8542 (p90) REVERT: Q 145 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5314 (m-80) REVERT: R 5 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7382 (mmt90) REVERT: R 33 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7782 (tpp80) REVERT: R 37 GLU cc_start: 0.8617 (tt0) cc_final: 0.7997 (mt-10) REVERT: R 92 ASP cc_start: 0.7656 (t0) cc_final: 0.7411 (t0) REVERT: S 10 GLN cc_start: 0.7825 (mt0) cc_final: 0.6665 (pp30) REVERT: S 75 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6518 (mtm-85) REVERT: S 117 ILE cc_start: 0.6348 (mt) cc_final: 0.5598 (tp) REVERT: T 35 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.7778 (p0) REVERT: T 36 THR cc_start: 0.5157 (OUTLIER) cc_final: 0.4550 (p) REVERT: T 83 GLN cc_start: 0.7779 (tp40) cc_final: 0.7217 (pt0) REVERT: U 67 LYS cc_start: 0.8520 (mttt) cc_final: 0.8029 (tttm) REVERT: U 75 LYS cc_start: 0.6363 (mttm) cc_final: 0.6007 (mttt) REVERT: U 76 THR cc_start: 0.9335 (m) cc_final: 0.9122 (p) REVERT: U 78 ASP cc_start: 0.6276 (m-30) cc_final: 0.5943 (m-30) REVERT: U 91 LEU cc_start: 0.8498 (mt) cc_final: 0.7958 (tp) REVERT: U 107 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: V 21 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8839 (t0) REVERT: V 39 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8871 (p) REVERT: V 40 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8823 (t70) REVERT: V 65 SER cc_start: 0.9439 (p) cc_final: 0.9148 (m) REVERT: V 72 LEU cc_start: 0.8943 (mt) cc_final: 0.8468 (mt) REVERT: V 76 ASP cc_start: 0.8792 (t0) cc_final: 0.8341 (t0) REVERT: W 56 HIS cc_start: 0.9219 (OUTLIER) cc_final: 0.8941 (m-70) REVERT: W 111 MET cc_start: 0.8917 (ptp) cc_final: 0.8673 (ptp) REVERT: X 90 CYS cc_start: 0.9228 (m) cc_final: 0.8503 (m) REVERT: X 100 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9219 (m) REVERT: Y 6 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8687 (p) REVERT: Y 23 MET cc_start: 0.9164 (ptp) cc_final: 0.8711 (ptp) REVERT: Y 106 GLN cc_start: 0.8882 (mm110) cc_final: 0.8679 (mm-40) REVERT: Y 109 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8496 (mm-30) REVERT: Y 117 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.9015 (m) REVERT: Z 68 ILE cc_start: 0.7340 (mt) cc_final: 0.6984 (mp) REVERT: a 67 LEU cc_start: 0.9041 (tp) cc_final: 0.8824 (tt) REVERT: b 20 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8684 (pttm) REVERT: b 26 GLN cc_start: 0.8966 (mt0) cc_final: 0.8713 (mp10) REVERT: c 43 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6950 (mt) REVERT: c 67 ARG cc_start: 0.8590 (ttt180) cc_final: 0.7862 (ttp-170) REVERT: d 34 TYR cc_start: 0.6547 (m-80) cc_final: 0.6040 (m-80) REVERT: d 40 ARG cc_start: 0.5268 (OUTLIER) cc_final: 0.4798 (ptm160) REVERT: e 34 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.7183 (mpt-90) REVERT: e 36 MET cc_start: 0.8122 (ttp) cc_final: 0.7914 (tmm) REVERT: g 30 MET cc_start: 0.2776 (ptp) cc_final: 0.2470 (ptp) REVERT: g 150 TRP cc_start: 0.6613 (m-10) cc_final: 0.4452 (m-10) REVERT: g 155 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.5508 (mpt180) REVERT: g 246 TYR cc_start: 0.6149 (t80) cc_final: 0.5650 (t80) REVERT: g 271 LYS cc_start: 0.7358 (pttt) cc_final: 0.7062 (tptm) REVERT: h 9 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8758 (ttp80) REVERT: h 21 ARG cc_start: 0.8590 (ttt180) cc_final: 0.8187 (ttp-170) REVERT: r 168 GLU cc_start: 0.9121 (pt0) cc_final: 0.7795 (mm-30) REVERT: r 170 ARG cc_start: 0.8547 (ttm170) cc_final: 0.8108 (ttm110) REVERT: w 91 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7727 (mmp) outliers start: 337 outliers final: 192 residues processed: 1058 average time/residue: 0.8017 time to fit residues: 1422.7444 Evaluate side-chains 1001 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 752 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 232 ASN Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 149 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 22 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 ARG Chi-restraints excluded: chain I residue 186 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 101 ARG Chi-restraints excluded: chain L residue 121 GLN Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain Q residue 145 TYR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 94 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 75 ARG Chi-restraints excluded: chain S residue 139 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 56 HIS Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 VAL Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 0.9980 chunk 455 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 406 optimal weight: 20.0000 chunk 608 optimal weight: 8.9990 chunk 643 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 576 optimal weight: 5.9990 chunk 173 optimal weight: 50.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 193 HIS ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 59 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 GLN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 18 GLN L 121 GLN Q 80 GLN R 116 ASN R 127 ASN S 17 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 305 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 86006 Z= 0.278 Angle : 0.697 10.559 125306 Z= 0.354 Chirality : 0.041 0.370 15565 Planarity : 0.005 0.086 8764 Dihedral : 25.015 179.812 35777 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 7.51 % Allowed : 22.42 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4859 helix: 0.22 (0.12), residues: 1608 sheet: -0.48 (0.16), residues: 938 loop : -0.93 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 67 HIS 0.007 0.001 HIS B 208 PHE 0.018 0.002 PHE T 92 TYR 0.017 0.002 TYR g 194 ARG 0.006 0.001 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 787 time to evaluate : 4.521 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: A 44 ASP cc_start: 0.7755 (m-30) cc_final: 0.7402 (t0) REVERT: A 73 ASP cc_start: 0.8621 (m-30) cc_final: 0.8282 (m-30) REVERT: A 130 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8317 (p0) REVERT: A 131 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7138 (p90) REVERT: A 165 ASN cc_start: 0.9165 (p0) cc_final: 0.8686 (p0) REVERT: A 177 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: A 189 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 195 TRP cc_start: 0.8885 (t60) cc_final: 0.8367 (t60) REVERT: A 200 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8476 (m-30) REVERT: B 68 GLU cc_start: 0.8375 (tp30) cc_final: 0.7918 (mm-30) REVERT: B 76 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7812 (p0) REVERT: B 78 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7131 (mm-30) REVERT: B 83 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8736 (mtpp) REVERT: B 97 LEU cc_start: 0.9161 (mt) cc_final: 0.8708 (mt) REVERT: B 110 MET cc_start: 0.8740 (tpp) cc_final: 0.8485 (tpp) REVERT: B 180 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7481 (p0) REVERT: B 198 GLU cc_start: 0.8762 (tp30) cc_final: 0.8271 (tp30) REVERT: B 232 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: C 80 GLU cc_start: 0.8211 (tp30) cc_final: 0.7921 (tp30) REVERT: C 104 ASP cc_start: 0.8955 (p0) cc_final: 0.8349 (p0) REVERT: C 160 LEU cc_start: 0.9395 (tp) cc_final: 0.9175 (tt) REVERT: C 216 MET cc_start: 0.8673 (mtm) cc_final: 0.7942 (mtp) REVERT: C 227 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8569 (ttt90) REVERT: D 31 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6177 (pm20) REVERT: D 46 THR cc_start: 0.6023 (m) cc_final: 0.5684 (t) REVERT: D 94 ARG cc_start: 0.8836 (ptt180) cc_final: 0.7905 (ptm160) REVERT: D 150 MET cc_start: 0.4363 (mtt) cc_final: 0.4048 (mmt) REVERT: E 19 MET cc_start: 0.8318 (mmp) cc_final: 0.8028 (mmm) REVERT: E 60 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8018 (mt-10) REVERT: E 66 MET cc_start: 0.9035 (mmm) cc_final: 0.8696 (mmm) REVERT: E 133 THR cc_start: 0.8423 (m) cc_final: 0.8045 (p) REVERT: E 145 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (ttm110) REVERT: F 44 LYS cc_start: 0.8993 (pttt) cc_final: 0.8581 (tmtt) REVERT: F 70 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8124 (tm-30) REVERT: F 77 MET cc_start: 0.7535 (ptp) cc_final: 0.6852 (ptp) REVERT: F 82 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6010 (p0) REVERT: F 110 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7373 (mm-40) REVERT: F 116 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8838 (mt) REVERT: F 148 ASN cc_start: 0.8733 (m110) cc_final: 0.8527 (m110) REVERT: F 160 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7734 (tt0) REVERT: F 179 ASN cc_start: 0.8980 (m-40) cc_final: 0.8628 (m110) REVERT: G 25 ARG cc_start: 0.9052 (mmt90) cc_final: 0.8774 (mmt90) REVERT: G 28 TYR cc_start: 0.8811 (m-10) cc_final: 0.8078 (m-10) REVERT: G 152 ASP cc_start: 0.8329 (t0) cc_final: 0.8118 (t0) REVERT: G 156 TYR cc_start: 0.8537 (m-80) cc_final: 0.7902 (m-80) REVERT: H 25 GLN cc_start: 0.8872 (mt0) cc_final: 0.8664 (mm-40) REVERT: H 41 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8352 (ptp-110) REVERT: H 87 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7801 (t80) REVERT: H 127 ASP cc_start: 0.8331 (t0) cc_final: 0.7911 (t0) REVERT: H 159 ASP cc_start: 0.9021 (t0) cc_final: 0.8623 (t70) REVERT: I 105 ASP cc_start: 0.8320 (m-30) cc_final: 0.8086 (m-30) REVERT: I 130 THR cc_start: 0.7581 (p) cc_final: 0.6691 (p) REVERT: I 134 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: I 165 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8644 (mt0) REVERT: J 64 ASP cc_start: 0.7732 (t0) cc_final: 0.7109 (p0) REVERT: J 65 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8207 (tm-30) REVERT: J 102 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9164 (tp) REVERT: J 103 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8304 (mm-30) REVERT: J 108 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.7763 (mmp-170) REVERT: J 143 ASN cc_start: 0.9059 (t0) cc_final: 0.8129 (t0) REVERT: J 150 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8508 (mtt180) REVERT: L 37 TYR cc_start: 0.8985 (p90) cc_final: 0.8779 (p90) REVERT: L 39 ASN cc_start: 0.8704 (t0) cc_final: 0.8197 (t0) REVERT: L 40 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8275 (mm) REVERT: L 49 