Starting phenix.real_space_refine on Sat Jan 25 01:00:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xp2_38548/01_2025/8xp2_38548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xp2_38548/01_2025/8xp2_38548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xp2_38548/01_2025/8xp2_38548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xp2_38548/01_2025/8xp2_38548.map" model { file = "/net/cci-nas-00/data/ceres_data/8xp2_38548/01_2025/8xp2_38548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xp2_38548/01_2025/8xp2_38548.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 1739 5.49 5 S 186 5.16 5 C 41464 2.51 5 N 14062 2.21 5 O 19039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 76494 Number of models: 1 Model: "" Number of chains: 40 Chain: "Ln" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "S2" Number of atoms: 36896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1740, 36896 Classifications: {'DNA': 15, 'RNA': 1725} Modifications used: {'5*END': 1, 'rna2p_pur': 155, 'rna2p_pyr': 129, 'rna3p_pur': 751, 'rna3p_pyr': 687} Link IDs: {'rna2p': 283, 'rna3p': 1456} Chain breaks: 4 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {' G:plan2': 3, ' A:plan': 1, ' C:plan': 11, ' U:plan': 3, ' G:plan': 3, ' C:plan2': 11, ' A:plan2': 1} Unresolved non-hydrogen planarities: 203 Chain: "SA" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1747 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "SB" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1738 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "SD" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "SE" 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: "SF" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "SH" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1497 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 176} Chain breaks: 1 Chain: "SI" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "SK" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 827 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "SL" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1182 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "SP" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1045 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "SQ" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SR" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "SS" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1198 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "ST" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "SU" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "SV" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "SX" 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: "Sa" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "Sc" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "Sd" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "Sg" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "SC" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "SG" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "SJ" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "SM" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "SN" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SO" 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: "SW" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "SY" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1022 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "SZ" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Sb" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "Se" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "Sf" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 497 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "JD" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain breaks: 1 Chain: "Sa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 59425 SG CYSSa 23 84.877 174.203 113.514 1.00 56.03 S ATOM 59446 SG CYSSa 26 84.513 172.865 110.017 1.00 55.65 S ATOM 59829 SG CYSSa 74 87.053 171.179 112.487 1.00 54.28 S ATOM 59848 SG CYSSa 77 87.810 174.366 110.955 1.00 54.19 S ATOM 74753 SG CYSSb 37 62.654 156.238 177.038 1.00 86.84 S ATOM 74770 SG CYSSb 40 60.224 156.793 179.298 1.00 87.45 S ATOM 74896 SG CYSSb 56 58.654 155.554 175.894 1.00 89.34 S ATOM 75830 SG CYSSf 121 170.280 163.793 28.510 1.00131.35 S ATOM 75984 SG CYSSf 141 166.915 162.943 29.420 1.00118.79 S ATOM 76003 SG CYSSf 144 167.687 165.783 31.456 1.00120.02 S Time building chain proxies: 32.80, per 1000 atoms: 0.43 Number of scatterers: 76494 At special positions: 0 Unit cell: (205.134, 262.434, 210.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 186 16.00 P 1739 15.00 O 19039 8.00 N 14062 7.00 C 41464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.64 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNSa 201 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 77 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 26 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 74 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 23 " pdb=" ZNSb 101 " pdb="ZN ZNSb 101 " - pdb=" SG CYSSb 56 " pdb="ZN ZNSb 101 " - pdb=" SG CYSSb 40 " pdb="ZN ZNSb 101 " - pdb=" SG CYSSb 37 " pdb=" ZNSf 200 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 144 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 121 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 141 " Number of angles added : 6 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9194 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 58 sheets defined 36.1% alpha, 18.9% beta 530 base pairs and 881 stacking pairs defined. Time for finding SS restraints: 25.95 Creating SS restraints... Processing helix chain 'Ln' and resid 2 through 24 removed outlier: 3.533A pdb=" N LYSLn 7 " --> pdb=" O ALALn 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSLn 8 " --> pdb=" O LYSLn 4 " (cutoff:3.500A) Processing helix chain 'SA' and resid 11 through 22 Processing helix chain 'SA' and resid 50 through 67 removed outlier: 3.577A pdb=" N ALASA 67 " --> pdb=" O ARGSA 63 " (cutoff:3.500A) Processing helix chain 'SA' and resid 70 through 72 No H-bonds generated for 'chain 'SA' and resid 70 through 72' Processing helix chain 'SA' and resid 83 through 95 Processing helix chain 'SA' and resid 130 through 138 removed outlier: 3.565A pdb=" N LEUSA 134 " --> pdb=" O ASPSA 130 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SERSA 138 " --> pdb=" O LEUSA 134 " (cutoff:3.500A) Processing helix chain 'SA' and resid 167 through 186 removed outlier: 3.664A pdb=" N GLYSA 172 " --> pdb=" O ALASA 168 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUSA 173 " --> pdb=" O HISSA 169 " (cutoff:3.500A) Processing helix chain 'SA' and resid 198 through 203 removed outlier: 3.864A pdb=" N TYRSA 202 " --> pdb=" O PROSA 199 " (cutoff:3.500A) Processing helix chain 'SA' and resid 206 through 223 Processing helix chain 'SB' and resid 57 through 62 Processing helix chain 'SB' and resid 72 through 74 No H-bonds generated for 'chain 'SB' and resid 72 through 74' Processing helix chain 'SB' and resid 106 through 114 removed outlier: 3.801A pdb=" N VALSB 114 " --> pdb=" O METSB 110 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 175 Processing helix chain 'SB' and resid 180 through 189 removed outlier: 3.660A pdb=" N VALSB 184 " --> pdb=" O ASPSB 180 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VALSB 185 " --> pdb=" O LEUSB 181 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASNSB 186 " --> pdb=" O LYSSB 182 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 removed outlier: 3.579A pdb=" N LYSSB 195 " --> pdb=" O ASPSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 233 removed outlier: 4.285A pdb=" N LEUSB 228 " --> pdb=" O GLUSB 224 " (cutoff:3.500A) Processing helix chain 'SD' and resid 6 through 29 Processing helix chain 'SD' and resid 54 through 60 Processing helix chain 'SD' and resid 63 through 78 removed outlier: 3.770A pdb=" N ARGSD 67 " --> pdb=" O GLYSD 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VALSD 72 " --> pdb=" O GLUSD 68 " (cutoff:3.500A) Processing helix chain 'SD' and resid 93 through 96 Processing helix chain 'SD' and resid 97 through 111 Processing helix chain 'SD' and resid 114 through 130 removed outlier: 3.528A pdb=" N TYRSD 120 " --> pdb=" O ARGSD 116 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHESD 125 " --> pdb=" O GLYSD 121 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLYSD 130 " --> pdb=" O ILESD 126 " (cutoff:3.500A) Processing helix chain 'SD' and resid 162 through 167 removed outlier: 4.012A pdb=" N TYRSD 166 " --> pdb=" O ASPSD 162 " (cutoff:3.500A) Processing helix chain 'SE' and resid 37 through 41 removed outlier: 3.631A pdb=" N GLUSE 40 " --> pdb=" O LYSSE 37 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYSSE 41 " --> pdb=" O LEUSE 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'SE' and resid 37 through 41' Processing helix chain 'SE' and resid 43 through 49 Processing helix chain 'SE' and resid 57 through 66 removed outlier: 3.540A pdb=" N LYSSE 62 " --> pdb=" O GLYSE 58 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYSSE 63 " --> pdb=" O ASPSE 59 " (cutoff:3.500A) Processing helix chain 'SE' and resid 247 through 263 removed outlier: 3.696A pdb=" N GLNSE 260 " --> pdb=" O LEUSE 256 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SERSE 261 " --> pdb=" O ALASE 257 " (cutoff:3.500A) Processing helix chain 'SF' and resid 20 through 22 No H-bonds generated for 'chain 'SF' and resid 20 through 22' Processing helix chain 'SF' and resid 67 through 76 removed outlier: 3.511A pdb=" N METSF 76 " --> pdb=" O LEUSF 72 " (cutoff:3.500A) Processing helix chain 'SF' and resid 79 through 83 Processing helix chain 'SF' and resid 85 through 104 Processing helix chain 'SF' and resid 107 through 120 Processing helix chain 'SF' and resid 142 through 162 removed outlier: 3.501A pdb=" N TRPSF 152 " --> pdb=" O ASNSF 148 " (cutoff:3.500A) Processing helix chain 'SF' and resid 168 through 182 Processing helix chain 'SF' and resid 187 through 203 Processing helix chain 'SH' and resid 17 through 32 removed outlier: 3.723A pdb=" N GLYSH 22 " --> pdb=" O GLUSH 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N METSH 32 " --> pdb=" O LEUSH 28 " (cutoff:3.500A) Processing helix chain 'SH' and resid 33 through 41 removed outlier: 5.476A pdb=" N LEUSH 36 " --> pdb=" O ASNSH 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALASH 38 " --> pdb=" O ASPSH 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEUSH 40 " --> pdb=" O LYSSH 37 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARGSH 41 " --> pdb=" O ALASH 38 " (cutoff:3.500A) Processing helix chain 'SH' and resid 65 through 67 No H-bonds generated for 'chain 'SH' and resid 65 through 67' Processing helix chain 'SH' and resid 68 through 87 removed outlier: 3.738A pdb=" N ILESH 75 " --> pdb=" O SERSH 71 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VALSH 77 " --> pdb=" O GLNSH 73 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARGSH 78 " --> pdb=" O LYSSH 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARGSH 81 " --> pdb=" O VALSH 77 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLUSH 84 " --> pdb=" O VALSH 80 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYSSH 85 " --> pdb=" O ARGSH 81 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYSSH 86 " --> pdb=" O GLUSH 82 " (cutoff:3.500A) Processing helix chain 'SH' and resid 117 through 120 Processing helix chain 'SH' and resid 121 through 134 removed outlier: 3.501A pdb=" N VALSH 125 " --> pdb=" O THRSH 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VALSH 134 " --> pdb=" O LEUSH 130 " (cutoff:3.500A) Processing helix chain 'SH' and resid 162 through 168 removed outlier: 4.559A pdb=" N GLUSH 167 " --> pdb=" O ASNSH 164 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N HISSH 168 " --> pdb=" O ASNSH 165 " (cutoff:3.500A) Processing helix chain 'SH' and resid 169 through 181 removed outlier: 3.581A pdb=" N GLYSH 175 " --> pdb=" O GLUSH 171 " (cutoff:3.500A) Processing helix chain 'SI' and resid 25 through 27 No H-bonds generated for 'chain 'SI' and resid 25 through 27' Processing helix chain 'SI' and resid 88 through 93 removed outlier: 3.586A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 