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7996 (tp30) REVERT: N 49 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8523 (mm-40) REVERT: N 107 LYS cc_start: 0.8452 (tptt) cc_final: 0.8120 (tptt) REVERT: N 140 LYS cc_start: 0.9366 (tttt) cc_final: 0.8836 (tttp) REVERT: O 44 VAL cc_start: 0.9509 (t) cc_final: 0.9210 (p) REVERT: O 52 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9149 (p) REVERT: O 61 LYS cc_start: 0.8746 (mmpt) cc_final: 0.8421 (mmtt) REVERT: O 72 TYR cc_start: 0.8720 (t80) cc_final: 0.7918 (t80) REVERT: O 124 MET cc_start: 0.8083 (tpp) cc_final: 0.7689 (tpp) REVERT: O 135 ILE cc_start: 0.9152 (tt) cc_final: 0.8868 (pt) REVERT: P 40 ARG cc_start: 0.5358 (tpt170) cc_final: 0.2036 (ptp-170) REVERT: P 108 LYS cc_start: 0.4549 (mmtp) cc_final: 0.4228 (mmtt) REVERT: Q 41 MET cc_start: 0.0519 (tpp) cc_final: 0.0296 (tpt) REVERT: Q 43 GLU cc_start: 0.3206 (OUTLIER) cc_final: 0.1564 (mm-30) REVERT: Q 132 PHE cc_start: 0.8812 (p90) cc_final: 0.8585 (p90) REVERT: Q 145 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.5496 (m-80) REVERT: R 5 ARG cc_start: 0.8016 (mmt180) cc_final: 0.7762 (mmt90) REVERT: R 18 GLU cc_start: 0.8843 (tt0) cc_final: 0.7799 (tp30) REVERT: R 33 ARG cc_start: 0.8477 (mmt180) cc_final: 0.7778 (mpt180) REVERT: R 37 GLU cc_start: 0.8716 (tt0) cc_final: 0.8030 (mt-10) REVERT: R 130 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8511 (p) REVERT: S 10 GLN cc_start: 0.7713 (mt0) cc_final: 0.6384 (pp30) REVERT: S 117 ILE cc_start: 0.5929 (mt) cc_final: 0.5182 (tp) REVERT: T 35 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.7749 (p0) REVERT: T 36 THR cc_start: 0.5253 (OUTLIER) cc_final: 0.4163 (p) REVERT: T 83 GLN cc_start: 0.7768 (tp40) cc_final: 0.7186 (pt0) REVERT: T 91 HIS cc_start: 0.4563 (OUTLIER) cc_final: 0.4185 (m-70) REVERT: U 24 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7791 (mm) REVERT: U 62 ARG cc_start: 0.6932 (mtt180) cc_final: 0.6710 (ptt180) REVERT: U 67 LYS cc_start: 0.8513 (mttt) cc_final: 0.7948 (tttm) REVERT: U 75 LYS cc_start: 0.6579 (mttm) cc_final: 0.6293 (mmtp) REVERT: U 76 THR cc_start: 0.9328 (m) cc_final: 0.9105 (p) REVERT: U 78 ASP cc_start: 0.6429 (m-30) cc_final: 0.6185 (m-30) REVERT: U 82 MET cc_start: 0.7307 (tmm) cc_final: 0.6774 (tmm) REVERT: U 91 LEU cc_start: 0.8475 (mt) cc_final: 0.7949 (tp) REVERT: U 107 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.5831 (mp0) REVERT: V 34 MET cc_start: 0.8955 (tpp) cc_final: 0.8726 (ttm) REVERT: V 39 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8885 (p) REVERT: V 53 TYR cc_start: 0.8325 (m-10) cc_final: 0.8120 (m-10) REVERT: V 65 SER cc_start: 0.9329 (p) cc_final: 0.9115 (m) REVERT: V 70 LEU cc_start: 0.9239 (tp) cc_final: 0.9030 (tp) REVERT: V 72 LEU cc_start: 0.8942 (mt) cc_final: 0.8540 (mt) REVERT: V 76 ASP cc_start: 0.8771 (t0) cc_final: 0.8483 (t0) REVERT: W 56 HIS cc_start: 0.9101 (OUTLIER) cc_final: 0.8882 (m-70) REVERT: W 111 MET cc_start: 0.8801 (ptp) cc_final: 0.8597 (ptp) REVERT: X 26 GLN cc_start: 0.7288 (mt0) cc_final: 0.7050 (mt0) REVERT: X 32 LEU cc_start: 0.8956 (tp) cc_final: 0.8682 (tp) REVERT: X 90 CYS cc_start: 0.9120 (m) cc_final: 0.8547 (m) REVERT: X 100 VAL cc_start: 0.9412 (OUTLIER) cc_final: 0.9168 (m) REVERT: Y 6 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8674 (p) REVERT: Y 23 MET cc_start: 0.9087 (ptp) cc_final: 0.8620 (ptp) REVERT: Y 98 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8164 (mm-30) REVERT: Y 106 GLN cc_start: 0.8872 (mm110) cc_final: 0.8628 (mm-40) REVERT: Y 109 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8572 (mm-30) REVERT: Y 117 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8999 (m) REVERT: Z 68 ILE cc_start: 0.7261 (mt) cc_final: 0.6950 (mp) REVERT: a 26 CYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7552 (m) REVERT: a 77 CYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6858 (m) REVERT: b 20 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8680 (pttm) REVERT: b 82 LYS cc_start: 0.8187 (mttt) cc_final: 0.7812 (mttm) REVERT: c 67 ARG cc_start: 0.8622 (ttt180) cc_final: 0.7932 (ttp-170) REVERT: d 40 ARG cc_start: 0.5273 (OUTLIER) cc_final: 0.4829 (ptm160) REVERT: e 34 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.7116 (mpt-90) REVERT: g 90 TRP cc_start: 0.7109 (m100) cc_final: 0.5996 (m100) REVERT: g 150 TRP cc_start: 0.6621 (m-10) cc_final: 0.4739 (m-10) REVERT: g 217 MET cc_start: 0.6449 (mmm) cc_final: 0.5795 (mmm) REVERT: g 235 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7480 (mm) REVERT: g 246 TYR cc_start: 0.6393 (t80) cc_final: 0.5852 (t80) REVERT: g 271 LYS cc_start: 0.7392 (pttt) cc_final: 0.7001 (tptm) REVERT: h 9 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8693 (ttp80) REVERT: h 21 ARG cc_start: 0.8568 (ttt180) cc_final: 0.8119 (tmm-80) REVERT: r 168 GLU cc_start: 0.9120 (pt0) cc_final: 0.7819 (mm-30) REVERT: r 170 ARG cc_start: 0.8569 (ttm170) cc_final: 0.8133 (ttm110) REVERT: w 91 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (mmp) outliers start: 319 outliers final: 194 residues processed: 1011 average time/residue: 0.8126 time to fit residues: 1395.9818 Evaluate side-chains 977 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 742 time to evaluate : 4.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain L residue 18 GLN Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain Q residue 145 TYR Chi-restraints excluded: chain R residue 26 ASN Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 94 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 40 TYR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 139 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 35 ASP Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 56 HIS Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 52 ASP Chi-restraints excluded: chain a residue 53 ILE Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 8.9990 chunk 365 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 479 optimal weight: 2.9990 chunk 265 optimal weight: 9.9990 chunk 549 optimal weight: 0.9980 chunk 444 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 577 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 HIS K 44 HIS L 18 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN S 17 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN W 113 HIS ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS d 26 ASN d 28 HIS e 37 GLN ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 296 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 86006 Z= 0.260 Angle : 0.682 11.484 125306 Z= 0.345 Chirality : 0.040 0.354 15565 Planarity : 0.005 0.106 8764 Dihedral : 24.880 179.162 35725 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 7.51 % Allowed : 22.89 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 4859 helix: 0.47 (0.13), residues: 1625 sheet: -0.48 (0.16), residues: 936 loop : -0.82 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 25 HIS 0.006 0.001 HIS d 28 PHE 0.033 0.002 PHE D 17 TYR 0.019 0.002 TYR E 121 ARG 0.007 0.001 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 788 time to evaluate : 4.493 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: A 73 ASP cc_start: 0.8616 (m-30) cc_final: 0.8280 (m-30) REVERT: A 130 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8352 (p0) REVERT: A 131 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7127 (p90) REVERT: A 165 ASN cc_start: 0.9170 (p0) cc_final: 0.8622 (p0) REVERT: A 186 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8903 (tpp80) REVERT: A 189 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 195 TRP cc_start: 0.8902 (t60) cc_final: 0.8615 (t60) REVERT: A 200 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8499 (m-30) REVERT: B 76 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7783 (p0) REVERT: B 78 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7181 (mm-30) REVERT: B 83 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8443 (mtmt) REVERT: B 97 LEU cc_start: 0.9170 (mt) cc_final: 0.8769 (mt) REVERT: B 106 THR cc_start: 0.8898 (m) cc_final: 0.8453 (p) REVERT: B 168 MET cc_start: 0.7971 (mtm) cc_final: 0.7561 (mtt) REVERT: B 180 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7449 (p0) REVERT: B 198 GLU cc_start: 0.8756 (tp30) cc_final: 0.8287 (tp30) REVERT: B 232 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7138 (t-90) REVERT: C 80 GLU cc_start: 0.8376 (tp30) cc_final: 0.7804 (tp30) REVERT: C 104 ASP cc_start: 0.8904 (p0) cc_final: 0.8330 (p0) REVERT: C 120 GLN cc_start: 0.7493 (mt0) cc_final: 0.7135 (mt0) REVERT: C 123 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8065 (mtp180) REVERT: C 156 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9144 (tp) REVERT: C 160 LEU cc_start: 0.9406 (tp) cc_final: 0.8928 (tt) REVERT: C 216 MET cc_start: 0.8702 (mtm) cc_final: 0.7938 (mtp) REVERT: C 227 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8619 (ttt90) REVERT: D 14 ASP cc_start: 0.8500 (m-30) cc_final: 0.8089 (p0) REVERT: D 46 THR cc_start: 0.6167 (m) cc_final: 0.5859 (t) REVERT: D 94 ARG cc_start: 0.8831 (ptt180) cc_final: 0.7914 (ptm160) REVERT: D 145 GLN cc_start: 0.6056 (pp30) cc_final: 0.5721 (pp30) REVERT: D 154 ASP cc_start: 0.6928 (t0) cc_final: 0.6714 (t0) REVERT: D 189 MET cc_start: 0.8894 (ttt) cc_final: 0.8494 (tpp) REVERT: E 60 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8115 (mt-10) REVERT: E 133 THR cc_start: 0.8272 (m) cc_final: 0.7897 (p) REVERT: F 38 TYR cc_start: 0.8135 (m-80) cc_final: 0.7909 (m-80) REVERT: F 70 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8173 (tm-30) REVERT: F 77 MET cc_start: 0.7523 (ptp) cc_final: 0.6930 (ptp) REVERT: F 116 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8819 (mt) REVERT: F 160 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7733 (tt0) REVERT: G 25 ARG cc_start: 0.9133 (mmt90) cc_final: 0.8898 (mmt90) REVERT: G 28 TYR cc_start: 0.8772 (m-10) cc_final: 0.8022 (m-10) REVERT: G 58 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: H 25 GLN cc_start: 0.8881 (mt0) cc_final: 0.8622 (mm-40) REVERT: H 32 MET cc_start: 0.9063 (mmm) cc_final: 0.8572 (ptt) REVERT: H 41 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8343 (ptp-110) REVERT: H 87 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7982 (t80) REVERT: H 127 ASP cc_start: 