118 removed outlier: 3.794A pdb=" N TRPSI 112 " --> pdb=" O PROSI 108 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLUSI 114 " --> pdb=" O ARGSI 110 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SERSI 115 " --> pdb=" O GLNSI 111 " (cutoff:3.500A) Processing helix chain 'SI' and resid 129 through 138 Processing helix chain 'SI' and resid 142 through 155 removed outlier: 3.717A pdb=" N LYSSI 148 " --> pdb=" O LYSSI 144 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLUSI 151 " --> pdb=" O LYSSI 147 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYSSI 154 " --> pdb=" O ASPSI 150 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASNSI 155 " --> pdb=" O GLUSI 151 " (cutoff:3.500A) Processing helix chain 'SI' and resid 159 through 167 removed outlier: 3.539A pdb=" N GLUSI 164 " --> pdb=" O SERSI 160 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLNSI 165 " --> pdb=" O LEUSI 161 " (cutoff:3.500A) Processing helix chain 'SI' and resid 191 through 207 removed outlier: 3.577A pdb=" N LYSSI 201 " --> pdb=" O PHESI 197 " (cutoff:3.500A) Processing helix chain 'SK' and resid 5 through 18 removed outlier: 3.733A pdb=" N LEUSK 15 " --> pdb=" O ILESK 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHESK 16 " --> pdb=" O TYRSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 41 through 55 removed outlier: 3.620A pdb=" N ALASK 48 " --> pdb=" O HISSK 44 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SERSK 51 " --> pdb=" O LYSSK 47 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEUSK 52 " --> pdb=" O ALASK 48 " (cutoff:3.500A) Processing helix chain 'SK' and resid 72 through 84 removed outlier: 3.546A pdb=" N GLNSK 77 " --> pdb=" O ASNSK 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASPSK 81 " --> pdb=" O GLNSK 77 " (cutoff:3.500A) Processing helix chain 'SL' and resid 47 through 52 removed outlier: 3.779A pdb=" N ILESL 51 " --> pdb=" O PROSL 47 " (cutoff:3.500A) Processing helix chain 'SP' and resid 22 through 28 removed outlier: 3.661A pdb=" N LEUSP 26 " --> pdb=" O LEUSP 22 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASPSP 27 " --> pdb=" O ASPSP 23 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N METSP 28 " --> pdb=" O GLNSP 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'SP' and resid 22 through 28' Processing helix chain 'SP' and resid 29 through 35 removed outlier: 3.521A pdb=" N LEUSP 33 " --> pdb=" O SERSP 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLNSP 35 " --> pdb=" O GLUSP 31 " (cutoff:3.500A) Processing helix chain 'SP' and resid 38 through 47 removed outlier: 3.612A pdb=" N ARGSP 43 " --> pdb=" O ALASP 39 " (cutoff:3.500A) Processing helix chain 'SP' and resid 50 through 64 removed outlier: 3.503A pdb=" N HISSP 54 " --> pdb=" O ARGSP 50 " (cutoff:3.500A) Processing helix chain 'SP' and resid 108 through 112 removed outlier: 4.131A pdb=" N ILESP 112 " --> pdb=" O PROSP 109 " (cutoff:3.500A) Processing helix chain 'SP' and resid 116 through 120 removed outlier: 3.737A pdb=" N PHESP 119 " --> pdb=" O LEUSP 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SERSP 120 " --> pdb=" O GLYSP 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'SP' and resid 116 through 120' Processing helix chain 'SQ' and resid 44 through 46 No H-bonds generated for 'chain 'SQ' and resid 44 through 46' Processing helix chain 'SQ' and resid 47 through 52 removed outlier: 3.516A pdb=" N LEUSQ 51 " --> pdb=" O LEUSQ 47 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 57 Processing helix chain 'SQ' and resid 76 through 100 removed outlier: 4.126A pdb=" N ARGSQ 85 " --> pdb=" O ILESQ 81 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLNSQ 86 " --> pdb=" O TYRSQ 82 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 101 through 115 removed outlier: 3.823A pdb=" N GLUSQ 107 " --> pdb=" O ALASQ 103 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILESQ 111 " --> pdb=" O GLUSQ 107 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 116 through 120 Processing helix chain 'SR' and resid 6 through 19 removed outlier: 3.755A pdb=" N ALASR 12 " --> pdb=" O THRSR 8 " (cutoff:3.500A) Processing helix chain 'SR' and resid 27 through 38 removed outlier: 3.683A pdb=" N ARGSR 33 " --> pdb=" O HISSR 29 " (cutoff:3.500A) Processing helix chain 'SR' and resid 43 through 64 removed outlier: 3.512A pdb=" N LYSSR 59 " --> pdb=" O THRSR 55 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLNSR 62 " --> pdb=" O METSR 58 " (cutoff:3.500A) Processing helix chain 'SR' and resid 71 through 82 removed outlier: 3.556A pdb=" N GLUSR 76 " --> pdb=" O LYSSR 72 " (cutoff:3.500A) Processing helix chain 'SR' and resid 99 through 108 Processing helix chain 'SS' and resid 25 through 30 removed outlier: 4.086A pdb=" N ILESS 30 " --> pdb=" O ILESS 26 " (cutoff:3.500A) Processing helix chain 'SS' and resid 31 through 33 No H-bonds generated for 'chain 'SS' and resid 31 through 33' Processing helix chain 'SS' and resid 37 through 49 removed outlier: 3.620A pdb=" N LEUSS 45 " --> pdb=" O ALASS 41 " (cutoff:3.500A) Processing helix chain 'SS' and resid 60 through 73 removed outlier: 3.545A pdb=" N ARGSS 66 " --> pdb=" O ASPSS 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N METSS 71 " --> pdb=" O VALSS 67 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASNSS 73 " --> pdb=" O THRSS 69 " (cutoff:3.500A) Processing helix chain 'SS' and resid 74 through 78 removed outlier: 3.501A pdb=" N LYSSS 78 " --> pdb=" O ARGSS 75 " (cutoff:3.500A) Processing helix chain 'SS' and resid 80 through 84 removed outlier: 3.802A pdb=" N LEUSS 84 " --> pdb=" O ASPSS 81 " (cutoff:3.500A) Processing helix chain 'SS' and resid 100 through 118 removed outlier: 3.524A pdb=" N ASPSS 104 " --> pdb=" O ALASS 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSSS 106 " --> pdb=" O GLYSS 102 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYSSS 116 " --> pdb=" O GLUSS 112 " (cutoff:3.500A) Processing helix chain 'SS' and resid 119 through 127 removed outlier: 3.576A pdb=" N ARGSS 124 " --> pdb=" O HISSS 120 " (cutoff:3.500A) Processing helix chain 'ST' and resid 10 through 25 removed outlier: 3.522A pdb=" N LYSST 23 " --> pdb=" O ALAST 19 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYSST 24 " --> pdb=" O ALAST 20 " (cutoff:3.500A) Processing helix chain 'ST' and resid 31 through 36 removed outlier: 3.776A pdb=" N VALST 34 " --> pdb=" O PROST 31 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASPST 35 " --> pdb=" O GLUST 32 " (cutoff:3.500A) Processing helix chain 'ST' and resid 51 through 67 removed outlier: 3.824A pdb=" N TYRST 65 " --> pdb=" O ALAST 61 " (cutoff:3.500A) Processing helix chain 'ST' and resid 71 through 79 removed outlier: 3.673A pdb=" N LYSST 77 " --> pdb=" O GLYST 73 " (cutoff:3.500A) Processing helix chain 'ST' and resid 96 through 110 removed outlier: 3.559A pdb=" N ALAST 100 " --> pdb=" O SERST 96 " (cutoff:3.500A) Processing helix chain 'ST' and resid 124 through 144 removed outlier: 3.656A pdb=" N ASPST 132 " --> pdb=" O GLNST 128 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARGST 133 " --> pdb=" O ARGST 129 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VALST 138 " --> pdb=" O ILEST 134 " (cutoff:3.500A) Processing helix chain 'SU' and resid 28 through 46 Processing helix chain 'SU' and resid 96 through 105 removed outlier: 3.816A pdb=" N GLNSU 100 " --> pdb=" O GLUSU 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILESU 101 " --> pdb=" O ILESU 97 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SERSU 105 " --> pdb=" O ILESU 101 " (cutoff:3.500A) Processing helix chain 'SV' and resid 56 through 63 removed outlier: 3.620A pdb=" N ARGSV 60 " --> pdb=" O CYSSV 56 " (cutoff:3.500A) Processing helix chain 'SV' and resid 64 through 77 removed outlier: 3.592A pdb=" N SERSV 68 " --> pdb=" O GLUSV 64 " (cutoff:3.500A) Processing helix chain 'SX' and resid 9 through 22 removed outlier: 3.979A pdb=" N TRPSX 22 " --> pdb=" O ARGSX 18 " (cutoff:3.500A) Processing helix chain 'SX' and resid 24 through 32 Processing helix chain 'SX' and resid 33 through 39 Processing helix chain 'SX' and resid 129 through 135 Processing helix chain 'Sa' and resid 49 through 56 Processing helix chain 'Sa' and resid 74 through 81 Processing helix chain 'Sa' and resid 88 through 93 removed outlier: 4.161A pdb=" N LYSSa 93 " --> pdb=" O ARGSa 89 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 3 through 8 removed outlier: 4.419A pdb=" N TRPSd 8 " --> pdb=" O GLNSd 4 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 32 through 36 Processing helix chain 'Sd' and resid 40 through 46 Processing helix chain 'Sd' and resid 46 through 51 Processing helix chain 'SC' and resid 64 through 72 Processing helix chain 'SC' and resid 78 through 84 removed outlier: 3.611A pdb=" N TYRSC 82 " --> pdb=" O LEUSC 78 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHESC 84 " --> pdb=" O GLUSC 80 " (cutoff:3.500A) Processing helix chain 'SC' and resid 91 through 98 removed outlier: 3.903A pdb=" N ASPSC 95 " --> pdb=" O SERSC 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHESC 97 " --> pdb=" O ILESC 93 " (cutoff:3.500A) Processing helix chain 'SC' and resid 146 through 161 Processing helix chain 'SC' and resid 207 through 217 removed outlier: 3.642A pdb=" N LEUSC 213 " --> pdb=" O VALSC 209 " (cutoff:3.500A) Processing helix chain 'SC' and resid 232 through 246 removed outlier: 3.679A pdb=" N THRSC 240 " --> pdb=" O PHESC 236 " (cutoff:3.500A) Processing helix chain 'SC' and resid 252 through 256 removed outlier: 3.516A pdb=" N TRPSC 256 " --> pdb=" O PROSC 253 " (cutoff:3.500A) Processing helix chain 'SC' and resid 264 through 269 removed outlier: 3.527A pdb=" N PHESC 269 " --> pdb=" O PROSC 265 " (cutoff:3.500A) Processing helix chain 'SC' and resid 269 through 277 removed outlier: 3.543A pdb=" N LYSSC 275 " --> pdb=" O ASPSC 271 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THRSC 276 " --> pdb=" O HISSC 272 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HISSC 277 " --> pdb=" O LEUSC 273 " (cutoff:3.500A) Processing helix chain 'SG' and resid 20 through 25 removed outlier: 3.653A pdb=" N LEUSG 24 " --> pdb=" O ASPSG 20 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 145 removed outlier: 3.559A pdb=" N PHESG 145 " --> pdb=" O ILESG 141 " (cutoff:3.500A) Processing helix chain 'SG' and resid 152 through 157 removed outlier: 4.170A pdb=" N VALSG 157 " --> pdb=" O ARGSG 154 " (cutoff:3.500A) Processing helix chain 'SG' and resid 181 through 229 removed outlier: 3.524A pdb=" N GLNSG 186 " --> pdb=" O PROSG 182 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYSSG 196 " --> pdb=" O ILESG 192 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYSSG 218 " --> pdb=" O ALASG 214 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLUSG 219 " --> pdb=" O LYSSG 215 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILESG 228 " --> pdb=" O ARGSG 224 " (cutoff:3.500A) Processing helix chain 'SG' and resid 229 through 237 Processing helix chain 'SJ' and resid 21 through 36 removed outlier: 3.617A pdb=" N LEUSJ 31 " --> pdb=" O GLNSJ 27 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 40 through 63 removed outlier: 3.754A pdb=" N VALSJ 46 " --> pdb=" O GLUSJ 42 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEUSJ 63 " --> pdb=" O GLUSJ 59 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 67 through 84 removed outlier: 3.514A pdb=" N LEUSJ 77 " --> pdb=" O GLUSJ 73 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 93 through 97 Processing helix chain 'SJ' and resid 101 through 108 removed outlier: 3.874A pdb=" N PHESJ 105 " --> pdb=" O LYSSJ 101 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARGSJ 108 " --> pdb=" O ASPSJ 104 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 109 through 117 removed outlier: 3.590A pdb=" N PHESJ 115 " --> pdb=" O GLNSJ 111 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 122 through 132 removed outlier: 3.632A pdb=" N ILESJ 130 " --> pdb=" O ALASJ 126 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 150 through 156 removed outlier: 3.943A pdb=" N LYSSJ 155 " --> pdb=" O LEUSJ 151 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HISSJ 156 " --> pdb=" O ASPSJ 152 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 171 through 185 removed outlier: 3.675A pdb=" N ALASJ 185 " --> pdb=" O GLYSJ 181 " (cutoff:3.500A) Processing helix chain 'SM' and resid 16 through 29 removed outlier: 4.112A pdb=" N GLUSM 20 " --> pdb=" O THRSM 16 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALSM 21 " --> pdb=" O ALASM 17 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALASM 25 " --> pdb=" O VALSM 21 " (cutoff:3.500A) Processing helix chain 'SM' and resid 34 through 44 Processing helix chain 'SM' and resid 58 through 72 removed outlier: 3.920A pdb=" N LYSSM 63 " --> pdb=" O PROSM 59 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUSM 64 " --> pdb=" O METSM 60 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HISSM 72 " --> pdb=" O LEUSM 68 " (cutoff:3.500A) Processing helix chain 'SM' and resid 81 through 89 removed outlier: 3.640A pdb=" N GLYSM 86 " --> pdb=" O ASNSM 82 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLUSM 87 " --> pdb=" O LYSSM 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRPSM 88 " --> pdb=" O LYSSM 84 " (cutoff:3.500A) Processing helix chain 'SM' and resid 119 through 132 removed outlier: 3.903A pdb=" N GLUSM 125 " --> pdb=" O LYSSM 121 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLUSM 126 " --> pdb=" O ASPSM 122 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHESM 128 " --> pdb=" O ILESM 124 " (cutoff:3.500A) Processing helix chain 'SN' and resid 29 through 43 removed outlier: 3.605A pdb=" N VALSN 33 " --> pdb=" O THRSN 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSSN 34 " --> pdb=" O SERSN 30 " (cutoff:3.500A) Processing helix chain 'SN' and resid 46 through 57 removed outlier: 3.691A pdb=" N VALSN 52 " --> pdb=" O SERSN 48 " (cutoff:3.500A) Processing helix chain 'SN' and resid 62 through 67 Processing helix chain 'SN' and resid 70 through 79 Processing helix chain 'SN' and resid 85 through 105 removed outlier: 3.633A pdb=" N HISSN 90 " --> pdb=" O GLUSN 86 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEUSN 91 " --> pdb=" O ASPSN 87 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARGSN 104 " --> pdb=" O LYSSN 100 " (cutoff:3.500A) Processing helix chain 'SN' and resid 108 through 132 removed outlier: 3.567A pdb=" N ILESN 116 " --> pdb=" O LYSSN 112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUSN 117 " --> pdb=" O PHESN 113 " (cutoff:3.500A) Processing helix chain 'SN' and resid 145 through 150 removed outlier: 3.658A pdb=" N VALSN 150 " --> pdb=" O ALASN 146 " (cutoff:3.500A) Processing helix chain 'SO' and resid 58 through 62 Processing helix chain 'SO' and resid 70 through 89 removed outlier: 3.749A pdb=" N GLYSO 89 " --> pdb=" O CYSSO 85 " (cutoff:3.500A) Processing helix chain 'SO' and resid 110 through 123 removed outlier: 4.231A pdb=" N SERSO 114 " --> pdb=" O PROSO 110 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALASO 120 " --> pdb=" O LEUSO 116 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLYSO 123 " --> pdb=" O LEUSO 119 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 21 removed outlier: 3.756A pdb=" N ASPSW 9 " --> pdb=" O ASNSW 5 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALASW 10 " --> pdb=" O VALSW 6 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 44 removed outlier: 3.527A pdb=" N VALSW 35 " --> pdb=" O SERSW 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALSW 40 " --> pdb=" O ARGSW 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N METSW 41 " --> pdb=" O PHESW 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HISSW 44 " --> pdb=" O VALSW 40 " (cutoff:3.500A) Processing helix chain 'SW' and resid 85 through 94 removed outlier: 3.512A pdb=" N ASNSW 92 " --> pdb=" O LYSSW 88 " (cutoff:3.500A) Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SY' and resid 36 through 49 removed outlier: 3.513A pdb=" N GLUSY 42 " --> pdb=" O THRSY 38 " (cutoff:3.500A) Processing helix chain 'SY' and resid 51 through 53 No H-bonds generated for 'chain 'SY' and resid 51 through 53' Processing helix chain 'SY' and resid 78 through 85 removed outlier: 3.557A pdb=" N LYSSY 84 " --> pdb=" O ASPSY 80 " (cutoff:3.500A) Processing helix chain 'SY' and resid 87 through 93 removed outlier: 3.553A pdb=" N LEUSY 91 " --> pdb=" O PROSY 87 " (cutoff:3.500A) Processing helix chain 'SY' and resid 103 through 117 removed outlier: 3.596A pdb=" N GLUSY 109 " --> pdb=" O LYSSY 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARGSY 110 " --> pdb=" O GLNSY 106 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALSY 117 " --> pdb=" O ARGSY 113 " (cutoff:3.500A) Processing helix chain 'SY' and resid 120 through 126 removed outlier: 3.804A pdb=" N ASNSY 124 " --> pdb=" O THRSY 120 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 51 through 62 removed outlier: 3.574A pdb=" N VALSZ 62 " --> pdb=" O LEUSZ 58 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 63 through 65 No H-bonds generated for 'chain 'SZ' and resid 63 through 65' Processing helix chain 'SZ' and resid 69 through 78 removed outlier: 3.503A pdb=" N LEUSZ 77 " --> pdb=" O VALSZ 73 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 81 through 94 removed outlier: 3.887A pdb=" N LEUSZ 88 " --> pdb=" O ALASZ 84 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLNSZ 89 " --> pdb=" O ARGSZ 85 " (cutoff:3.500A) Processing helix chain 'Sb' and resid 11 through 17 removed outlier: 3.643A pdb=" N ARGSb 17 " --> pdb=" O GLUSb 13 " (cutoff:3.500A) Processing helix chain 'Se' and resid 10 through 16 Processing helix chain 'Se' and resid 30 through 42 removed outlier: 3.615A pdb=" N ARGSe 41 " --> pdb=" O GLNSe 37 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHESe 42 " --> pdb=" O TYRSe 38 " (cutoff:3.500A) Processing helix chain 'Sf' and resid 100 through 105 removed outlier: 3.968A pdb=" N LYSSf 104 " --> pdb=" O LEUSf 100 " (cutoff:3.500A) Processing helix chain 'Sf' and resid 123 through 127 removed outlier: 4.111A pdb=" N GLYSf 127 " --> pdb=" O ASPSf 124 " (cutoff:3.500A) Processing helix chain 'JD' and resid 590 through 615 removed outlier: 3.568A pdb=" N GLUJD 597 " --> pdb=" O LYSJD 593 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILEJD 602 " --> pdb=" O LEUJD 598 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASNJD 603 " --> pdb=" O ALAJD 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASPJD 604 " --> pdb=" O LYSJD 600 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLNJD 611 " --> pdb=" O PHEJD 607 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUJD 613 " --> pdb=" O TYRJD 609 " (cutoff:3.500A) Processing helix chain 'JD' and resid 639 through 647 removed outlier: 3.616A pdb=" N PHEJD 643 " --> pdb=" O SERJD 639 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SA' and resid 38 through 41 removed outlier: 7.011A pdb=" N ILESA 48 " --> pdb=" O TYRSA 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SA' and resid 97 through 100 removed outlier: 6.755A pdb=" N VALSA 74 " --> pdb=" O THRSA 97 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILESA 99 " --> pdb=" O VALSA 74 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VALSA 76 " --> pdb=" O ILESA 99 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SERSA 75 " --> pdb=" O VALSA 123 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THRSA 144 " --> pdb=" O ILESA 159 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILESA 161 " --> pdb=" O THRSA 144 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALASA 146 " --> pdb=" O ILESA 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SB' and resid 43 through 50 removed outlier: 4.206A pdb=" N GLYSB 45 " --> pdb=" O VALSB 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VALSB 33 " --> pdb=" O GLYSB 45 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N CYSSB 96 " --> pdb=" O TRPSB 30 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASPSB 32 " --> pdb=" O CYSSB 96 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THRSB 98 " --> pdb=" O ASPSB 32 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LYSSB 34 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N PHESB 100 " --> pdb=" O LYSSB 34 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N CYSSB 96 " --> pdb=" O VALSB 91 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VALSB 91 " --> pdb=" O CYSSB 96 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THRSB 98 " --> pdb=" O GLUSB 89 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLUSB 89 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N PHESB 100 " --> pdb=" O ILESB 87 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILESB 87 " --> pdb=" O PHESB 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SB' and resid 43 through 50 removed outlier: 4.206A pdb=" N GLYSB 45 " --> pdb=" O VALSB 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VALSB 33 " --> pdb=" O GLYSB 45 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N CYSSB 96 " --> pdb=" O TRPSB 30 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASPSB 32 " --> pdb=" O CYSSB 96 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THRSB 98 " --> pdb=" O ASPSB 32 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LYSSB 34 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N PHESB 100 " --> pdb=" O LYSSB 34 " (cutoff:3.500A) removed outlier: 12.863A pdb=" N ASNSB 99 " --> pdb=" O LYSSB 219 " (cutoff:3.500A) removed outlier: 12.688A pdb=" N LYSSB 219 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N HISSB 101 " --> pdb=" O METSB 217 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ARGSB 213 " --> pdb=" O LEUSB 105 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VALSB 212 " --> pdb=" O VALSB 140 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VALSB 140 " --> pdb=" O VALSB 212 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEUSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'SD' and resid 34 through 40 removed outlier: 3.545A pdb=" N ILESD 50 " --> pdb=" O TYRSD 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SD' and resid 148 through 155 removed outlier: 3.791A pdb=" N GLYSD 133 " --> pdb=" O METSD 189 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SERSD 139 " --> pdb=" O GLYSD 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'SR' and resid 39 through 40 Processing sheet with id=AA8, first strand: chain 'SD' and resid 223 through 224 removed outlier: 4.336A pdb=" N LEUSg 173 " --> pdb=" O GLYSg 169 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VALSg 166 " --> pdb=" O ARGSg 155 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGSg 155 " --> pdb=" O VALSg 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SE' and resid 75 through 76 removed outlier: 4.271A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SE' and resid 102 through 103 removed outlier: 4.375A pdb=" N ILESE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'SE' and resid 146 through 148 removed outlier: 3.544A pdb=" N ILESE 136 " --> pdb=" O GLYSE 132 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASPSE 171 " --> pdb=" O GLNSE 161 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASPSE 163 " --> pdb=" O ILESE 169 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILESE 169 " --> pdb=" O ASPSE 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SE' and resid 217 through 221 removed outlier: 6.742A pdb=" N VALSE 207 " --> pdb=" O ARGSE 198 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARGSE 198 " --> pdb=" O VALSE 207 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HISSE 209 " --> pdb=" O THRSE 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SE' and resid 229 through 230 removed outlier: 3.532A pdb=" N LYSSE 233 " --> pdb=" O LYSSE 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SF' and resid 18 through 19 Processing sheet with id=AB6, first strand: chain 'SF' and resid 123 through 125 removed outlier: 8.178A pdb=" N ALASF 138 " --> pdb=" O ASNSc 45 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LYSSc 47 " --> pdb=" O ALASF 138 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASPSF 140 " --> pdb=" O LYSSc 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLYSc 19 " --> pdb=" O GLNSc 29 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARGSc 31 " --> pdb=" O VALSc 17 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VALSc 17 " --> pdb=" O ARGSc 31 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N GLUSc 33 " --> pdb=" O THRSc 15 