0.8311 (t0) cc_final: 0.7882 (t0) REVERT: H 159 ASP cc_start: 0.9011 (t0) cc_final: 0.8735 (t0) REVERT: H 181 THR cc_start: 0.9240 (p) cc_final: 0.8952 (p) REVERT: I 23 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8750 (pttt) REVERT: I 130 THR cc_start: 0.7424 (p) cc_final: 0.6564 (p) REVERT: I 134 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: I 165 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8738 (mt0) REVERT: I 184 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8711 (mtt180) REVERT: J 41 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7375 (ttp-170) REVERT: J 64 ASP cc_start: 0.7751 (t0) cc_final: 0.6927 (p0) REVERT: J 65 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8051 (tm-30) REVERT: J 102 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9142 (tp) REVERT: J 103 GLU cc_start: 0.8682 (mm-30) cc_final: 0.7970 (mm-30) REVERT: J 108 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.7867 (mmp-170) REVERT: J 143 ASN cc_start: 0.9044 (t0) cc_final: 0.8192 (t0) REVERT: J 150 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8513 (mtt180) REVERT: K 14 LEU cc_start: 0.7436 (mp) cc_final: 0.6826 (tt) REVERT: L 37 TYR cc_start: 0.8998 (p90) cc_final: 0.8759 (p90) REVERT: L 39 ASN cc_start: 0.8631 (t0) cc_final: 0.8100 (t0) REVERT: L 40 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8243 (mm) REVERT: M 12 MET cc_start: 0.4257 (OUTLIER) cc_final: 0.3909 (ppp) REVERT: M 80 ASP cc_start: 0.6814 (m-30) cc_final: 0.5996 (p0) REVERT: N 49 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8573 (mm-40) REVERT: N 86 GLU cc_start: 0.8327 (pm20) cc_final: 0.7952 (pp20) REVERT: N 107 LYS cc_start: 0.8442 (tptt) cc_final: 0.8120 (tptt) REVERT: N 140 LYS cc_start: 0.9234 (tttt) cc_final: 0.8986 (tttp) REVERT: O 44 VAL cc_start: 0.9523 (t) cc_final: 0.9253 (p) REVERT: O 52 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9102 (p) REVERT: O 61 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8465 (mmtt) REVERT: O 63 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7186 (mmmt) REVERT: O 124 MET cc_start: 0.7989 (tpp) cc_final: 0.7761 (tpp) REVERT: O 135 ILE cc_start: 0.9198 (tt) cc_final: 0.8984 (pt) REVERT: P 40 ARG cc_start: 0.5522 (tpt170) cc_final: 0.1971 (ptp-170) REVERT: Q 43 GLU cc_start: 0.3345 (OUTLIER) cc_final: 0.1708 (mm-30) REVERT: Q 132 PHE cc_start: 0.8805 (p90) cc_final: 0.8426 (p90) REVERT: R 11 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7749 (ptmt) REVERT: R 18 GLU cc_start: 0.8863 (tt0) cc_final: 0.7816 (tp30) REVERT: R 33 ARG cc_start: 0.8471 (mmt180) cc_final: 0.7779 (mpt180) REVERT: R 37 GLU cc_start: 0.8733 (tt0) cc_final: 0.8097 (mt-10) REVERT: R 69 ILE cc_start: 0.8293 (pt) cc_final: 0.7723 (tt) REVERT: S 10 GLN cc_start: 0.7750 (mt0) cc_final: 0.6318 (pp30) REVERT: S 117 ILE cc_start: 0.5670 (mt) cc_final: 0.4970 (tp) REVERT: T 83 GLN cc_start: 0.7733 (tt0) cc_final: 0.7140 (pt0) REVERT: T 91 HIS cc_start: 0.4619 (OUTLIER) cc_final: 0.4209 (m-70) REVERT: U 24 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7767 (mm) REVERT: U 62 ARG cc_start: 0.6946 (mtt180) cc_final: 0.6738 (ptt180) REVERT: U 75 LYS cc_start: 0.6540 (mttm) cc_final: 0.6271 (mmtp) REVERT: U 76 THR cc_start: 0.9344 (m) cc_final: 0.9101 (p) REVERT: U 78 ASP cc_start: 0.6372 (m-30) cc_final: 0.6088 (m-30) REVERT: U 82 MET cc_start: 0.7142 (tmm) cc_final: 0.6781 (tmm) REVERT: U 91 LEU cc_start: 0.8454 (mt) cc_final: 0.7973 (tp) REVERT: U 107 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: V 53 TYR cc_start: 0.8360 (m-10) cc_final: 0.8132 (m-10) REVERT: V 72 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8492 (mt) REVERT: V 76 ASP cc_start: 0.8862 (t0) cc_final: 0.8500 (t0) REVERT: W 56 HIS cc_start: 0.9142 (OUTLIER) cc_final: 0.8876 (m-70) REVERT: X 32 LEU cc_start: 0.8926 (tp) cc_final: 0.8681 (tp) REVERT: X 90 CYS cc_start: 0.9089 (m) cc_final: 0.8558 (m) REVERT: X 100 VAL cc_start: 0.9420 (OUTLIER) cc_final: 0.9163 (m) REVERT: Y 6 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8653 (p) REVERT: Y 23 MET cc_start: 0.9065 (ptp) cc_final: 0.8639 (ptp) REVERT: Y 98 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8149 (mm-30) REVERT: Y 106 GLN cc_start: 0.8874 (mm110) cc_final: 0.8626 (mm-40) REVERT: Y 109 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8564 (mm-30) REVERT: Y 117 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9063 (m) REVERT: Z 68 ILE cc_start: 0.7249 (mt) cc_final: 0.6907 (mp) REVERT: a 26 CYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7379 (m) REVERT: a 77 CYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6710 (m) REVERT: b 8 LEU cc_start: 0.8572 (mt) cc_final: 0.8189 (mt) REVERT: b 20 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8713 (pttm) REVERT: b 82 LYS cc_start: 0.8227 (mttt) cc_final: 0.7971 (mttm) REVERT: c 42 ILE cc_start: 0.8492 (mt) cc_final: 0.8270 (tt) REVERT: c 67 ARG cc_start: 0.8645 (ttt180) cc_final: 0.7965 (ttp-170) REVERT: d 40 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.4794 (ptm160) REVERT: e 34 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.7383 (mpt-90) REVERT: g 90 TRP cc_start: 0.7104 (m100) cc_final: 0.6022 (m100) REVERT: g 143 GLN cc_start: 0.8040 (pm20) cc_final: 0.6619 (tp40) REVERT: g 150 TRP cc_start: 0.6469 (m-10) cc_final: 0.4925 (m-10) REVERT: g 155 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5713 (mpt180) REVERT: g 217 MET cc_start: 0.6596 (mmm) cc_final: 0.6143 (mmm) REVERT: g 235 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7657 (mm) REVERT: g 246 TYR cc_start: 0.6384 (t80) cc_final: 0.5835 (t80) REVERT: g 271 LYS cc_start: 0.7676 (pttt) cc_final: 0.7168 (tptm) REVERT: h 9 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8691 (ttp80) REVERT: h 21 ARG cc_start: 0.8561 (ttt180) cc_final: 0.7986 (tmm-80) REVERT: r 168 GLU cc_start: 0.9117 (pt0) cc_final: 0.7820 (mm-30) REVERT: r 170 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8116 (ttm110) REVERT: w 91 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7817 (mmp) outliers start: 319 outliers final: 199 residues processed: 1013 average time/residue: 0.7768 time to fit residues: 1336.6094 Evaluate side-chains 982 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 741 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 232 ASN Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 ARG Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 40 TYR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 139 THR Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 27 ILE Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 56 HIS Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain X residue 135 LYS Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 234 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 294 ASP Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 2.9990 chunk 579 optimal weight: 0.8980 chunk 127 optimal weight: 30.0000 chunk 377 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 644 optimal weight: 5.9990 chunk 534 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 338 optimal weight: 0.0060 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 193 HIS ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN H 112 ASN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN S 17 ASN ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 ASN g 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 86006 Z= 0.181 Angle : 0.625 9.487 125306 Z= 0.317 Chirality : 0.037 0.318 15565 Planarity : 0.004 0.104 8764 Dihedral : 24.730 179.359 35715 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 6.00 % Allowed : 24.56 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 4859 helix: 0.84 (0.13), residues: 1619 sheet: -0.40 (0.16), residues: 929 loop : -0.68 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 69 HIS 0.012 0.001 HIS d 28 PHE 0.021 0.001 PHE C 269 TYR 0.022 0.001 TYR f 140 ARG 0.009 0.000 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 796 time to evaluate : 4.496 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: A 73 ASP cc_start: 0.8607 (m-30) cc_final: 0.8239 (m-30) REVERT: A 130 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8471 (p0) REVERT: A 131 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7126 (p90) REVERT: A 165 ASN cc_start: 0.9115 (p0) cc_final: 0.8571 (p0) REVERT: A 186 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8836 (tpp80) REVERT: A 209 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: A 213 GLU cc_start: 0.7681 (mm-30) cc_final: 0.6918 (mm-30) REVERT: B 76 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7692 (p0) REVERT: B 78 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 83 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8358 (mtmm) REVERT: B 97 LEU cc_start: 0.9166 (mt) cc_final: 0.8775 (mt) REVERT: B 106 THR cc_start: 0.8815 (m) cc_final: 0.8604 (p) REVERT: B 110 MET cc_start: 0.8779 (tpp) cc_final: 0.8494 (tpp) REVERT: B 168 MET cc_start: 0.7959 (mtm) cc_final: 0.7676 (mtm) REVERT: B 180 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7470 (p0) REVERT: B 198 GLU cc_start: 0.8732 (tp30) cc_final: 0.8304 (tp30) REVERT: B 232 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7064 (t-90) REVERT: C 80 GLU cc_start: 0.8360 (tp30) cc_final: 0.7847 (tp30) REVERT: C 104 ASP cc_start: 0.8859 (p0) cc_final: 0.8285 (p0) REVERT: C 120 GLN cc_start: 0.7364 (mt0) cc_final: 0.6924 (mt0) REVERT: C 160 LEU cc_start: 0.9384 (tp) cc_final: 0.8942 (tt) REVERT: C 216 MET cc_start: 0.8684 (mtm) cc_final: 0.7881 (mtp) REVERT: C 227 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8657 (ttt90) REVERT: D 14 ASP cc_start: 0.8449 (m-30) cc_final: 0.8008 (p0) REVERT: D 46 THR cc_start: 0.6472 (m) cc_final: 0.5997 (t) REVERT: D 94 ARG cc_start: 0.8764 (ptt180) cc_final: 0.7810 (ptm160) REVERT: D 145 GLN cc_start: 0.6322 (pp30) cc_final: 0.6069 (pp30) REVERT: D 189 MET cc_start: 0.8813 (ttt) cc_final: 0.8441 (tpp) REVERT: E 19 MET cc_start: 0.8478 (mtm) cc_final: 0.8243 (ttm) REVERT: E 41 CYS cc_start: 0.8563 (p) cc_final: 0.8305 (p) REVERT: E 60 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8060 (mt-10) REVERT: E 133 THR cc_start: 0.8021 (m) cc_final: 0.7620 (p) REVERT: E 158 ASP cc_start: 0.8950 (t0) cc_final: 0.8731 (t0) REVERT: E 184 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.8928 (t) REVERT: F 77 MET cc_start: 0.7608 (ptp) cc_final: 0.6972 (ptp) REVERT: F 116 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8798 (mp) REVERT: F 160 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7583 (tt0) REVERT: F 179 ASN cc_start: 0.8959 (m-40) cc_final: 0.8613 (m110) REVERT: G 28 TYR cc_start: 0.8692 (m-10) cc_final: 0.7946 (m-10) REVERT: G 56 ASN cc_start: 0.8003 (m110) cc_final: 0.7694 (m-40) REVERT: G 57 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.7089 (p0) REVERT: G 152 ASP cc_start: 0.8376 (t0) cc_final: 0.7203 (p0) REVERT: H 25 GLN cc_start: 0.8892 (mt0) cc_final: 0.8639 (mm-40) REVERT: H 41 ARG cc_start: 0.8595 (ttm110) cc_final: 0.8355 (ptp-110) REVERT: H 87 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7938 (t80) REVERT: H 127 ASP cc_start: 0.8300 (t0) cc_final: 0.7865 (t0) REVERT: H 159 ASP cc_start: 0.8977 (t0) cc_final: 0.8678 (t0) REVERT: H 181 THR cc_start: 0.9188 (p) cc_final: 0.8891 (p) REVERT: I 23 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8537 (pttt) REVERT: I 130 THR cc_start: 0.7909 (p) cc_final: 0.7170 (p) REVERT: I 134 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: I 184 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8538 (mtt-85) REVERT: I 195 LEU cc_start: 0.9206 (tp) cc_final: 0.8995 (tp) REVERT: J 21 GLU cc_start: 0.7851 (pm20) cc_final: 0.7321 (pm20) REVERT: J 41 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7246 (ttp-170) REVERT: J 103 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8028 (mm-30) REVERT: J 108 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8008 (mmp-170) REVERT: J 143 ASN cc_start: 0.8982 (t0) cc_final: 0.8267 (t0) REVERT: J 150 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8521 (mtt180) REVERT: K 14 LEU cc_start: 0.7394 (mp) cc_final: 0.6781 (tt) REVERT: L 39 ASN cc_start: 0.8484 (t0) cc_final: 0.7730 (p0) REVERT: M 12 MET cc_start: 0.4002 (tmm) cc_final: 0.3612 (ppp) REVERT: M 60 MET cc_start: 0.7004 (ttt) cc_final: 0.5311 (pmm) REVERT: M 80 ASP cc_start: 0.6901 (m-30) cc_final: 0.6128 (p0) REVERT: N 49 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8472 (mm-40) REVERT: N 107 LYS cc_start: 0.8397 (tptt) cc_final: 0.8066 (tptt) REVERT: N 140 LYS cc_start: 0.9258 (tttt) cc_final: 0.8734 (tttp) REVERT: N 142 GLU cc_start: 0.8030 (pm20) cc_final: 0.7795 (pm20) REVERT: O 44 VAL cc_start: 0.9545 (t) cc_final: 0.9231 (p) REVERT: O 52 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9077 (p) REVERT: O 61 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8344 (mmtt) REVERT: O 63 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7188 (mmmt) REVERT: O 72 TYR cc_start: 0.8577 (t80) cc_final: 0.7165 (t80) REVERT: O 124 MET cc_start: 0.7971 (tpp) cc_final: 0.7587 (tpp) REVERT: P 40 ARG cc_start: 0.5634 (tpt170) cc_final: 0.1954 (ptp-170) REVERT: P 72 LYS cc_start: 0.5436 (tptt) cc_final: 0.4984 (tptt) REVERT: P 83 MET cc_start: 0.3535 (tpt) cc_final: 0.2912 (mtp) REVERT: P 84 ILE cc_start: 0.4338 (OUTLIER) cc_final: 0.3200 (tp) REVERT: Q 43 GLU cc_start: 0.3187 (OUTLIER) cc_final: 0.2267 (mp0) REVERT: Q 132 PHE cc_start: 0.8702 (p90) cc_final: 0.8148 (p90) REVERT: Q 140 ARG cc_start: 0.7751 (mmm-85) cc_final: 0.7064 (mmm-85) REVERT: R 33 ARG cc_start: 0.8280 (mmt180) cc_final: 0.7663 (mpt180) REVERT: R 37 GLU cc_start: 0.8720 (tt0) cc_final: 0.8070 (mt-10) REVERT: R 130 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8419 (p) REVERT: S 50 ILE cc_start: 0.6371 (OUTLIER) cc_final: 0.5823 (mp) REVERT: S 117 ILE cc_start: 0.5204 (mt) cc_final: 0.4530 (tp) REVERT: T 13 GLU cc_start: 0.7211 (mp0) cc_final: 0.6801 (mp0) REVERT: T 83 GLN cc_start: 0.7675 (tt0) cc_final: 0.7070 (pt0) REVERT: T 91 HIS cc_start: 0.4840 (OUTLIER) cc_final: 0.4618 (m-70) REVERT: T 126 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8126 (tm-30) REVERT: U 24 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7730 (mm) REVERT: U 75 LYS cc_start: 0.6404 (mttm) cc_final: 0.6168 (mmtp) REVERT: U 76 THR cc_start: 0.9354 (m) cc_final: 0.9076 (p) REVERT: U 78 ASP cc_start: 0.6309 (m-30) cc_final: 0.6032 (m-30) REVERT: U 82 MET cc_start: 0.7072 (tmm) cc_final: 0.6683 (tmm) REVERT: U 91 LEU cc_start: 0.8448 (mt) cc_final: 0.7942 (tp) REVERT: U 107 GLU cc_start: 0.7678 (tp30) cc_final: 0.5875 (mp0) REVERT: V 53 TYR cc_start: 0.8274 (m-10) cc_final: 0.8052 (m-10) REVERT: V 72 LEU cc_start: 0.8920 (mt) cc_final: 0.8529 (mt) REVERT: V 76 ASP cc_start: 0.8860 (t0) cc_final: 0.8508 (t0) REVERT: X 32 LEU cc_start: 0.8948 (tp) cc_final: 0.8719 (tp) REVERT: X 90 CYS cc_start: 0.8997 (m) cc_final: 0.8501 (m) REVERT: X 100 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.9123 (m) REVERT: Y 23 MET cc_start: 0.9009 (ptp) cc_final: 0.8609 (ptp) REVERT: Y 98 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8062 (mm-30) REVERT: Y 106 GLN cc_start: 0.8952 (mm110) cc_final: 0.8742 (mm-40) REVERT: Y 117 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9036 (m) REVERT: Z 68 ILE cc_start: 0.7264 (mt) cc_final: 0.6971 (mp) REVERT: a 26 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7280 (m) REVERT: a 77 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6801 (m) REVERT: b 8 LEU cc_start: 0.8474 (mt) cc_final: 0.8031 (mt) REVERT: c 67 ARG cc_start: 0.8632 (ttt180) cc_final: 0.7962 (ttp-170) REVERT: d 40 ARG cc_start: 0.4985 (OUTLIER) cc_final: 0.4052 (ptt180) REVERT: e 34 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.7608 (mpt-90) REVERT: g 90 TRP cc_start: 0.7224 (m100) cc_final: 0.5812 (m100) REVERT: g 143 GLN cc_start: 0.8166 (pm20) cc_final: 0.6940 (tp40) REVERT: g 150 TRP cc_start: 0.6507 (m-10) cc_final: 0.5115 (m-10) REVERT: g 155 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.5899 (mpt180) REVERT: g 196 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6685 (m-40) REVERT: g 217 MET cc_start: 0.6678 (mmm) cc_final: 0.6240 (mmm) REVERT: g 246 TYR cc_start: 0.6452 (t80) cc_final: 0.5915 (t80) REVERT: g 271 LYS cc_start: 0.7784 (pttt) cc_final: 0.7208 (tptm) REVERT: h 6 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7449 (mmt90) REVERT: h 9 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8670 (ttp80) REVERT: h 21 ARG cc_start: 0.8693 (ttt180) cc_final: 0.8390 (tmm-80) REVERT: r 167 LYS cc_start: 0.8905 (tptp) cc_final: 0.8419 (tptp) REVERT: r 168 GLU cc_start: 0.9082 (pt0) cc_final: 0.7725 (mm-30) REVERT: r 170 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8137 (ttm110) REVERT: w 91 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7811 (mmp) outliers start: 255 outliers final: 165 residues processed: 968 average time/residue: 0.7941 time to fit residues: 1299.3478 Evaluate side-chains 937 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 736 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 ARG Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 127 ASN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain S residue 21 ASP Chi-restraints excluded: chain S residue 40 TYR Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 74 MET Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 60 ASP Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain g residue 196 ASN Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 294 ASP Chi-restraints excluded: chain h residue 6 ARG Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 chunk 367 optimal weight: 9.9990 chunk 470 optimal weight: 9.9990 chunk 364 optimal weight: 5.9990 chunk 542 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 641 optimal weight: 30.0000 chunk 401 optimal weight: 8.9990 chunk 391 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN F 82 ASN ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN K 44 HIS N 101 HIS N 105 ASN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN ** S 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS d 28 HIS ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 HIS ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 305 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 86006 Z= 0.337 Angle : 0.719 10.744 125306 Z= 0.361 Chirality : 0.041 0.355 15565 Planarity : 0.005 0.100 8764 Dihedral : 24.758 179.454 35691 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.23 % Favored : 94.63 % Rotamer: Outliers : 6.80 % Allowed : 25.03 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 4859 helix: 0.67 (0.13), residues: 1627 sheet: -0.52 (0.16), residues: 934 loop : -0.74 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 69 HIS 0.009 0.001 HIS K 66 PHE 0.029 0.002 PHE C 269 TYR 0.037 0.002 TYR g 194 ARG 0.020 0.001 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 741 time to evaluate : 4.607 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: A 73 ASP cc_start: 0.8552 (m-30) cc_final: 0.8204 (m-30) REVERT: A 130 ASP cc_start: 0.9260 (OUTLIER) cc_final: 0.8482 (p0) REVERT: A 131 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.7234 (p90) REVERT: A 186 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8835 (tpp80) REVERT: A 209 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 213 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6966 (mm-30) REVERT: B 76 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7807 (p0) REVERT: B 78 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 83 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8610 (mtmm) REVERT: B 97 LEU cc_start: 0.9139 (mt) cc_final: 0.8773 (mt) REVERT: B 106 THR cc_start: 0.8906 (m) cc_final: 0.8545 (p) REVERT: B 110 MET cc_start: 0.8677 (tpp) cc_final: 0.8402 (tpp) REVERT: B 168 MET cc_start: 0.8075 (mtm) cc_final: 0.7752 (mtm) REVERT: B 198 GLU cc_start: 0.8745 (tp30) cc_final: 0.8269 (tp30) REVERT: C 80 GLU cc_start: 0.8401 (tp30) cc_final: 0.7862 (tp30) REVERT: C 104 ASP cc_start: 0.8890 (p0) cc_final: 0.8327 (p0) REVERT: C 120 GLN cc_start: 0.7618 (mt0) cc_final: 0.7161 (mt0) REVERT: C 160 LEU cc_start: 0.9388 (tp) cc_final: 0.8961 (tt) REVERT: C 216 MET cc_start: 0.8784 (mtm) cc_final: 0.8051 (mtp) REVERT: C 227 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8555 (ttt90) REVERT: D 46 THR cc_start: 0.6538 (m) cc_final: 0.6068 (t) REVERT: D 94 ARG cc_start: 0.8741 (ptt180) cc_final: 0.7778 (ptm160) REVERT: D 145 GLN cc_start: 0.6405 (pp30) cc_final: 0.6146 (pp30) REVERT: E 60 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8043 (mt-10) REVERT: E 133 THR cc_start: 0.8183 (m) cc_final: 0.7812 (p) REVERT: E 232 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8635 (m-40) REVERT: F 73 THR cc_start: 0.8959 (p) cc_final: 0.8727 (t) REVERT: F 160 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7689 (pt0) REVERT: G 28 TYR cc_start: 0.8780 (m-10) cc_final: 0.8076 (m-10) REVERT: G 58 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8704 (mttp) REVERT: H 25 GLN cc_start: 0.8928 (mt0) cc_final: 0.8626 (mm-40) REVERT: H 32 MET cc_start: 0.9051 (mmm) cc_final: 0.8598 (ptt) REVERT: H 41 ARG cc_start: 0.8409 (ttm110) cc_final: 0.8169 (ptp-110) REVERT: H 87 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.7963 (t80) REVERT: H 127 ASP cc_start: 0.8358 (t0) cc_final: 0.7934 (t0) REVERT: H 159 ASP cc_start: 0.9021 (t0) cc_final: 0.8808 (t70) REVERT: H 181 THR cc_start: 0.9234 (p) cc_final: 0.8956 (p) REVERT: I 23 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8454 (ptpp) REVERT: I 130 THR cc_start: 0.7778 (p) cc_final: 0.6987 (p) REVERT: I 134 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: I 184 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8564 (mtt-85) REVERT: J 21 GLU cc_start: 0.8046 (pm20) cc_final: 0.7307 (pm20) REVERT: J 41 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7388 (ttp-170) REVERT: J 66 LYS cc_start: 0.9135 (pttm) cc_final: 0.8880 (mmtt) REVERT: J 103 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8174 (mm-30) REVERT: J 108 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8033 (mmp-170) REVERT: J 143 ASN cc_start: 0.9078 (t0) cc_final: 0.8337 (t0) REVERT: J 150 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8509 (mtt180) REVERT: K 14 LEU cc_start: 0.7436 (mp) cc_final: 0.6821 (tt) REVERT: K 47 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6571 (tttt) REVERT: L 39 ASN cc_start: 0.8507 (t0) cc_final: 0.8184 (t0) REVERT: M 12 MET cc_start: 0.4057 (tmm) cc_final: 0.3647 (ppp) REVERT: M 80 ASP cc_start: 0.6761 (m-30) cc_final: 0.5959 (p0) REVERT: N 49 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8597 (mm-40) REVERT: N 86 GLU cc_start: 0.8333 (pm20) cc_final: 0.7988 (pp20) REVERT: N 107 LYS cc_start: 0.8514 (tptt) cc_final: 0.8155 (tptt) REVERT: N 140 LYS cc_start: 0.9282 (tttt) cc_final: 0.8839 (tttp) REVERT: O 44 VAL cc_start: 0.9519 (t) cc_final: 0.9234 (p) REVERT: O 52 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.9116 (p) REVERT: O 63 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7230 (mmmt) REVERT: O 124 MET cc_start: 0.8337 (tpp) cc_final: 0.7960 (tpp) REVERT: P 40 ARG cc_start: 0.5559 (tpt170) cc_final: 0.1682 (ptt-90) REVERT: P 72 LYS cc_start: 0.5282 (tptt) cc_final: 0.5017 (tptt) REVERT: Q 43 GLU cc_start: 0.3804 (OUTLIER) cc_final: 0.2924 (mp0) REVERT: Q 132 PHE cc_start: 0.8615 (p90) cc_final: 0.8328 (p90) REVERT: R 11 LYS cc_start: 0.7917 (pttt) cc_final: 0.7686 (ptmt) REVERT: R 33 ARG cc_start: 0.8400 (mmt180) cc_final: 0.7696 (mpt180) REVERT: R 37 GLU cc_start: 0.8696 (tt0) cc_final: 0.8063 (mt-10) REVERT: R 130 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8565 (p) REVERT: S 117 ILE cc_start: 0.5273 (mt) cc_final: 0.4600 (tp) REVERT: T 83 GLN cc_start: 0.7691 (tt0) cc_final: 0.7074 (pt0) REVERT: T 91 HIS cc_start: 0.4917 (OUTLIER) cc_final: 0.4604 (m-70) REVERT: T 126 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8112 (tm-30) REVERT: U 24 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7839 (mm) REVERT: U 62 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6771 (ptt180) REVERT: U 75 LYS cc_start: 0.6455 (mttm) cc_final: 0.6230 (mmtp) REVERT: U 76 THR cc_start: 0.9299 (m) cc_final: 0.9033 (p) REVERT: U 78 ASP cc_start: 0.6312 (m-30) cc_final: 0.6056 (m-30) REVERT: U 82 MET cc_start: 0.7237 (tmm) cc_final: 0.6922 (tmm) REVERT: U 91 LEU cc_start: 0.8478 (mt) cc_final: 0.8003 (tp) REVERT: U 107 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.5754 (mp0) REVERT: V 72 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8451 (mt) REVERT: V 76 ASP cc_start: 0.8888 (t0) cc_final: 0.8532 (t0) REVERT: W 25 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8611 (m) REVERT: W 115 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8521 (mm-30) REVERT: X 32 LEU cc_start: 0.9021 (tp) cc_final: 0.8801 (tp) REVERT: X 53 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: X 90 CYS cc_start: 0.9082 (m) cc_final: 0.8591 (m) REVERT: X 100 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9162 (m) REVERT: Y 6 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8678 (p) REVERT: Y 23 MET cc_start: 0.9068 (ptp) cc_final: 0.8699 (ptp) REVERT: Y 117 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9062 (m) REVERT: Z 68 ILE cc_start: 0.7431 (mt) cc_final: 0.7075 (mp) REVERT: a 26 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7419 (m) REVERT: a 73 TYR cc_start: 0.9278 (OUTLIER) cc_final: 0.8409 (m-10) REVERT: a 77 CYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6638 (m) REVERT: b 8 LEU cc_start: 0.8459 (mt) cc_final: 0.8069 (mt) REVERT: c 67 ARG cc_start: 0.8675 (ttt180) cc_final: 0.7972 (ttp-170) REVERT: d 40 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.4626 (ptm160) REVERT: e 34 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.7289 (mpt-90) REVERT: g 90 TRP cc_start: 0.7077 (m100) cc_final: 0.5852 (m100) REVERT: g 143 GLN cc_start: 0.8031 (pm20) cc_final: 0.6930 (tp40) REVERT: g 150 TRP cc_start: 0.6780 (m-10) cc_final: 0.5558 (m-10) REVERT: g 155 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5826 (mpt180) REVERT: g 217 MET cc_start: 0.6355 (mmm) cc_final: 0.5947 (mmm) REVERT: g 246 TYR cc_start: 0.6260 (t80) cc_final: 0.5791 (t80) REVERT: g 271 LYS cc_start: 0.7925 (pttt) cc_final: 0.7341 (tptm) REVERT: h 6 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7601 (mmt90) REVERT: h 21 ARG cc_start: 0.8637 (ttt180) cc_final: 0.8301 (tmm-80) REVERT: r 167 LYS cc_start: 0.8803 (tptp) cc_final: 0.8450 (tptp) REVERT: r 168 GLU cc_start: 0.9127 (pt0) cc_final: 0.7867 (mm-30) REVERT: r 170 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8022 (ttm110) REVERT: w 91 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7817 (mmp) outliers start: 289 outliers final: 217 residues processed: 935 average time/residue: 0.7932 time to fit residues: 1255.8027 Evaluate side-chains 964 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 711 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 232 ASN Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 ARG Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 96 LYS Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 105 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 76 GLU Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain S residue 40 TYR Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain U residue 116 ILE Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 30 CYS Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 112 ASP Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 53 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 73 TYR Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 86 THR Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 294 ASP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain h residue 6 ARG Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 89 ASP Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 383 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 124 optimal weight: 50.0000 chunk 408 optimal weight: 0.9980 chunk 437 optimal weight: 9.9990 chunk 317 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 504 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 GLN S 101 ASN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS d 28 HIS e 56 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 86006 Z= 0.283 Angle : 0.686 15.140 125306 Z= 0.346 Chirality : 0.040 0.362 15565 Planarity : 0.005 0.098 8764 Dihedral : 24.768 179.724 35691 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.88 % Favored : 94.98 % Rotamer: Outliers : 6.17 % Allowed : 25.81 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4859 helix: 0.74 (0.13), residues: 1625 sheet: -0.62 (0.16), residues: 924 loop : -0.74 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 69 HIS 0.007 0.001 HIS K 66 PHE 0.028 0.002 PHE C 269 TYR 0.021 0.002 TYR E 103 ARG 0.011 0.001 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 741 time to evaluate : 4.607 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: A 73 ASP cc_start: 0.8572 (m-30) cc_final: 0.8213 (m-30) REVERT: A 130 ASP cc_start: 0.9274 (OUTLIER) cc_final: 0.8719 (p0) REVERT: A 131 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7211 (p90) REVERT: A 209 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: A 213 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7087 (tp30) REVERT: B 76 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7846 (p0) REVERT: B 78 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7326 (mm-30) REVERT: B 83 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8616 (mtmm) REVERT: B 97 LEU cc_start: 0.9106 (mt) cc_final: 0.8698 (mt) REVERT: B 106 THR cc_start: 0.8722 (m) cc_final: 0.8335 (p) REVERT: B 168 MET cc_start: 0.8022 (mtm) cc_final: 0.7727 (mtm) REVERT: B 180 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 198 GLU cc_start: 0.8765 (tp30) cc_final: 0.8289 (tp30) REVERT: B 232 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7045 (t-90) REVERT: C 80 GLU cc_start: 0.8381 (tp30) cc_final: 0.7854 (tp30) REVERT: C 104 ASP cc_start: 0.8894 (p0) cc_final: 0.8321 (p0) REVERT: C 120 GLN cc_start: 0.7568 (mt0) cc_final: 0.7056 (mt0) REVERT: C 123 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8506 (mtp85) REVERT: C 160 LEU cc_start: 0.9362 (tp) cc_final: 0.8967 (tt) REVERT: C 216 MET cc_start: 0.8712 (mtm) cc_final: 0.7928 (mtp) REVERT: C 227 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8583 (ttt90) REVERT: D 14 ASP cc_start: 0.8453 (m-30) cc_final: 0.7919 (p0) REVERT: D 46 THR cc_start: 0.6524 (m) cc_final: 0.6047 (t) REVERT: D 94 ARG cc_start: 0.8744 (ptt180) cc_final: 0.7786 (ptm160) REVERT: D 145 GLN cc_start: 0.6492 (pp30) cc_final: 0.6215 (pp30) REVERT: D 154 ASP cc_start: 0.7964 (p0) cc_final: 0.7654 (p0) REVERT: D 189 MET cc_start: 0.8866 (ttt) cc_final: 0.8311 (tpp) REVERT: E 11 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8867 (tpp-160) REVERT: E 19 MET cc_start: 0.8365 (mtt) cc_final: 0.8077 (mmm) REVERT: E 60 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8030 (mt-10) REVERT: E 133 THR cc_start: 0.8246 (m) cc_final: 0.7887 (p) REVERT: F 79 HIS cc_start: 0.6425 (OUTLIER) cc_final: 0.6169 (m-70) REVERT: F 160 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7703 (tt0) REVERT: G 25 ARG cc_start: 0.8793 (mmt90) cc_final: 0.8562 (mmt90) REVERT: G 28 TYR cc_start: 0.8665 (m-10) cc_final: 0.7918 (m-10) REVERT: G 152 ASP cc_start: 0.8423 (t0) cc_final: 0.7288 (p0) REVERT: H 25 GLN cc_start: 0.8942 (mt0) cc_final: 0.8616 (mm-40) REVERT: H 32 MET cc_start: 0.9055 (mmm) cc_final: 0.8628 (ptt) REVERT: H 41 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8261 (ptp-110) REVERT: H 87 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7892 (t80) REVERT: H 112 ASN cc_start: 0.8001 (t0) cc_final: 0.7265 (m-40) REVERT: H 127 ASP cc_start: 0.8337 (t0) cc_final: 0.7902 (t0) REVERT: H 159 ASP cc_start: 0.9034 (t0) cc_final: 0.8825 (t70) REVERT: H 181 THR cc_start: 0.9246 (p) cc_final: 0.9013 (p) REVERT: I 130 THR cc_start: 0.7995 (p) cc_final: 0.7181 (p) REVERT: I 134 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: J 21 GLU cc_start: 0.8086 (pm20) cc_final: 0.7386 (pm20) REVERT: J 41 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8381 (ttm110) REVERT: J 66 LYS cc_start: 0.9114 (pttm) cc_final: 0.8735 (tppt) REVERT: J 103 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8172 (mm-30) REVERT: J 108 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8027 (mmp-170) REVERT: J 143 ASN cc_start: 0.9045 (t0) cc_final: 0.8402 (t0) REVERT: J 150 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8536 (mtt180) REVERT: K 14 LEU cc_start: 0.7533 (mp) cc_final: 0.6876 (tt) REVERT: K 46 MET cc_start: 0.6932 (ppp) cc_final: 0.6630 (ppp) REVERT: K 47 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7007 (tttt) REVERT: K 64 TRP cc_start: 0.6244 (m-10) cc_final: 0.5922 (m-10) REVERT: L 39 ASN cc_start: 0.8399 (t0) cc_final: 0.7887 (p0) REVERT: L 49 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7795 (tp30) REVERT: M 12 MET cc_start: 0.4179 (OUTLIER) cc_final: 0.3744 (ppp) REVERT: M 80 ASP cc_start: 0.6782 (m-30) cc_final: 0.6036 (p0) REVERT: N 49 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8516 (mm-40) REVERT: N 107 LYS cc_start: 0.8461 (tptt) cc_final: 0.8133 (tptt) REVERT: N 140 LYS cc_start: 0.9165 (tttt) cc_final: 0.8897 (tttp) REVERT: O 44 VAL cc_start: 0.9479 (t) cc_final: 0.9212 (p) REVERT: O 52 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9042 (p) REVERT: O 63 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7249 (mmmt) REVERT: P 40 ARG cc_start: 0.5361 (tpt170) cc_final: 0.1517 (ptp90) REVERT: P 72 LYS cc_start: 0.5383 (tptt) cc_final: 0.5125 (tptt) REVERT: P 84 ILE cc_start: 0.4297 (OUTLIER) cc_final: 0.3413 (tp) REVERT: Q 43 GLU cc_start: 0.3479 (OUTLIER) cc_final: 0.2644 (mp0) REVERT: Q 132 PHE cc_start: 0.8564 (p90) cc_final: 0.7960 (p90) REVERT: Q 140 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.6661 (mmm-85) REVERT: R 33 ARG cc_start: 0.8394 (mmt180) cc_final: 0.7725 (mmt-90) REVERT: R 37 GLU cc_start: 0.8656 (tt0) cc_final: 0.8008 (mt-10) REVERT: R 82 ASP cc_start: 0.7982 (t70) cc_final: 0.7779 (t0) REVERT: R 92 ASP cc_start: 0.8235 (t0) cc_final: 0.8009 (t0) REVERT: R 130 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8546 (p) REVERT: S 117 ILE cc_start: 0.5226 (mt) cc_final: 0.4584 (tp) REVERT: T 83 GLN cc_start: 0.8030 (tt0) cc_final: 0.7243 (pt0) REVERT: T 91 HIS cc_start: 0.4924 (OUTLIER) cc_final: 0.4363 (m-70) REVERT: T 126 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8122 (tm-30) REVERT: U 24 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7792 (mm) REVERT: U 62 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6630 (mtm-85) REVERT: U 75 LYS cc_start: 0.6472 (mttm) cc_final: 0.6229 (mmtp) REVERT: U 76 THR cc_start: 0.9286 (m) cc_final: 0.9017 (p) REVERT: U 78 ASP cc_start: 0.6228 (m-30) cc_final: 0.5985 (m-30) REVERT: U 82 MET cc_start: 0.7252 (tmm) cc_final: 0.6853 (tmm) REVERT: U 91 LEU cc_start: 0.8486 (mt) cc_final: 0.8006 (tp) REVERT: U 107 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: V 36 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9279 (p) REVERT: V 72 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8546 (mt) REVERT: W 111 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8527 (ptt) REVERT: X 32 LEU cc_start: 0.9002 (tp) cc_final: 0.8789 (tp) REVERT: X 53 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: X 90 CYS cc_start: 0.8983 (m) cc_final: 0.8512 (m) REVERT: X 100 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9122 (m) REVERT: Y 6 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8542 (p) REVERT: Y 23 MET cc_start: 0.9047 (ptp) cc_final: 0.8696 (ptp) REVERT: Y 98 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8101 (mm-30) REVERT: Z 57 LYS cc_start: 0.8564 (tppt) cc_final: 0.8291 (ttpp) REVERT: Z 65 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: Z 68 ILE cc_start: 0.7417 (mt) cc_final: 0.7073 (mp) REVERT: Z 85 ARG cc_start: 0.7530 (ttm-80) cc_final: 0.7089 (mtm-85) REVERT: Z 102 LYS cc_start: 0.7031 (tttt) cc_final: 0.6781 (tttt) REVERT: a 22 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8446 (mmt90) REVERT: a 26 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7344 (m) REVERT: a 40 VAL cc_start: 0.9638 (t) cc_final: 0.9386 (p) REVERT: a 73 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8383 (m-10) REVERT: a 77 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6556 (m) REVERT: c 67 ARG cc_start: 0.8661 (ttt180) cc_final: 0.8052 (ttp-170) REVERT: d 40 ARG cc_start: 0.4828 (OUTLIER) cc_final: 0.4391 (ptm160) REVERT: e 34 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.7364 (mpt-90) REVERT: f 93 HIS cc_start: 0.3688 (t70) cc_final: 0.3166 (p-80) REVERT: g 90 TRP cc_start: 0.6962 (m100) cc_final: 0.5729 (m100) REVERT: g 143 GLN cc_start: 0.7997 (pm20) cc_final: 0.7108 (tp40) REVERT: g 150 TRP cc_start: 0.6907 (m-10) cc_final: 0.5654 (m-10) REVERT: g 155 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.5949 (mpt180) REVERT: g 217 MET cc_start: 0.6655 (mmm) cc_final: 0.6248 (mmm) REVERT: g 235 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8135 (mm) REVERT: g 246 TYR cc_start: 0.6353 (t80) cc_final: 0.5743 (t80) REVERT: g 271 LYS cc_start: 0.7912 (pttt) cc_final: 0.7309 (tptm) REVERT: h 6 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7591 (mmt90) REVERT: h 21 ARG cc_start: 0.8615 (ttt180) cc_final: 0.8303 (tmm-80) REVERT: r 168 GLU cc_start: 0.9150 (pt0) cc_final: 0.7897 (mm-30) REVERT: r 170 ARG cc_start: 0.8604 (ttm170) cc_final: 0.8148 (ttm110) REVERT: w 91 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7901 (mmp) outliers start: 262 outliers final: 196 residues processed: 917 average time/residue: 0.8082 time to fit residues: 1258.4369 Evaluate side-chains 959 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 723 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 133 THR Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 76 GLU Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 83 ASN Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain S residue 40 TYR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 111 MET Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 53 GLU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 ARG Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 73 TYR Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 33 GLU Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 80 ARG Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 294 ASP Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain h residue 6 ARG Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 89 ASP Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 5.9990 chunk 614 optimal weight: 8.9990 chunk 561 optimal weight: 4.9990 chunk 598 optimal weight: 7.9990 chunk 360 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 469 optimal weight: 0.1980 chunk 183 optimal weight: 30.0000 chunk 540 optimal weight: 10.0000 chunk 565 optimal weight: 2.9990 chunk 596 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 HIS F 82 ASN ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 GLN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS d 28 HIS e 56 ASN g 305 ASN w 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 86006 Z= 0.219 Angle : 0.649 13.631 125306 Z= 0.327 Chirality : 0.038 0.336 15565 Planarity : 0.004 0.104 8764 Dihedral : 24.665 179.891 35685 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 5.79 % Allowed : 26.23 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4859 helix: 0.91 (0.13), residues: 1618 sheet: -0.60 (0.16), residues: 926 loop : -0.66 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 69 HIS 0.008 0.001 HIS d 28 PHE 0.027 0.002 PHE C 269 TYR 0.022 0.001 TYR K 68 ARG 0.009 0.000 ARG O 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 749 time to evaluate : 4.425 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: A 73 ASP cc_start: 0.8620 (m-30) cc_final: 0.8257 (m-30) REVERT: A 130 ASP cc_start: 0.9261 (OUTLIER) cc_final: 0.8689 (p0) REVERT: A 131 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7210 (p90) REVERT: B 76 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7669 (p0) REVERT: B 78 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 83 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8609 (mtmm) REVERT: B 97 LEU cc_start: 0.9171 (mt) cc_final: 0.8835 (mt) REVERT: B 106 THR cc_start: 0.8722 (m) cc_final: 0.8347 (p) REVERT: B 168 MET cc_start: 0.7983 (mtm) cc_final: 0.7416 (mtt) REVERT: B 198 GLU cc_start: 0.8743 (tp30) cc_final: 0.8295 (tp30) REVERT: B 232 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7001 (t-90) REVERT: C 80 GLU cc_start: 0.8419 (tp30) cc_final: 0.7975 (tp30) REVERT: C 104 ASP cc_start: 0.8860 (p0) cc_final: 0.8277 (p0) REVERT: C 120 GLN cc_start: 0.7509 (mt0) cc_final: 0.6958 (mt0) REVERT: C 121 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7911 (tmt170) REVERT: C 123 ARG cc_start: 0.8747 (mtp180) cc_final: 0.8101 (mtp180) REVERT: C 216 MET cc_start: 0.8645 (mtm) cc_final: 0.7906 (mtp) REVERT: C 227 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8566 (ttt90) REVERT: D 14 ASP cc_start: 0.8445 (m-30) cc_final: 0.7915 (p0) REVERT: D 46 THR cc_start: 0.6593 (m) cc_final: 0.6147 (t) REVERT: D 94 ARG cc_start: 0.8684 (ptt180) cc_final: 0.7734 (ptm160) REVERT: D 145 GLN cc_start: 0.6321 (pp30) cc_final: 0.6077 (pp30) REVERT: D 189 MET cc_start: 0.8867 (ttt) cc_final: 0.8362 (tpp) REVERT: E 60 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8002 (mt-10) REVERT: E 133 THR cc_start: 0.8134 (m) cc_final: 0.7739 (p) REVERT: E 184 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9068 (t) REVERT: F 160 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7596 (pt0) REVERT: G 28 TYR cc_start: 0.8652 (m-10) cc_final: 0.7895 (m-10) REVERT: H 25 GLN cc_start: 0.8940 (mt0) cc_final: 0.8620 (mm-40) REVERT: H 32 MET cc_start: 0.9063 (mmm) cc_final: 0.8562 (ptt) REVERT: H 87 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.7870 (t80) REVERT: H 112 ASN cc_start: 0.7876 (t0) cc_final: 0.7270 (m-40) REVERT: H 127 ASP cc_start: 0.8361 (t0) cc_final: 0.7928 (t0) REVERT: H 159 ASP cc_start: 0.9030 (t0) cc_final: 0.8826 (t70) REVERT: I 130 THR cc_start: 0.8085 (p) cc_final: 0.7383 (p) REVERT: I 134 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: I 165 GLN cc_start: 0.9052 (mt0) cc_final: 0.8812 (mt0) REVERT: J 21 GLU cc_start: 0.8060 (pm20) cc_final: 0.7358 (pm20) REVERT: J 41 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7300 (ttp-170) REVERT: J 66 LYS cc_start: 0.9052 (pttm) cc_final: 0.8725 (tppt) REVERT: J 103 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7933 (mm-30) REVERT: J 107 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: J 108 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.8109 (mmp-170) REVERT: J 143 ASN cc_start: 0.8974 (t0) cc_final: 0.8373 (t0) REVERT: J 150 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8486 (mtt180) REVERT: J 161 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9177 (pp) REVERT: K 14 LEU cc_start: 0.7509 (mp) cc_final: 0.6854 (tt) REVERT: K 46 MET cc_start: 0.6723 (ppp) cc_final: 0.6316 (ppp) REVERT: K 47 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.6970 (tttt) REVERT: K 64 TRP cc_start: 0.6321 (m-10) cc_final: 0.6039 (m-10) REVERT: L 39 ASN cc_start: 0.8287 (t0) cc_final: 0.7873 (p0) REVERT: L 49 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7795 (tp30) REVERT: M 12 MET cc_start: 0.4343 (OUTLIER) cc_final: 0.3959 (ppp) REVERT: M 80 ASP cc_start: 0.6709 (m-30) cc_final: 0.5984 (p0) REVERT: N 49 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8527 (mm-40) REVERT: N 107 LYS cc_start: 0.8435 (tptt) cc_final: 0.8118 (tptt) REVERT: N 140 LYS cc_start: 0.9114 (tttt) cc_final: 0.8830 (tttp) REVERT: O 44 VAL cc_start: 0.9536 (t) cc_final: 0.9250 (p) REVERT: O 52 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.8989 (p) REVERT: O 63 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7092 (mmmt) REVERT: O 72 TYR cc_start: 0.8422 (t80) cc_final: 0.7067 (t80) REVERT: P 40 ARG cc_start: 0.5403 (tpt170) cc_final: 0.1574 (ptp90) REVERT: P 72 LYS cc_start: 0.5326 (tptt) cc_final: 0.5101 (tptt) REVERT: P 84 ILE cc_start: 0.4088 (OUTLIER) cc_final: 0.3301 (tp) REVERT: Q 43 GLU cc_start: 0.3390 (OUTLIER) cc_final: 0.2568 (mp0) REVERT: Q 132 PHE cc_start: 0.8640 (p90) cc_final: 0.8006 (p90) REVERT: Q 140 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.6925 (mmm-85) REVERT: R 33 ARG cc_start: 0.8393 (mmt180) cc_final: 0.7644 (mmt-90) REVERT: R 37 GLU cc_start: 0.8677 (tt0) cc_final: 0.7953 (mt-10) REVERT: R 82 ASP cc_start: 0.8045 (t70) cc_final: 0.7722 (t0) REVERT: R 130 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8504 (p) REVERT: S 117 ILE cc_start: 0.5144 (mt) cc_final: 0.4460 (tp) REVERT: T 83 GLN cc_start: 0.8000 (tt0) cc_final: 0.7206 (pt0) REVERT: T 126 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8142 (tm-30) REVERT: U 24 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7838 (mm) REVERT: U 75 LYS cc_start: 0.6581 (mttm) cc_final: 0.6278 (mmtp) REVERT: U 76 THR cc_start: 0.9218 (m) cc_final: 0.8925 (p) REVERT: U 78 ASP cc_start: 0.6269 (m-30) cc_final: 0.6066 (m-30) REVERT: U 82 MET cc_start: 0.7157 (tmm) cc_final: 0.6824 (tmm) REVERT: U 91 LEU cc_start: 0.8477 (mt) cc_final: 0.7994 (tp) REVERT: U 107 GLU cc_start: 0.7677 (tp30) cc_final: 0.5358 (mp0) REVERT: V 36 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9277 (p) REVERT: V 72 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8523 (mt) REVERT: W 111 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8420 (ptt) REVERT: X 32 LEU cc_start: 0.8960 (tp) cc_final: 0.8747 (tp) REVERT: X 53 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: X 90 CYS cc_start: 0.8914 (m) cc_final: 0.8445 (m) REVERT: X 100 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9114 (m) REVERT: Y 6 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8587 (p) REVERT: Y 23 MET cc_start: 0.9013 (ptp) cc_final: 0.8656 (ptp) REVERT: Z 57 LYS cc_start: 0.8628 (tppt) cc_final: 0.8363 (ttpp) REVERT: Z 65 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6407 (m-80) REVERT: Z 68 ILE cc_start: 0.7257 (mt) cc_final: 0.6930 (mp) REVERT: Z 102 LYS cc_start: 0.7021 (tttt) cc_final: 0.6775 (tttt) REVERT: a 26 CYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7378 (m) REVERT: a 40 VAL cc_start: 0.9627 (t) cc_final: 0.9368 (p) REVERT: a 73 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: a 77 CYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6532 (m) REVERT: a 89 ARG cc_start: 0.8696 (ttm170) cc_final: 0.8369 (ttp-170) REVERT: b 75 GLU cc_start: 0.8529 (tp30) cc_final: 0.8202 (tp30) REVERT: c 67 ARG cc_start: 0.8650 (ttt180) cc_final: 0.8052 (ttp-170) REVERT: d 40 ARG cc_start: 0.4929 (OUTLIER) cc_final: 0.4498 (ptm160) REVERT: e 5 SER cc_start: 0.8323 (p) cc_final: 0.8062 (m) REVERT: e 34 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7473 (mpt-90) REVERT: f 93 HIS cc_start: 0.3696 (t70) cc_final: 0.3144 (p-80) REVERT: g 26 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: g 90 TRP cc_start: 0.7018 (m100) cc_final: 0.5716 (m100) REVERT: g 143 GLN cc_start: 0.7884 (pm20) cc_final: 0.7206 (tp40) REVERT: g 150 TRP cc_start: 0.7267 (m-10) cc_final: 0.5758 (m-10) REVERT: g 191 HIS cc_start: 0.6913 (m90) cc_final: 0.6614 (m-70) REVERT: g 235 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8073 (mm) REVERT: g 246 TYR cc_start: 0.6324 (t80) cc_final: 0.5856 (t80) REVERT: g 271 LYS cc_start: 0.7904 (pttt) cc_final: 0.7132 (tptm) REVERT: h 6 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7566 (mmt90) REVERT: h 21 ARG cc_start: 0.8610 (ttt180) cc_final: 0.8298 (tmm-80) REVERT: r 168 GLU cc_start: 0.9169 (pt0) cc_final: 0.7932 (mm-30) REVERT: r 170 ARG cc_start: 0.8584 (ttm170) cc_final: 0.8126 (ttm110) REVERT: w 91 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7905 (mmp) outliers start: 246 outliers final: 193 residues processed: 919 average time/residue: 0.7843 time to fit residues: 1220.6146 Evaluate side-chains 946 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 717 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 97 TYR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 76 GLU Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain S residue 40 TYR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 MET Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 53 GLU Chi-restraints excluded: chain X residue 61 GLN Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 90 GLU Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 73 TYR Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 33 GLU Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 26 GLN Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 294 ASP Chi-restraints excluded: chain g residue 305 ASN Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain h residue 6 ARG Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 89 ASP Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 7.9990 chunk 632 optimal weight: 7.9990 chunk 386 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 663 optimal weight: 2.9990 chunk 610 optimal weight: 20.0000 chunk 528 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 408 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 86006 Z= 0.305 Angle : 0.702 59.071 125306 Z= 0.365 Chirality : 0.039 0.387 15565 Planarity : 0.005 0.160 8764 Dihedral : 24.661 179.818 35673 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 5.70 % Allowed : 26.40 % Favored : 67.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4859 helix: 0.91 (0.13), residues: 1618 sheet: -0.60 (0.16), residues: 926 loop : -0.65 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 67 HIS 0.021 0.001 HIS d 28 PHE 0.030 0.002 PHE P 15 TYR 0.075 0.002 TYR P 17 ARG 0.015 0.001 ARG f 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9718 Ramachandran restraints generated. 