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THRSc 15 " --> pdb=" O GLUSc 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SH' and resid 47 through 52 removed outlier: 3.784A pdb=" N HISSH 91 " --> pdb=" O LYSSH 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SH' and resid 184 through 188 removed outlier: 7.105A pdb=" N ARGSH 152 " --> pdb=" O ASPSH 184 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASNSH 186 " --> pdb=" O ARGSH 152 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILESH 154 " --> pdb=" O ASNSH 186 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLUSH 188 " --> pdb=" O ILESH 154 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VALSH 156 " --> pdb=" O GLUSH 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYSSH 142 " --> pdb=" O ASPSW 54 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHESW 50 " --> pdb=" O VALSH 146 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLUSW 49 " --> pdb=" O ASNSW 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VALSW 63 " --> pdb=" O VALSW 25 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VALSW 25 " --> pdb=" O VALSW 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SI' and resid 3 through 4 removed outlier: 3.758A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SI' and resid 37 through 38 removed outlier: 6.565A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SI' and resid 72 through 74 removed outlier: 6.976A pdb=" N SERSI 66 " --> pdb=" O VALSI 189 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILESI 175 " --> pdb=" O CYSSI 100 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N CYSSI 100 " --> pdb=" O ILESI 175 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILESI 101 " --> pdb=" O VALSI 82 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASPSI 80 " --> pdb=" O LEUSI 103 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASPSI 105 " --> pdb=" O ILESI 78 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILESI 78 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SK' and resid 21 through 24 removed outlier: 3.799A pdb=" N METSK 21 " --> pdb=" O TRPSK 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRPSK 69 " --> pdb=" O METSK 21 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALASK 23 " --> pdb=" O PHESK 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SL' and resid 72 through 79 removed outlier: 17.860A pdb=" N ILESL 72 " --> pdb=" O LEUSL 93 " (cutoff:3.500A) removed outlier: 15.255A pdb=" N LEUSL 93 " --> pdb=" O ILESL 72 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N SERSL 74 " --> pdb=" O ASPSL 91 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASPSL 91 " --> pdb=" O SERSL 74 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VALSL 87 " --> pdb=" O THRSL 78 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARGSL 90 " --> pdb=" O LYSSL 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYSSL 107 " --> pdb=" O ARGSL 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARGSL 101 " --> pdb=" O ILESL 96 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N VALSL 138 " --> pdb=" O ASNSL 108 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SERSL 110 " --> pdb=" O VALSL 138 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHESL 140 " --> pdb=" O SERSL 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VALSL 142 " --> pdb=" O HISSL 112 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THRSL 127 " --> pdb=" O LEUSL 143 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VALSL 145 " --> pdb=" O ILESL 125 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILESL 125 " --> pdb=" O VALSL 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'SP' and resid 76 through 78 removed outlier: 6.189A pdb=" N VALSP 76 " --> pdb=" O GLYSP 95 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N TYRSP 97 " --> pdb=" O VALSP 76 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THRSP 78 " --> pdb=" O TYRSP 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'SQ' and resid 9 through 16 Processing sheet with id=AC7, first strand: chain 'SR' and resid 96 through 98 removed outlier: 5.940A pdb=" N ILESR 96 " --> pdb=" O GLNSR 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'SS' and resid 12 through 13 Processing sheet with id=AC9, first strand: chain 'ST' and resid 81 through 83 Processing sheet with id=AD1, first strand: chain 'ST' and resid 113 through 115 Processing sheet with id=AD2, first strand: chain 'SU' and resid 51 through 55 removed outlier: 4.025A pdb=" N ASPSU 90 " --> pdb=" O LYSSU 51 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEUSU 88 " --> pdb=" O PROSU 53 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARGSU 55 " --> pdb=" O LYSSU 86 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LYSSU 86 " --> pdb=" O ARGSU 55 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'SU' and resid 51 through 55 removed outlier: 4.025A pdb=" N ASPSU 90 " --> pdb=" O LYSSU 51 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEUSU 88 " --> pdb=" O PROSU 53 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARGSU 55 " --> pdb=" O LYSSU 86 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LYSSU 86 " --> pdb=" O ARGSU 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'SV' and resid 32 through 39 removed outlier: 5.416A pdb=" N GLNSV 49 " --> pdb=" O GLUSV 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'SX' and resid 56 through 58 removed outlier: 10.457A pdb=" N PHESX 120 " --> pdb=" O LYSSX 80 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THRSX 82 " --> pdb=" O PHESX 120 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VALSX 122 " --> pdb=" O THRSX 82 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHESX 84 " --> pdb=" O VALSX 122 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LYSSX 124 " --> pdb=" O PHESX 84 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VALSX 125 " --> pdb=" O GLUSX 99 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLUSX 99 " --> pdb=" O VALSX 125 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARGSX 71 " --> pdb=" O LEUSX 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Sa' and resid 20 through 22 Processing sheet with id=AD7, first strand: chain 'Sa' and resid 36 through 43 Processing sheet with id=AD8, first strand: chain 'Sd' and resid 30 through 31 Processing sheet with id=AD9, first strand: chain 'Sg' and resid 4 through 12 removed outlier: 5.802A pdb=" N METSg 5 " --> pdb=" O THRSg 313 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THRSg 313 " --> pdb=" O METSg 5 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEUSg 7 " --> pdb=" O GLNSg 311 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLNSg 311 " --> pdb=" O LEUSg 7 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLYSg 9 " --> pdb=" O VALSg 309 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEUSg 306 " --> pdb=" O TYRSg 302 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARGSg 308 " --> pdb=" O ALASg 300 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALASg 300 " --> pdb=" O ARGSg 308 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THRSg 297 " --> pdb=" O TRPSg 291 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TRPSg 291 " --> pdb=" O THRSg 297 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHESg 299 " --> pdb=" O LEUSg 289 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEUSg 289 " --> pdb=" O PHESg 299 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLYSg 301 " --> pdb=" O THRSg 287 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Sg' and resid 18 through 23 removed outlier: 3.797A pdb=" N ILESg 31 " --> pdb=" O TRPSg 43 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THRSg 39 " --> pdb=" O SERSg 35 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARGSg 57 " --> pdb=" O METSg 42 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYSSg 44 " --> pdb=" O PROSg 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Sg' and resid 66 through 71 removed outlier: 6.643A pdb=" N GLYSg 81 " --> pdb=" O SERSg 67 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VALSg 69 " --> pdb=" O LEUSg 79 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEUSg 79 " --> pdb=" O VALSg 69 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILESg 71 " --> pdb=" O PHESg 77 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHESg 77 " --> pdb=" O ILESg 71 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEUSg 87 " --> pdb=" O ARGSg 100 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARGSg 100 " --> pdb=" O LEUSg 87 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEUSg 89 " --> pdb=" O THRSg 98 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Sg' and resid 108 through 113 removed outlier: 3.894A pdb=" N ILESg 120 " --> pdb=" O TRPSg 132 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Sg' and resid 195 through 200 removed outlier: 7.341A pdb=" N GLYSg 210 " --> pdb=" O ASNSg 196 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VALSg 198 " --> pdb=" O ALASg 208 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALASg 208 " --> pdb=" O VALSg 198 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VALSg 200 " --> pdb=" O LEUSg 206 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEUSg 206 " --> pdb=" O VALSg 200 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYRSg 228 " --> pdb=" O LEUSg 218 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASPSg 220 " --> pdb=" O HISSg 226 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HISSg 226 " --> pdb=" O ASPSg 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Sg' and resid 236 through 241 removed outlier: 6.429A pdb=" N ALASg 251 " --> pdb=" O ASNSg 237 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEUSg 239 " --> pdb=" O CYSSg 249 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYSSg 249 " --> pdb=" O LEUSg 239 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILESg 256 " --> pdb=" O GLUSg 269 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLUSg 269 " --> pdb=" O ILESg 256 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILESg 258 " --> pdb=" O VALSg 267 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASPSg 260 " --> pdb=" O ILESg 265 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILESg 265 " --> pdb=" O ASPSg 260 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'SC' and resid 103 through 116 removed outlier: 5.091A pdb=" N ASPSC 104 " --> pdb=" O GLYSC 131 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLYSC 131 " --> pdb=" O ASPSC 104 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VALSC 106 " --> pdb=" O ALASC 129 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALASC 129 " --> pdb=" O VALSC 106 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYSSC 108 " --> pdb=" O PHESC 127 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VALSC 137 " --> pdb=" O VALSC 163 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'SC' and resid 184 through 188 Processing sheet with id=AE8, first strand: chain 'SG' and resid 14 through 17 removed outlier: 6.585A pdb=" N LYSSG 2 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEUSG 111 " --> pdb=" O LYSSG 2 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASNSG 4 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILESG 113 " --> pdb=" O ASNSG 4 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SERSG 6 " --> pdb=" O ILESG 113 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYSSG 115 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VALSG 108 " --> pdb=" O GLYSG 55 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLYSG 55 " --> pdb=" O VALSG 108 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASNSG 110 " --> pdb=" O SERSG 53 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VALSG 49 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'SG' and resid 14 through 17 removed outlier: 6.585A pdb=" N LYSSG 2 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEUSG 111 " --> pdb=" O LYSSG 2 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASNSG 4 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILESG 113 " --> pdb=" O ASNSG 4 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SERSG 6 " --> pdb=" O ILESG 113 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N LYSSG 115 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VALSG 108 " --> pdb=" O GLYSG 55 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLYSG 55 " --> pdb=" O VALSG 108 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASNSG 110 " --> pdb=" O SERSG 53 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VALSG 49 " --> pdb=" O VALSG 114 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLYSG 55 " --> pdb=" O PROSG 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'SG' and resid 72 through 77 Processing sheet with id=AF2, first strand: chain 'SG' and resid 160 through 162 removed outlier: 3.502A pdb=" N ARGSG 170 " --> pdb=" O LEUSG 162 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'SJ' and resid 140 through 141 removed outlier: 3.542A pdb=" N ASPSJ 158 " --> pdb=" O ARGSJ 136 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'SM' and resid 32 through 33 removed outlier: 3.549A pdb=" N VALSM 110 " --> pdb=" O ALASM 32 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEUSM 49 " --> pdb=" O VALSM 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYSSM 50 " --> pdb=" O ILESM 77 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VALSM 79 " --> pdb=" O CYSSM 50 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEUSM 52 " --> pdb=" O VALSM 79 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'SO' and resid 52 through 57 removed outlier: 3.586A pdb=" N CYSSO 54 " --> pdb=" O VALSO 44 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILESO 95 " --> pdb=" O GLYSO 127 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILESO 129 " --> pdb=" O ILESO 95 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEUSO 97 " --> pdb=" O ILESO 129 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASPSO 131 " --> pdb=" O LEUSO 97 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'SW' and resid 72 through 73 Processing sheet with id=AF7, first strand: chain 'SW' and resid 72 through 73 removed outlier: 6.676A pdb=" N VALSW 103 " --> pdb=" O LEUSW 126 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHESW 128 " --> pdb=" O PHESW 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHESW 101 " --> pdb=" O PHESW 128 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'SY' and resid 6 through 15 removed outlier: 5.758A pdb=" N ILESY 7 " --> pdb=" O LEUSY 28 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEUSY 28 " --> pdb=" O ILESY 7 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THRSY 9 " --> pdb=" O ASPSY 26 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASPSY 26 " --> pdb=" O THRSY 9 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYSSY 11 " --> pdb=" O VALSY 24 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VALSY 24 " --> pdb=" O LYSSY 11 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N METSY 23 " --> pdb=" O GLYSY 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLYSY 67 " --> pdb=" O HISSY 29 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THRSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHESY 60 " --> pdb=" O THRSY 70 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'SZ' and resid 97 through 99 Processing sheet with id=AG1, first strand: chain 'Sb' and resid 44 through 47 removed outlier: 3.741A pdb=" N THRSb 44 " --> pdb=" O VALSb 35 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Sb' and resid 54 through 55 removed outlier: 6.346A pdb=" N VALSb 54 " --> pdb=" O LEUSb 63 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Sf' and resid 106 through 109 Processing sheet with id=AG4, first strand: chain 'Sf' and resid 138 through 140 1457 hydrogen bonds defined for protein. 4143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1308 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 530 basepair parallelities 881 stacking parallelities Total time for adding SS restraints: 66.41 Time building geometry restraints manager: 16.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11667 1.33 - 1.45: 30059 1.45 - 1.57: 36029 1.57 - 1.70: 3462 1.70 - 1.82: 286 Bond restraints: 81503 Sorted by residual: bond pdb=" O3' GS21450 " pdb=" P GS21451 " ideal model delta sigma weight residual 1.607 1.536 0.071 1.50e-02 4.44e+03 2.24e+01 bond pdb=" CA ASNSZ 45 " pdb=" CB ASNSZ 45 " ideal model delta sigma weight residual 1.525 1.589 -0.065 1.47e-02 4.63e+03 1.93e+01 bond pdb=" N ARGSL 35 " pdb=" CA ARGSL 35 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.24e-02 6.50e+03 1.20e+01 bond pdb=" N ASPSR 27 " pdb=" CA ASPSR 27 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" O3' CS2 358 " pdb=" P US2 359 " ideal model delta sigma weight residual 1.607 1.557 0.050 1.50e-02 4.44e+03 1.10e+01 ... (remaining 81498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 117237 3.35 - 6.70: 925 6.70 - 10.05: 94 10.05 - 13.40: 7 13.40 - 16.75: 2 Bond angle restraints: 118265 Sorted by residual: angle pdb=" C LEUSR 109 " pdb=" N ASPSR 110 " pdb=" CA ASPSR 110 " ideal model delta sigma weight residual 121.54 138.29 -16.75 1.91e+00 2.74e-01 7.69e+01 angle pdb=" C ILESg 129 " pdb=" N LYSSg 130 " pdb=" CA LYSSg 130 " ideal model delta sigma weight residual 121.54 135.14 -13.60 1.91e+00 2.74e-01 5.07e+01 angle pdb=" O3' GS2 291 " pdb=" C3' GS2 291 " pdb=" C2' GS2 291 " ideal model delta sigma weight residual 113.70 123.37 -9.67 1.50e+00 4.44e-01 4.16e+01 angle pdb=" C PHESc 34 " pdb=" N METSc 35 " pdb=" CA METSc 35 " ideal model delta sigma weight residual 121.54 132.14 -10.60 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C TYRSL 36 " pdb=" CA TYRSL 36 " pdb=" CB TYRSL 36 " ideal model delta sigma weight residual 110.29 101.38 8.91 1.64e+00 3.72e-01 2.95e+01 ... (remaining 118260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 46996 35.93 - 71.86: 4439 71.86 - 107.78: 538 107.78 - 143.71: 7 143.71 - 179.64: 14 Dihedral angle restraints: 51994 sinusoidal: 37747 harmonic: 14247 Sorted by residual: dihedral pdb=" CA GLUSQ 43 " pdb=" C GLUSQ 43 " pdb=" N PROSQ 44 " pdb=" CA PROSQ 44 " ideal model delta harmonic sigma weight residual 180.00 -117.89 -62.11 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" O4' US2 427 " pdb=" C1' US2 427 " pdb=" N1 US2 427 " pdb=" C2 US2 427 " ideal model delta sinusoidal sigma weight residual 200.00 43.51 156.49 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' CS2 325 " pdb=" C1' CS2 325 " pdb=" N1 CS2 325 " pdb=" C2 CS2 325 " ideal model delta sinusoidal sigma weight residual 200.00 44.88 155.12 1 1.50e+01 4.44e-03 8.14e+01 ... (remaining 51991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 13349 0.077 - 0.154: 1153 0.154 - 0.231: 79 0.231 - 0.308: 15 0.308 - 0.385: 3 Chirality restraints: 14599 Sorted by residual: chirality pdb=" CB VALSI 97 " pdb=" CA VALSI 97 " pdb=" CG1 VALSI 97 " pdb=" CG2 VALSI 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB ILESL 72 " pdb=" CA ILESL 72 " pdb=" CG1 ILESL 72 " pdb=" CG2 ILESL 72 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASPSD 162 " pdb=" N ASPSD 162 " pdb=" C ASPSD 162 " pdb=" CB ASPSD 162 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 14596 not shown) Planarity restraints: 8596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GS2 841 " -0.024 2.00e-02 2.50e+03 3.75e-02 4.23e+01 pdb=" N9 GS2 841 " 0.042 2.00e-02 2.50e+03 pdb=" C8 GS2 841 " 0.010 2.00e-02 2.50e+03 pdb=" N7 GS2 841 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GS2 841 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GS2 841 " -0.047 2.00e-02 2.50e+03 pdb=" O6 GS2 841 " 0.026 2.00e-02 2.50e+03 pdb=" N1 GS2 841 " 0.017 2.00e-02 2.50e+03 pdb=" C2 GS2 841 " -0.088 2.00e-02 2.50e+03 pdb=" N2 GS2 841 " 0.059 2.00e-02 2.50e+03 pdb=" N3 GS2 841 " 0.005 2.00e-02 2.50e+03 pdb=" C4 GS2 841 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CS2 839 " -0.013 2.00e-02 2.50e+03 2.88e-02 1.86e+01 pdb=" N1 CS2 839 " 0.003 2.00e-02 2.50e+03 pdb=" C2 CS2 839 " 0.062 2.00e-02 2.50e+03 pdb=" O2 CS2 839 " -0.032 2.00e-02 2.50e+03 pdb=" N3 CS2 839 " -0.016 2.00e-02 2.50e+03 pdb=" C4 CS2 839 " 0.037 2.00e-02 2.50e+03 pdb=" N4 CS2 839 " -0.026 2.00e-02 2.50e+03 pdb=" C5 CS2 839 " -0.006 2.00e-02 2.50e+03 pdb=" C6 CS2 839 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' US2 918 " -0.054 2.00e-02 2.50e+03 2.75e-02 1.70e+01 pdb=" N1 US2 918 " 0.056 2.00e-02 2.50e+03 pdb=" C2 US2 918 " 0.014 2.00e-02 2.50e+03 pdb=" O2 US2 918 " 0.004 2.00e-02 2.50e+03 pdb=" N3 US2 918 " -0.008 2.00e-02 2.50e+03 pdb=" C4 US2 918 " -0.004 2.00e-02 2.50e+03 pdb=" O4 US2 918 " -0.019 2.00e-02 2.50e+03 pdb=" C5 US2 918 " 0.004 2.00e-02 2.50e+03 pdb=" C6 US2 918 " 0.007 2.00e-02 2.50e+03 ... (remaining 8593 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 815 2.59 - 3.17: 56269 3.17 - 3.74: 139956 3.74 - 4.32: 190445 4.32 - 4.90: 272150 Nonbonded interactions: 659635 Sorted by model distance: nonbonded pdb=" O2 CS2 834 " pdb=" O2 CS2 839 " model vdw 2.012 3.040 nonbonded pdb=" N4 CS2 834 " pdb=" N4 CS2 839 " model vdw 2.021 3.200 nonbonded pdb=" N3 CS2 834 " pdb=" N3 CS2 839 " model vdw 2.097 3.200 nonbonded pdb=" O2' CS21488 " pdb=" OP2 GS21490 " model vdw 2.144 3.040 nonbonded pdb=" NE1 TRPSK 64 " pdb="ZN ZNSd 101 " model vdw 2.200 2.310 ... (remaining 659630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 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: 2.500 Check model and map are aligned: 0.450 Set scattering table: 0.580 Process input model: 191.710 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.003 0.077 81503 Z= 0.209 Angle : 0.786 16.751 118265 Z= 0.409 Chirality : 0.043 0.385 14599 Planarity : 0.007 0.096 8596 Dihedral : 22.009 179.641 42800 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 4879 helix: -2.82 (0.09), residues: 1558 sheet: -0.41 (0.18), residues: 832 loop : -1.30 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPSI 8 HIS 0.018 0.001 HISSg 226 PHE 0.038 0.002 PHESH 19 TYR 0.039 0.002 TYRSK 78 ARG 0.022 0.001 ARGSP 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1572 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1570 time to evaluate : 4.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 68 GLU cc_start: 0.7763 (pp20) cc_final: 0.5675 (pp20) REVERT: SD 127 MET cc_start: 0.8524 (mmm) cc_final: 0.7922 (mmm) REVERT: SF 104 THR cc_start: 0.8421 (p) cc_final: 0.8184 (p) REVERT: SF 168 THR cc_start: 0.8798 (p) cc_final: 0.7639 (p) REVERT: SK 39 ASN cc_start: 0.8208 (t0) cc_final: 0.7959 (t0) REVERT: SP 98 ASN cc_start: 0.8169 (p0) cc_final: 0.7827 (p0) REVERT: SP 111 MET cc_start: 0.7807 (mmp) cc_final: 0.7604 (mmm) REVERT: SQ 114 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7538 (tm-30) REVERT: SS 101 ASN cc_start: 0.8168 (p0) cc_final: 0.7934 (p0) REVERT: ST 134 ILE cc_start: 0.8899 (tp) cc_final: 0.8544 (tt) REVERT: SU 38 ASP cc_start: 0.8309 (m-30) cc_final: 0.7992 (m-30) REVERT: SU 55 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7568 (mtt-85) REVERT: SU 115 THR cc_start: 0.7366 (m) cc_final: 0.6745 (m) REVERT: SV 67 ASP cc_start: 0.7570 (t0) cc_final: 0.7354 (t0) REVERT: Sc 58 LEU cc_start: 0.8942 (mp) cc_final: 0.8740 (mt) REVERT: Sd 20 SER cc_start: 0.8697 (t) cc_final: 0.8464 (p) REVERT: SC 113 GLN cc_start: 0.8341 (mt0) cc_final: 0.8056 (mt0) REVERT: SG 1 MET cc_start: 0.7969 (tmm) cc_final: 0.7737 (ttp) REVERT: SM 48 HIS cc_start: 0.7574 (m170) cc_final: 0.7337 (m-70) REVERT: SM 75 ASN cc_start: 0.6894 (p0) cc_final: 0.6334 (p0) REVERT: SZ 106 GLN cc_start: 0.8220 (tp40) cc_final: 0.7838 (tp40) REVERT: Sf 114 ILE cc_start: 0.5354 (mm) cc_final: 0.4969 (mm) REVERT: Sf 126 CYS cc_start: 0.3687 (m) cc_final: 0.3455 (m) REVERT: Sf 136 PHE cc_start: 0.8004 (p90) cc_final: 0.7710 (p90) REVERT: JD 608 TYR cc_start: 0.7464 (m-10) cc_final: 0.7207 (m-10) outliers start: 2 outliers final: 0 residues processed: 1570 average time/residue: 0.7958 time to fit residues: 2100.0925 Evaluate side-chains 1043 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1043 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 553 optimal weight: 2.9990 chunk 496 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 334 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 513 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 312 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 chunk 594 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 9 GLN SA 33 GLN ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SD 22 ASN ** SD 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 174 HIS SF 110 GLN SF 114 ASN ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 39 GLN ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SH 164 ASN ** SI 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 138 ASN SI 165 GLN SK 39 ASN SL 18 GLN SP 46 ASN SP 103 ASN SQ 11 GLN SQ 142 GLN SR 116 ASN SU 81 GLN SV 2 GLN Sd 26 ASN Sd 45 GLN SG 225 GLN SG 227 GLN SM 55 ASN SN 101 HIS SN 105 ASN SW 70 ASN SZ 46 ASN SZ 112 ASN Se 58 ASN JD 588 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.050163 restraints weight = 255509.044| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.07 r_work: 0.2731 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 81503 Z= 0.258 Angle : 0.649 11.712 118265 Z= 0.337 Chirality : 0.039 0.295 14599 Planarity : 0.006 0.101 8596 Dihedral : 23.005 179.674 32555 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 2.44 % Allowed : 13.89 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 4879 helix: -0.71 (0.12), residues: 1596 sheet: -0.46 (0.17), residues: 885 loop : -1.12 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPLn 5 HIS 0.012 0.001 HISSK 28 PHE 0.027 0.002 PHESN 65 TYR 0.020 0.002 TYRSG 48 ARG 0.010 0.001 ARGSD 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1043 time to evaluate : 4.612 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: SA 84 GLN cc_start: 0.8983 (mt0) cc_final: 0.8655 (mp10) REVERT: SB 76 ASN cc_start: 0.8505 (p0) cc_final: 0.8131 (p0) REVERT: SB 211 PHE cc_start: 0.8492 (m-80) cc_final: 0.8246 (m-80) REVERT: SB 227 LYS cc_start: 0.8854 (pttp) cc_final: 0.8521 (mmmm) REVERT: SD 50 ILE cc_start: 0.9616 (mt) cc_final: 0.9373 (tp) REVERT: SD 81 GLU cc_start: 0.8551 (tp30) cc_final: 0.8269 (tp30) REVERT: SD 87 TYR cc_start: 0.8631 (m-10) cc_final: 0.7983 (m-10) REVERT: SF 44 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9012 (mtpt) REVERT: SF 104 THR cc_start: 0.8920 (p) cc_final: 0.8642 (p) REVERT: SF 195 GLU cc_start: 0.9342 (tp30) cc_final: 0.9078 (tp30) REVERT: SI 6 ASP cc_start: 0.8924 (p0) cc_final: 0.8451 (p0) REVERT: SK 13 GLU cc_start: 0.8676 (pt0) cc_final: 0.8471 (pt0) REVERT: SK 18 GLU cc_start: 0.8489 (tp30) cc_final: 0.7974 (tp30) REVERT: SK 26 ASP cc_start: 0.8652 (t0) cc_final: 0.8435 (t0) REVERT: SK 31 LYS cc_start: 0.9270 (mttm) cc_final: 0.8854 (tptt) REVERT: SK 80 ARG cc_start: 0.8887 (ttm-80) cc_final: 0.8642 (tpp-160) REVERT: SL 11 GLN cc_start: 0.8111 (mm110) cc_final: 0.7901 (mm-40) REVERT: SP 34 MET cc_start: 0.9245 (mmm) cc_final: 0.8614 (mmt) REVERT: SP 41 GLN cc_start: 0.8857 (mp10) cc_final: 0.8569 (mp10) REVERT: SP 103 ASN cc_start: 0.8979 (m110) cc_final: 0.8721 (m-40) REVERT: SQ 80 GLN cc_start: 0.8962 (mt0) cc_final: 0.8722 (mt0) REVERT: SQ 114 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8433 (tm-30) REVERT: SR 1 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6206 (tpp) REVERT: SR 75 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9119 (mm-30) REVERT: SS 63 GLU cc_start: 0.8711 (pt0) cc_final: 0.7847 (pm20) REVERT: SS 95 TYR cc_start: 0.8767 (m-10) cc_final: 0.8397 (m-10) REVERT: ST 5 THR cc_start: 0.9070 (m) cc_final: 0.8692 (m) REVERT: ST 10 ASN cc_start: 0.9089 (t0) cc_final: 0.8877 (t0) REVERT: SU 18 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8319 (t-90) REVERT: SV 1 MET cc_start: 0.6992 (ppp) cc_final: 0.6285 (ppp) REVERT: SX 127 ASN cc_start: 0.9070 (t0) cc_final: 0.8784 (t0) REVERT: Sc 10 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8601 (ttmm) REVERT: Sc 16 LYS cc_start: 0.8769 (ttpp) cc_final: 0.8424 (ttpp) REVERT: Sc 31 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8230 (ttm-80) REVERT: Sc 37 ASP cc_start: 0.6934 (p0) cc_final: 0.6125 (p0) REVERT: Sc 54 ASP cc_start: 0.7678 (m-30) cc_final: 0.7373 (m-30) REVERT: Sc 58 LEU cc_start: 0.9305 (mp) cc_final: 0.8893 (mt) REVERT: Sd 34 TYR cc_start: 0.9013 (m-80) cc_final: 0.8668 (m-80) REVERT: Sg 140 TYR cc_start: 0.8124 (t80) cc_final: 0.7709 (t80) REVERT: SC 221 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8680 (m-30) REVERT: SG 43 GLU cc_start: 0.7922 (pp20) cc_final: 0.7718 (pm20) REVERT: SG 45 TRP cc_start: 0.8940 (m100) cc_final: 0.8544 (m100) REVERT: SG 57 ASP cc_start: 0.8817 (t0) cc_final: 0.8574 (t0) REVERT: SG 227 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7353 (mm-40) REVERT: SJ 28 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8781 (mt-10) REVERT: SJ 48 PHE cc_start: 0.8861 (t80) cc_final: 0.8651 (t80) REVERT: SM 48 HIS cc_start: 0.8345 (m170) cc_final: 0.7825 (m-70) REVERT: SN 65 PHE cc_start: 0.8422 (m-80) cc_final: 0.8197 (m-80) REVERT: SN 144 SER cc_start: 0.9243 (m) cc_final: 0.9017 (p) REVERT: SO 60 MET cc_start: 0.8813 (mmt) cc_final: 0.8518 (mmp) REVERT: SO 124 MET cc_start: 0.8949 (mmp) cc_final: 0.8640 (tpp) REVERT: SW 15 ASN cc_start: 0.9225 (t0) cc_final: 0.8978 (t0) REVERT: SW 111 MET cc_start: 0.8317 (mtp) cc_final: 0.8093 (mtp) REVERT: SZ 60 LYS cc_start: 0.9301 (tppt) cc_final: 0.9038 (tppt) REVERT: SZ 90 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8789 (tm-30) REVERT: Sb 6 ASP cc_start: 0.8806 (t0) cc_final: 0.8532 (t0) REVERT: Sb 15 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8057 (mm-30) REVERT: Sf 132 MET cc_start: 0.7784 (ttt) cc_final: 0.7043 (tpp) REVERT: JD 643 PHE cc_start: 0.6116 (t80) cc_final: 0.5792 (t80) outliers start: 104 outliers final: 65 residues processed: 1098 average time/residue: 0.7175 time to fit residues: 1354.6233 Evaluate side-chains 1019 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 948 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 20 MET Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SB residue 44 ILE Chi-restraints excluded: chain SB residue 121 ILE Chi-restraints excluded: chain SB residue 198 GLU Chi-restraints excluded: chain SB residue 231 LEU Chi-restraints excluded: chain SD residue 149 SER Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 44 LYS Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SH residue 49 LYS Chi-restraints excluded: chain SH residue 172 THR Chi-restraints excluded: chain SH residue 180 LEU Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 71 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SR residue 1 MET Chi-restraints excluded: chain SR residue 20 TYR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain ST residue 51 ASN Chi-restraints excluded: chain ST residue 66 LEU Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SV residue 2 GLN Chi-restraints excluded: chain SV residue 9 VAL Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 101 SER Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 227 GLN Chi-restraints excluded: chain SJ residue 22 LYS Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 160 SER Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 52 VAL Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SW residue 96 SER Chi-restraints excluded: chain SW residue 105 THR Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 46 ASN Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Sb residue 27 SER Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Se residue 53 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 406 optimal weight: 2.9990 chunk 652 optimal weight: 0.9980 chunk 580 optimal weight: 0.0000 chunk 41 optimal weight: 10.0000 chunk 618 optimal weight: 7.9990 chunk 392 optimal weight: 5.9990 chunk 442 optimal weight: 4.9990 chunk 592 optimal weight: 6.9990 chunk 520 optimal weight: 9.9990 chunk 176 optimal weight: 0.1980 chunk 208 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 22 ASN SH 33 ASN ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 18 GLN SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 116 ASN SU 81 GLN ** SU 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 2 GLN Sd 45 GLN ** SG 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 227 GLN SM 55 ASN SW 70 ASN SZ 106 GLN ** Se 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sf 135 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.050046 restraints weight = 255598.389| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.07 r_work: 0.2730 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 81503 Z= 0.191 Angle : 0.589 11.818 118265 Z= 0.305 Chirality : 0.037 0.277 14599 Planarity : 0.004 0.097 8596 Dihedral : 22.938 179.900 32555 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 2.95 % Allowed : 16.00 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4879 helix: 0.03 (0.13), residues: 1597 sheet: -0.49 (0.17), residues: 882 loop : -1.02 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPSM 88 HIS 0.012 0.001 HISSK 28 PHE 0.020 0.001 PHESN 65 TYR 0.017 0.001 TYRSD 34 ARG 0.010 0.000 ARGSB 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1000 time to evaluate : 6.051 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: Ln 2 ARG cc_start: 0.8025 (ttt180) cc_final: 0.7423 (ttt-90) REVERT: SA 11 LYS cc_start: 0.9349 (mmmt) cc_final: 0.9065 (mmmt) REVERT: SB 211 PHE cc_start: 0.8543 (m-80) cc_final: 0.8290 (m-80) REVERT: SB 227 LYS cc_start: 0.8733 (pttp) cc_final: 0.8397 (mmmm) REVERT: SD 50 ILE cc_start: 0.9630 (mt) cc_final: 0.9360 (tp) REVERT: SD 68 GLU cc_start: 0.8675 (pp20) cc_final: 0.7059 (pp20) REVERT: SD 87 TYR cc_start: 0.8689 (m-10) cc_final: 0.8071 (m-10) REVERT: SD 169 ASP cc_start: 0.8584 (t0) cc_final: 0.8291 (t0) REVERT: SF 38 TYR cc_start: 0.8801 (m-80) cc_final: 0.8574 (m-10) REVERT: SF 44 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9140 (mtpt) REVERT: SF 48 TYR cc_start: 0.8621 (m-80) cc_final: 0.8396 (m-80) REVERT: SF 104 THR cc_start: 0.8899 (p) cc_final: 0.8654 (p) REVERT: SH 33 ASN cc_start: 0.8073 (m110) cc_final: 0.7850 (m-40) REVERT: SH 97 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8511 (tp40) REVERT: SI 149 TYR cc_start: 0.8789 (m-80) cc_final: 0.8552 (m-80) REVERT: SK 8 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8267 (mmm-85) REVERT: SK 13 GLU cc_start: 0.8715 (pt0) cc_final: 0.8108 (pp20) REVERT: SK 17 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8547 (mmtt) REVERT: SK 26 ASP cc_start: 0.8744 (t0) cc_final: 0.8425 (t0) REVERT: SK 80 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8634 (tpp-160) REVERT: SL 3 ASP cc_start: 0.8285 (t0) cc_final: 0.7955 (t70) REVERT: SL 7 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: SL 11 GLN cc_start: 0.8068 (mm110) cc_final: 0.7664 (mm-40) REVERT: SL 49 GLU cc_start: 0.8770 (mp0) cc_final: 0.8554 (mt-10) REVERT: SP 34 MET cc_start: 0.9266 (mmm) cc_final: 0.8763 (mmt) REVERT: SP 56 LEU cc_start: 0.9404 (tp) cc_final: 0.9164 (tt) REVERT: SP 93 MET cc_start: 0.8951 (mmm) cc_final: 0.8612 (mmm) REVERT: SP 103 ASN cc_start: 0.8896 (m110) cc_final: 0.8672 (m-40) REVERT: SQ 114 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8608 (tm-30) REVERT: SR 74 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8180 (tm-30) REVERT: SR 75 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9156 (mm-30) REVERT: SS 63 GLU cc_start: 0.8698 (pt0) cc_final: 0.7898 (pm20) REVERT: SS 95 TYR cc_start: 0.8800 (m-10) cc_final: 0.8597 (m-10) REVERT: SS 101 ASN cc_start: 0.8700 (p0) cc_final: 0.8247 (t0) REVERT: SS 110 ASP cc_start: 0.8419 (m-30) cc_final: 0.8215 (m-30) REVERT: SS 113 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.8430 (ttp-110) REVERT: ST 10 ASN cc_start: 0.9056 (t0) cc_final: 0.8736 (t0) REVERT: ST 126 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7826 (tm-30) REVERT: ST 130 ASP cc_start: 0.9264 (p0) cc_final: 0.8879 (p0) REVERT: SU 18 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8307 (t-90) REVERT: SU 55 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.8184 (mtt-85) REVERT: SU 113 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8625 (tm-30) REVERT: SV 1 MET cc_start: 0.7476 (ppp) cc_final: 0.6774 (ppp) REVERT: Sa 25 ASN cc_start: 0.9223 (t0) cc_final: 0.8825 (t0) REVERT: Sc 10 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8630 (ttmm) REVERT: Sc 16 LYS cc_start: 0.8823 (ttpp) cc_final: 0.8034 (ttpp) REVERT: Sc 31 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8463 (ttm-80) REVERT: Sc 54 ASP cc_start: 0.7863 (m-30) cc_final: 0.7128 (m-30) REVERT: Sd 12 ARG cc_start: 0.8425 (mmt-90) cc_final: 0.8102 (mmt-90) REVERT: Sd 34 TYR cc_start: 0.8985 (m-80) cc_final: 0.8663 (m-80) REVERT: Sg 5 MET cc_start: 0.8333 (mmp) cc_final: 0.8071 (mmp) REVERT: SC 72 ASP cc_start: 0.9198 (m-30) cc_final: 0.8985 (m-30) REVERT: SC 113 GLN cc_start: 0.9062 (mt0) cc_final: 0.8771 (mt0) REVERT: SC 221 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8594 (m-30) REVERT: SG 43 GLU cc_start: 0.8060 (pp20) cc_final: 0.7831 (pm20) REVERT: SJ 28 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8772 (mt-10) REVERT: SJ 48 PHE cc_start: 0.8884 (t80) cc_final: 0.8542 (t80) REVERT: SJ 59 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8532 (tm-30) REVERT: SM 48 HIS cc_start: 0.8283 (m170) cc_final: 0.7739 (m-70) REVERT: SM 58 GLU cc_start: 0.6643 (mp0) cc_final: 0.6296 (mp0) REVERT: SO 60 MET cc_start: 0.8881 (mmt) cc_final: 0.8565 (mmp) REVERT: SW 85 ASP cc_start: 0.8584 (t0) cc_final: 0.8264 (t0) REVERT: SW 114 GLU cc_start: 0.8815 (tp30) cc_final: 0.8535 (tm-30) REVERT: SZ 60 LYS cc_start: 0.9326 (tppt) cc_final: 0.9071 (tppt) REVERT: SZ 89 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8479 (pm20) REVERT: Sb 15 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7916 (mm-30) REVERT: Se 40 ARG cc_start: 0.8470 (mmt-90) cc_final: 0.8253 (mmp80) REVERT: Sf 132 MET cc_start: 0.7802 (ttt) cc_final: 0.7092 (tpp) REVERT: JD 584 ARG cc_start: 0.8226 (ptp-170) cc_final: 0.7434 (ptp90) REVERT: JD 610 GLU cc_start: 0.7011 (tt0) cc_final: 0.6810 (tt0) REVERT: JD 638 ILE cc_start: 0.8629 (tp) cc_final: 0.8414 (tp) outliers start: 126 outliers final: 69 residues processed: 1074 average time/residue: 0.7361 time to fit residues: 1375.7069 Evaluate side-chains 1019 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 944 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SB residue 44 ILE Chi-restraints excluded: chain SB residue 198 GLU Chi-restraints excluded: chain SB residue 231 LEU Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 44 LYS Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SH residue 180 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 155 ASN Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 71 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 7 GLU Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 55 SER Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 113 ILE Chi-restraints excluded: chain SR residue 20 TYR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 26 ASN Chi-restraints excluded: chain SR residue 92 ASP Chi-restraints excluded: chain SR residue 116 ASN Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 60 THR Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain ST residue 51 ASN Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain ST residue 131 LEU Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SV residue 2 GLN Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain Sa residue 45 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 101 SER Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 160 SER Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 24 THR Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SW residue 105 THR Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Sb residue 27 SER Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Se residue 53 LYS Chi-restraints excluded: chain Sf residue 105 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 571 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 630 optimal weight: 1.9990 chunk 592 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 387 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 542 optimal weight: 9.9990 chunk 570 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 43 ASN SD 22 ASN SE 142 HIS SE 209 HIS ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 88 ASN SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SU 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sc 29 GLN Sd 45 GLN SG 110 ASN SW 70 ASN SZ 46 ASN ** Se 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JD 587 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.047112 restraints weight = 257651.406| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.09 r_work: 0.2648 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 81503 Z= 0.333 Angle : 0.638 12.516 118265 Z= 0.329 Chirality : 0.040 0.269 14599 Planarity : 0.005 0.096 8596 Dihedral : 22.887 179.329 32555 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 3.58 % Allowed : 17.94 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.76 (0.12), residues: 4879 helix: 0.36 (0.13), residues: 1617 sheet: -0.60 (0.17), residues: 897 loop : -1.01 (0.12), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPLn 5 HIS 0.011 0.001 HISSS 125 PHE 0.022 0.002 PHESN 65 TYR 0.020 0.002 TYRSD 34 ARG 0.012 0.001 ARGSD 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 933 time to evaluate : 4.643 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: Ln 1 MET cc_start: 0.6305 (ttm) cc_final: 0.5844 (ttt) REVERT: Ln 2 ARG cc_start: 0.8244 (ttt180) cc_final: 0.7534 (ttt-90) REVERT: SA 9 GLN cc_start: 0.9248 (mm-40) cc_final: 0.9037 (mm-40) REVERT: SA 11 LYS cc_start: 0.9286 (mmmt) cc_final: 0.9032 (mmtt) REVERT: SA 84 GLN cc_start: 0.9093 (mt0) cc_final: 0.8749 (mp10) REVERT: SB 76 ASN cc_start: 0.8419 (p0) cc_final: 0.8129 (p0) REVERT: SB 103 MET cc_start: 0.9181 (tmm) cc_final: 0.8911 (tmm) REVERT: SB 211 PHE cc_start: 0.8609 (m-80) cc_final: 0.8292 (m-80) REVERT: SD 87 TYR cc_start: 0.8730 (m-10) cc_final: 0.8402 (m-10) REVERT: SD 169 ASP cc_start: 0.8576 (t0) cc_final: 0.8259 (t0) REVERT: SE 199 GLU cc_start: 0.8804 (mp0) cc_final: 0.8554 (mp0) REVERT: SF 32 ASP cc_start: 0.9037 (t0) cc_final: 0.8835 (t0) REVERT: SF 48 TYR cc_start: 0.8752 (m-80) cc_final: 0.8476 (m-80) REVERT: SH 32 MET cc_start: 0.8406 (mpp) cc_final: 0.8178 (mpp) REVERT: SH 97 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8626 (tp40) REVERT: SI 88 ASN cc_start: 0.9215 (m-40) cc_final: 0.8729 (t0) REVERT: SK 9 ILE cc_start: 0.9365 (mm) cc_final: 0.9097 (mm) REVERT: SK 13 GLU cc_start: 0.8779 (pt0) cc_final: 0.8157 (pt0) REVERT: SK 17 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8607 (mmtt) REVERT: SK 26 ASP cc_start: 0.8748 (t0) cc_final: 0.8369 (t0) REVERT: SK 31 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9069 (tttp) REVERT: SK 39 ASN cc_start: 0.8952 (t0) cc_final: 0.8476 (t0) REVERT: SK 80 ARG cc_start: 0.8901 (ttm-80) cc_final: 0.8676 (tpp-160) REVERT: SL 3 ASP cc_start: 0.8371 (t0) cc_final: 0.8045 (t0) REVERT: SL 7 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: SL 49 GLU cc_start: 0.8846 (mp0) cc_final: 0.8623 (mt-10) REVERT: SL 119 ASP cc_start: 0.8079 (p0) cc_final: 0.7609 (p0) REVERT: SP 34 MET cc_start: 0.9251 (mmm) cc_final: 0.8925 (mmm) REVERT: SP 66 GLU cc_start: 0.8995 (pm20) cc_final: 0.8757 (pm20) REVERT: SP 103 ASN cc_start: 0.8883 (m110) cc_final: 0.8655 (m-40) REVERT: SQ 114 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8686 (tm-30) REVERT: SR 1 MET cc_start: 0.6464 (tpp) cc_final: 0.6224 (ttm) REVERT: SR 53 TYR cc_start: 0.9467 (t80) cc_final: 0.9241 (t80) REVERT: SR 74 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8221 (tm-30) REVERT: SR 75 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9185 (mm-30) REVERT: SR 76 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8846 (mp0) REVERT: SS 63 GLU cc_start: 0.8686 (pt0) cc_final: 0.7899 (pm20) REVERT: SS 83 PHE cc_start: 0.9008 (t80) cc_final: 0.8541 (t80) REVERT: SS 87 GLN cc_start: 0.7943 (mp10) cc_final: 0.7690 (mp10) REVERT: SS 91 LYS cc_start: 0.9383 (ttmm) cc_final: 0.8735 (tmtt) REVERT: SS 95 TYR cc_start: 0.8831 (m-10) cc_final: 0.8420 (m-10) REVERT: SS 96 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8830 (p) REVERT: ST 10 ASN cc_start: 0.9085 (t0) cc_final: 0.8760 (t0) REVERT: ST 49 ASP cc_start: 0.8911 (t0) cc_final: 0.8549 (t70) REVERT: ST 112 MET cc_start: 0.9005 (mmp) cc_final: 0.8176 (mpp) REVERT: ST 126 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7737 (tm-30) REVERT: ST 130 ASP cc_start: 0.9248 (p0) cc_final: 0.8964 (p0) REVERT: SU 18 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8394 (t-90) REVERT: SU 113 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8699 (tm-30) REVERT: SV 1 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6668 (ppp) REVERT: SV 66 ASP cc_start: 0.9074 (p0) cc_final: 0.8805 (p0) REVERT: SX 127 ASN cc_start: 0.9052 (t0) cc_final: 0.8785 (t0) REVERT: Sa 25 ASN cc_start: 0.9218 (t0) cc_final: 0.8829 (t0) REVERT: Sc 10 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8584 (ttmm) REVERT: Sc 31 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8536 (ttm-80) REVERT: Sd 12 ARG cc_start: 0.8524 (mmt-90) cc_final: 0.8150 (mmt-90) REVERT: Sd 34 TYR cc_start: 0.9061 (m-80) cc_final: 0.8740 (m-80) REVERT: Sg 5 MET cc_start: 0.8520 (mmp) cc_final: 0.7887 (mmm) REVERT: Sg 142 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8118 (p) REVERT: SC 105 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8037 (tm-30) REVERT: SG 57 ASP cc_start: 0.8947 (t0) cc_final: 0.8694 (t0) REVERT: SG 146 ASN cc_start: 0.9093 (t0) cc_final: 0.8819 (t0) REVERT: SJ 28 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8926 (mt-10) REVERT: SJ 59 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8561 (tm-30) REVERT: SM 48 HIS cc_start: 0.8309 (m170) cc_final: 0.7696 (m-70) REVERT: SM 68 LEU cc_start: 0.8659 (mm) cc_final: 0.8458 (mt) REVERT: SN 142 GLU cc_start: 0.8441 (pm20) cc_final: 0.8042 (pm20) REVERT: SN 144 SER cc_start: 0.9183 (m) cc_final: 0.8898 (p) REVERT: SO 60 MET cc_start: 0.8831 (mmt) cc_final: 0.8539 (mmm) REVERT: SW 85 ASP cc_start: 0.8739 (t0) cc_final: 0.8450 (t0) REVERT: SW 114 GLU cc_start: 0.8872 (tp30) cc_final: 0.8458 (tm-30) REVERT: SW 115 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.8819 (pt0) REVERT: SY 42 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8562 (tm-30) REVERT: SZ 46 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8091 (t0) REVERT: SZ 50 PHE cc_start: 0.8870 (m-80) cc_final: 0.8575 (m-80) REVERT: SZ 60 LYS cc_start: 0.9346 (tppt) cc_final: 0.9118 (tppt) REVERT: SZ 89 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: SZ 98 LYS cc_start: 0.8511 (mttt) cc_final: 0.8146 (mttm) REVERT: Sb 15 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8087 (mm-30) REVERT: Sf 132 MET cc_start: 0.7822 (ttt) cc_final: 0.7141 (tpp) REVERT: JD 610 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: JD 638 ILE cc_start: 0.8568 (tp) cc_final: 0.8269 (tp) outliers start: 153 outliers final: 103 residues processed: 1018 average time/residue: 0.7037 time to fit residues: 1242.5159 Evaluate side-chains 989 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 876 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 20 MET Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 152 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SB residue 44 ILE Chi-restraints excluded: chain SB residue 121 ILE Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 149 SER Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SD residue 160 SER Chi-restraints excluded: chain SD residue 224 SER Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 31 ASN Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 88 SER Chi-restraints excluded: chain SH residue 180 LEU Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 72 CYS Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 82 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 155 ASN Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 71 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 7 GLU Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 55 SER Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SR residue 20 TYR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 26 ASN Chi-restraints excluded: chain SR residue 92 ASP Chi-restraints excluded: chain SR residue 110 ASP Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 60 THR Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain SS residue 107 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 51 ASN Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 29 VAL Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 2 GLN Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain SV residue 79 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain SX residue 75 ILE Chi-restraints excluded: chain Sa residue 45 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 177 