4859 Oldfield, 0 Emsley, 4859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 717 time to evaluate : 4.557 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: A 73 ASP cc_start: 0.8625 (m-30) cc_final: 0.8259 (m-30) REVERT: A 130 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8696 (p0) REVERT: A 131 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7222 (p90) REVERT: A 209 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 213 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7062 (tp30) REVERT: B 76 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7674 (p0) REVERT: B 78 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7343 (mm-30) REVERT: B 83 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8613 (mtmm) REVERT: B 97 LEU cc_start: 0.9127 (mt) cc_final: 0.8772 (mt) REVERT: B 106 THR cc_start: 0.8733 (m) cc_final: 0.8357 (p) REVERT: B 168 MET cc_start: 0.7986 (mtm) cc_final: 0.7417 (mtt) REVERT: B 198 GLU cc_start: 0.8743 (tp30) cc_final: 0.8295 (tp30) REVERT: B 232 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7006 (t-90) REVERT: C 80 GLU cc_start: 0.8423 (tp30) cc_final: 0.7983 (tp30) REVERT: C 104 ASP cc_start: 0.8863 (p0) cc_final: 0.8284 (p0) REVERT: C 120 GLN cc_start: 0.7510 (mt0) cc_final: 0.6982 (mt0) REVERT: C 123 ARG cc_start: 0.8751 (mtp180) cc_final: 0.8533 (mtp85) REVERT: C 216 MET cc_start: 0.8649 (mtm) cc_final: 0.7912 (mtp) REVERT: C 227 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8571 (ttt90) REVERT: D 14 ASP cc_start: 0.8451 (m-30) cc_final: 0.7920 (p0) REVERT: D 46 THR cc_start: 0.6588 (m) cc_final: 0.6147 (t) REVERT: D 94 ARG cc_start: 0.8684 (ptt180) cc_final: 0.7735 (ptm160) REVERT: D 145 GLN cc_start: 0.6319 (pp30) cc_final: 0.6083 (pp30) REVERT: D 189 MET cc_start: 0.8864 (ttt) cc_final: 0.8365 (tpp) REVERT: E 60 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 133 THR cc_start: 0.8139 (m) cc_final: 0.7743 (p) REVERT: E 184 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9070 (t) REVERT: F 160 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7599 (pt0) REVERT: G 28 TYR cc_start: 0.8664 (m-10) cc_final: 0.7896 (m-10) REVERT: H 25 GLN cc_start: 0.8940 (mt0) cc_final: 0.8621 (mm-40) REVERT: H 32 MET cc_start: 0.9063 (mmm) cc_final: 0.8559 (ptt) REVERT: H 87 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7872 (t80) REVERT: H 112 ASN cc_start: 0.7878 (t0) cc_final: 0.7271 (m-40) REVERT: H 127 ASP cc_start: 0.8367 (t0) cc_final: 0.7935 (t0) REVERT: H 159 ASP cc_start: 0.9041 (t0) cc_final: 0.8828 (t70) REVERT: I 130 THR cc_start: 0.8084 (p) cc_final: 0.7387 (p) REVERT: I 134 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: I 165 GLN cc_start: 0.9057 (mt0) cc_final: 0.8831 (mt0) REVERT: I 184 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8656 (mtt180) REVERT: J 21 GLU cc_start: 0.8058 (pm20) cc_final: 0.7362 (pm20) REVERT: J 41 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7309 (ttp-170) REVERT: J 66 LYS cc_start: 0.9083 (pttm) cc_final: 0.8728 (tppt) REVERT: J 103 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7975 (mm-30) REVERT: J 107 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: J 108 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.8118 (mmp-170) REVERT: J 143 ASN cc_start: 0.8982 (t0) cc_final: 0.8381 (t0) REVERT: J 150 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8485 (mtt180) REVERT: J 161 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9180 (pp) REVERT: K 14 LEU cc_start: 0.7510 (mp) cc_final: 0.6857 (tt) REVERT: K 46 MET cc_start: 0.6677 (ppp) cc_final: 0.6332 (ppp) REVERT: K 47 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6968 (tttt) REVERT: K 64 TRP cc_start: 0.6332 (m-10) cc_final: 0.6061 (m-10) REVERT: L 39 ASN cc_start: 0.8292 (t0) cc_final: 0.7877 (p0) REVERT: L 49 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7796 (tp30) REVERT: M 12 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3960 (ppp) REVERT: M 80 ASP cc_start: 0.6711 (m-30) cc_final: 0.5985 (p0) REVERT: N 49 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8533 (mm-40) REVERT: N 107 LYS cc_start: 0.8440 (tptt) cc_final: 0.8122 (tptt) REVERT: N 140 LYS cc_start: 0.9101 (tttt) cc_final: 0.8827 (tttp) REVERT: O 44 VAL cc_start: 0.9518 (t) cc_final: 0.9255 (p) REVERT: O 52 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9033 (p) REVERT: O 63 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7096 (mmmt) REVERT: O 72 TYR cc_start: 0.8424 (t80) cc_final: 0.7072 (t80) REVERT: P 40 ARG cc_start: 0.5400 (tpt170) cc_final: 0.1577 (ptp90) REVERT: P 84 ILE cc_start: 0.4079 (OUTLIER) cc_final: 0.3292 (tp) REVERT: Q 43 GLU cc_start: 0.3399 (OUTLIER) cc_final: 0.2573 (mp0) REVERT: Q 132 PHE cc_start: 0.8645 (p90) cc_final: 0.8015 (p90) REVERT: Q 140 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.6944 (mmm-85) REVERT: R 33 ARG cc_start: 0.8392 (mmt180) cc_final: 0.7648 (mmt-90) REVERT: R 37 GLU cc_start: 0.8682 (tt0) cc_final: 0.7957 (mt-10) REVERT: R 82 ASP cc_start: 0.8014 (t70) cc_final: 0.7719 (t0) REVERT: R 130 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8536 (p) REVERT: S 117 ILE cc_start: 0.5134 (mt) cc_final: 0.4458 (tp) REVERT: T 83 GLN cc_start: 0.7997 (tt0) cc_final: 0.7206 (pt0) REVERT: T 126 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8143 (tm-30) REVERT: U 24 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7839 (mm) REVERT: U 75 LYS cc_start: 0.6586 (mttm) cc_final: 0.6281 (mmtp) REVERT: U 76 THR cc_start: 0.9221 (m) cc_final: 0.8931 (p) REVERT: U 78 ASP cc_start: 0.6132 (m-30) cc_final: 0.5914 (m-30) REVERT: U 82 MET cc_start: 0.7159 (tmm) cc_final: 0.6829 (tmm) REVERT: U 87 ARG cc_start: 0.4717 (mpt90) cc_final: 0.4147 (mpt90) REVERT: U 91 LEU cc_start: 0.8475 (mt) cc_final: 0.7995 (tp) REVERT: U 107 GLU cc_start: 0.7675 (tp30) cc_final: 0.5359 (mp0) REVERT: V 36 VAL cc_start: 0.9500 (OUTLIER) cc_final: 0.9280 (p) REVERT: V 72 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8527 (mt) REVERT: W 111 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8430 (ptt) REVERT: X 32 LEU cc_start: 0.8971 (tp) cc_final: 0.8753 (tp) REVERT: X 53 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: X 90 CYS cc_start: 0.8924 (m) cc_final: 0.8451 (m) REVERT: X 100 VAL cc_start: 0.9405 (OUTLIER) cc_final: 0.9122 (m) REVERT: Y 6 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8591 (p) REVERT: Y 23 MET cc_start: 0.9032 (ptp) cc_final: 0.8669 (ptp) REVERT: Z 57 LYS cc_start: 0.8628 (tppt) cc_final: 0.8365 (ttpp) REVERT: Z 65 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: Z 68 ILE cc_start: 0.7264 (mt) cc_final: 0.6927 (mp) REVERT: Z 102 LYS cc_start: 0.7022 (tttt) cc_final: 0.6777 (tttt) REVERT: a 26 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7385 (m) REVERT: a 40 VAL cc_start: 0.9630 (t) cc_final: 0.9372 (p) REVERT: a 73 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8342 (m-10) REVERT: a 77 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6545 (m) REVERT: a 89 ARG cc_start: 0.8703 (ttm170) cc_final: 0.8376 (ttp-170) REVERT: b 75 GLU cc_start: 0.8542 (tp30) cc_final: 0.8260 (tp30) REVERT: c 67 ARG cc_start: 0.8652 (ttt180) cc_final: 0.8053 (ttp-170) REVERT: d 40 ARG cc_start: 0.4930 (OUTLIER) cc_final: 0.4499 (ptm160) REVERT: e 5 SER cc_start: 0.8326 (p) cc_final: 0.8067 (m) REVERT: e 34 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7441 (mpt-90) REVERT: f 93 HIS cc_start: 0.3701 (t70) cc_final: 0.3145 (p-80) REVERT: g 26 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7091 (mp10) REVERT: g 90 TRP cc_start: 0.7020 (m100) cc_final: 0.5724 (m100) REVERT: g 143 GLN cc_start: 0.7881 (pm20) cc_final: 0.7206 (tp40) REVERT: g 150 TRP cc_start: 0.7251 (m-10) cc_final: 0.5760 (m-10) REVERT: g 191 HIS cc_start: 0.6840 (m90) cc_final: 0.6607 (m-70) REVERT: g 235 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8073 (mm) REVERT: g 246 TYR cc_start: 0.6328 (t80) cc_final: 0.5859 (t80) REVERT: g 271 LYS cc_start: 0.7913 (pttt) cc_final: 0.7135 (tptm) REVERT: h 6 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7575 (mmt90) REVERT: h 21 ARG cc_start: 0.8618 (ttt180) cc_final: 0.8300 (tmm-80) REVERT: r 168 GLU cc_start: 0.9164 (pt0) cc_final: 0.7930 (mm-30) REVERT: r 170 ARG cc_start: 0.8587 (ttm170) cc_final: 0.8131 (ttm110) REVERT: w 91 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7906 (mmp) outliers start: 242 outliers final: 193 residues processed: 886 average time/residue: 0.7836 time to fit residues: 1178.6219 Evaluate side-chains 948 residues out of total 4248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 717 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 25 PHE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 155 ASN Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 184 ARG Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 59 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 150 ARG Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 60 GLU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 83 ASP Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 76 GLU Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain S residue 40 TYR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 67 ARG Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 24 LEU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 74 SER Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 111 MET Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 3 LYS Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 26 GLN Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 53 GLU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain X residue 129 SER Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 65 TYR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 73 TYR Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 88 SER Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 33 GLU Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 40 ARG Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 34 ARG Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 26 GLN Chi-restraints excluded: chain g residue 65 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 155 ARG Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 294 ASP Chi-restraints excluded: chain g residue 313 THR Chi-restraints excluded: chain h residue 6 ARG Chi-restraints excluded: chain h residue 9 ARG Chi-restraints excluded: chain r residue 166 THR Chi-restraints excluded: chain w residue 89 ASP Chi-restraints excluded: chain w residue 91 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 4.9990 chunk 562 optimal weight: 0.2980 chunk 161 optimal weight: 10.0000 chunk 487 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 146 optimal weight: 30.0000 chunk 529 optimal weight: 20.0000 chunk 221 optimal weight: 0.9990 chunk 543 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090892 restraints weight = 189881.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091829 restraints weight = 415479.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092659 restraints weight = 205236.703| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 86006 Z= 0.233 Angle : 0.689 59.181 125306 Z= 0.355 Chirality : 0.038 0.438 15565 Planarity : 0.004 0.099 8764 Dihedral : 24.664 179.862 35673 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 5.82 % Allowed : 26.14 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 4859 helix: 0.90 (0.13), residues: 1624 sheet: -0.57 (0.16), residues: 934 loop : -0.64 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 67 HIS 0.010 0.001 HIS d 28 PHE 0.026 0.002 PHE D 24 TYR 0.034 0.002 TYR P 17 ARG 0.026 0.000 ARG c 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19467.75 seconds wall clock time: 343 minutes 52.68 seconds (20632.68 seconds total)