TRP Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SC residue 249 SER Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 46 VAL Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 35 ILE Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 24 THR Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SN residue 52 VAL Chi-restraints excluded: chain SN residue 60 VAL Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SW residue 115 GLU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 96 LEU Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 46 ASN Chi-restraints excluded: chain SZ residue 83 LEU Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Se residue 53 LYS Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 603 ASN Chi-restraints excluded: chain JD residue 610 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 16 optimal weight: 10.0000 chunk 458 optimal weight: 8.9990 chunk 412 optimal weight: 9.9990 chunk 542 optimal weight: 0.9990 chunk 367 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 401 optimal weight: 0.3980 chunk 242 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 22 ASN SE 142 HIS ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 84 ASN SL 18 GLN SP 104 GLN SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 83 GLN SU 81 GLN ** SU 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 2 GLN Sg 311 GLN SG 177 GLN SM 55 ASN SW 70 ASN SW 92 ASN Se 15 GLN JD 587 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048792 restraints weight = 256764.573| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.07 r_work: 0.2695 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 81503 Z= 0.182 Angle : 0.580 10.896 118265 Z= 0.300 Chirality : 0.037 0.279 14599 Planarity : 0.004 0.095 8596 Dihedral : 22.889 178.620 32555 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 3.07 % Allowed : 19.34 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.56 (0.12), residues: 4879 helix: 0.57 (0.13), residues: 1610 sheet: -0.53 (0.18), residues: 867 loop : -0.91 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLn 5 HIS 0.006 0.001 HISSS 125 PHE 0.026 0.001 PHESN 65 TYR 0.017 0.001 TYRSD 34 ARG 0.010 0.000 ARGSZ 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 946 time to evaluate : 4.589 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: Ln 1 MET cc_start: 0.6385 (ttm) cc_final: 0.5947 (ttt) REVERT: Ln 2 ARG cc_start: 0.8348 (ttt180) cc_final: 0.7518 (ttt-90) REVERT: SA 11 LYS cc_start: 0.9230 (mmmt) cc_final: 0.9007 (mmtt) REVERT: SB 76 ASN cc_start: 0.8434 (p0) cc_final: 0.8058 (p0) REVERT: SB 103 MET cc_start: 0.9098 (tmm) cc_final: 0.8821 (tmm) REVERT: SB 211 PHE cc_start: 0.8574 (m-80) cc_final: 0.8317 (m-80) REVERT: SB 223 PHE cc_start: 0.7983 (t80) cc_final: 0.7665 (t80) REVERT: SD 87 TYR cc_start: 0.8691 (m-10) cc_final: 0.8324 (m-10) REVERT: SD 123 LEU cc_start: 0.9320 (tp) cc_final: 0.9102 (tp) REVERT: SD 169 ASP cc_start: 0.8614 (t0) cc_final: 0.8179 (t0) REVERT: SE 199 GLU cc_start: 0.8658 (mp0) cc_final: 0.8346 (mp0) REVERT: SE 232 ASN cc_start: 0.9086 (t0) cc_final: 0.8870 (t0) REVERT: SF 48 TYR cc_start: 0.8713 (m-80) cc_final: 0.8436 (m-80) REVERT: SF 73 THR cc_start: 0.9462 (m) cc_final: 0.9250 (p) REVERT: SH 39 GLN cc_start: 0.8186 (mp-120) cc_final: 0.7906 (mp10) REVERT: SH 97 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8550 (tp40) REVERT: SI 88 ASN cc_start: 0.9191 (m-40) cc_final: 0.8706 (t0) REVERT: SK 9 ILE cc_start: 0.9394 (mm) cc_final: 0.9070 (mm) REVERT: SK 13 GLU cc_start: 0.8741 (pt0) cc_final: 0.8070 (pt0) REVERT: SK 17 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8609 (mmtt) REVERT: SK 26 ASP cc_start: 0.8819 (t0) cc_final: 0.8392 (t0) REVERT: SK 31 LYS cc_start: 0.9337 (mmmm) cc_final: 0.8902 (tptt) REVERT: SK 39 ASN cc_start: 0.8959 (t0) cc_final: 0.8579 (t0) REVERT: SK 80 ARG cc_start: 0.8895 (ttm-80) cc_final: 0.8665 (tpp-160) REVERT: SL 3 ASP cc_start: 0.8324 (t0) cc_final: 0.7991 (t0) REVERT: SL 7 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: SL 11 GLN cc_start: 0.8049 (mm110) cc_final: 0.7727 (mm-40) REVERT: SL 119 ASP cc_start: 0.8022 (p0) cc_final: 0.7558 (p0) REVERT: SP 34 MET cc_start: 0.9259 (mmm) cc_final: 0.8937 (mmm) REVERT: SP 66 GLU cc_start: 0.9014 (pm20) cc_final: 0.8788 (pm20) REVERT: SP 103 ASN cc_start: 0.8819 (m110) cc_final: 0.8609 (m-40) REVERT: SQ 80 GLN cc_start: 0.8903 (mt0) cc_final: 0.8518 (mt0) REVERT: SQ 114 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8676 (tm-30) REVERT: SR 1 MET cc_start: 0.6538 (tpp) cc_final: 0.6247 (mtm) REVERT: SR 74 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8215 (tm-30) REVERT: SS 58 GLU cc_start: 0.8169 (pm20) cc_final: 0.7938 (pm20) REVERT: SS 63 GLU cc_start: 0.8708 (pt0) cc_final: 0.7941 (pm20) REVERT: SS 89 ASP cc_start: 0.8028 (t0) cc_final: 0.7651 (t70) REVERT: SS 91 LYS cc_start: 0.9384 (ttmm) cc_final: 0.8855 (tmtt) REVERT: SS 101 ASN cc_start: 0.8844 (p0) cc_final: 0.8514 (t0) REVERT: ST 10 ASN cc_start: 0.9029 (t0) cc_final: 0.8693 (t0) REVERT: ST 49 ASP cc_start: 0.8887 (t0) cc_final: 0.8502 (t70) REVERT: ST 126 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7606 (tm-30) REVERT: ST 130 ASP cc_start: 0.9216 (p0) cc_final: 0.8959 (p0) REVERT: ST 137 GLN cc_start: 0.8665 (mp10) cc_final: 0.8400 (mp10) REVERT: SU 18 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8395 (t-90) REVERT: SU 55 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.8195 (mtt-85) REVERT: SU 113 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8540 (tm-30) REVERT: SV 1 MET cc_start: 0.7369 (ppp) cc_final: 0.6687 (ppp) REVERT: SX 127 ASN cc_start: 0.9053 (t0) cc_final: 0.8763 (t0) REVERT: Sa 25 ASN cc_start: 0.9234 (t0) cc_final: 0.8837 (t0) REVERT: Sc 10 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8680 (ttmm) REVERT: Sc 31 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8490 (ttm-80) REVERT: Sc 35 MET cc_start: 0.7468 (ptp) cc_final: 0.7000 (ptp) REVERT: Sd 12 ARG cc_start: 0.8419 (mmt-90) cc_final: 0.7997 (mmt-90) REVERT: Sd 34 TYR cc_start: 0.9053 (m-80) cc_final: 0.8827 (m-80) REVERT: Sg 5 MET cc_start: 0.8549 (mmp) cc_final: 0.8018 (mmm) REVERT: SC 72 ASP cc_start: 0.9257 (m-30) cc_final: 0.9031 (m-30) REVERT: SC 105 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8155 (tm-30) REVERT: SC 221 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: SC 248 TYR cc_start: 0.9436 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: SG 57 ASP cc_start: 0.8939 (t0) cc_final: 0.8705 (t0) REVERT: SG 110 ASN cc_start: 0.8324 (t160) cc_final: 0.7854 (t0) REVERT: SG 146 ASN cc_start: 0.9051 (t0) cc_final: 0.8761 (t0) REVERT: SJ 28 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8851 (mt-10) REVERT: SJ 59 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8501 (tm-30) REVERT: SJ 107 GLU cc_start: 0.9217 (tp30) cc_final: 0.8825 (tp30) REVERT: SM 31 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6527 (pp) REVERT: SM 48 HIS cc_start: 0.8294 (m170) cc_final: 0.7686 (m-70) REVERT: SN 142 GLU cc_start: 0.8480 (pm20) cc_final: 0.8127 (pm20) REVERT: SN 144 SER cc_start: 0.9141 (m) cc_final: 0.8858 (p) REVERT: SW 85 ASP cc_start: 0.8600 (t0) cc_final: 0.8317 (t0) REVERT: SW 111 MET cc_start: 0.8427 (mtp) cc_final: 0.8107 (mtp) REVERT: SW 114 GLU cc_start: 0.8809 (tp30) cc_final: 0.8465 (tm-30) REVERT: SY 42 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8682 (tp30) REVERT: SZ 50 PHE cc_start: 0.8947 (m-80) cc_final: 0.8652 (m-80) REVERT: SZ 60 LYS cc_start: 0.9297 (tppt) cc_final: 0.9087 (tppt) REVERT: SZ 89 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8438 (pm20) REVERT: SZ 98 LYS cc_start: 0.8568 (mttt) cc_final: 0.8343 (mttt) REVERT: Sb 15 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8148 (mm-30) REVERT: Sf 132 MET cc_start: 0.7894 (ttt) cc_final: 0.7315 (tpp) REVERT: JD 611 GLN cc_start: 0.9159 (mt0) cc_final: 0.8869 (mt0) REVERT: JD 638 ILE cc_start: 0.8593 (tp) cc_final: 0.8263 (tp) outliers start: 131 outliers final: 88 residues processed: 1026 average time/residue: 0.7604 time to fit residues: 1357.4377 Evaluate side-chains 991 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 896 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SD residue 160 SER Chi-restraints excluded: chain SD residue 162 ASP Chi-restraints excluded: chain SD residue 176 LEU Chi-restraints excluded: chain SD residue 224 SER Chi-restraints excluded: chain SE residue 98 ASN Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SF residue 31 ASN Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SF residue 172 CYS Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 88 SER Chi-restraints excluded: chain SH residue 180 LEU Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 72 CYS Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 45 VAL Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 7 GLU Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SR residue 20 TYR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 18 THR Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain ST residue 51 ASN Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain SV residue 79 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain Sa residue 45 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain Sg residue 177 TRP Chi-restraints excluded: chain SC residue 101 SER Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 46 VAL Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 35 ILE Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SN residue 60 VAL Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 96 LEU Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 83 LEU Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain SZ residue 97 ILE Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Se residue 53 LYS Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 603 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 332 optimal weight: 0.9990 chunk 414 optimal weight: 2.9990 chunk 267 optimal weight: 0.0470 chunk 301 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 580 optimal weight: 6.9990 chunk 393 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 531 optimal weight: 5.9990 chunk 629 optimal weight: 5.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 22 ASN SD 174 HIS SE 142 HIS ** SF 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 84 ASN SI 165 GLN ** SP 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 81 GLN ** SU 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sd 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sd 45 GLN SC 120 GLN SG 225 GLN SW 70 ASN SW 92 ASN SY 94 HIS SZ 45 ASN SZ 112 ASN JD 587 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049247 restraints weight = 255813.547| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.07 r_work: 0.2711 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 81503 Z= 0.170 Angle : 0.571 12.469 118265 Z= 0.294 Chirality : 0.036 0.286 14599 Planarity : 0.004 0.091 8596 Dihedral : 22.844 178.595 32555 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 3.14 % Allowed : 20.07 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.42 (0.12), residues: 4879 helix: 0.70 (0.13), residues: 1608 sheet: -0.41 (0.18), residues: 861 loop : -0.85 (0.13), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPSG 45 HIS 0.005 0.001 HISSS 125 PHE 0.023 0.001 PHESN 65 TYR 0.019 0.001 TYRSD 34 ARG 0.010 0.000 ARGSZ 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 944 time to evaluate : 4.728 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: Ln 1 MET cc_start: 0.6538 (ttm) cc_final: 0.6178 (ttt) REVERT: Ln 2 ARG cc_start: 0.8345 (ttt180) cc_final: 0.7527 (ttt-90) REVERT: SA 11 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8990 (mmtt) REVERT: SA 84 GLN cc_start: 0.9036 (mt0) cc_final: 0.8781 (mp10) REVERT: SB 76 ASN cc_start: 0.8448 (p0) cc_final: 0.8226 (p0) REVERT: SB 103 MET cc_start: 0.9095 (tmm) cc_final: 0.8874 (tmm) REVERT: SB 211 PHE cc_start: 0.8575 (m-80) cc_final: 0.8337 (m-80) REVERT: SD 87 TYR cc_start: 0.8662 (m-10) cc_final: 0.8354 (m-10) REVERT: SD 123 LEU cc_start: 0.9301 (tp) cc_final: 0.9099 (tp) REVERT: SD 169 ASP cc_start: 0.8490 (t0) cc_final: 0.8101 (t0) REVERT: SD 223 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7960 (mp) REVERT: SE 199 GLU cc_start: 0.8622 (mp0) cc_final: 0.8281 (mp0) REVERT: SE 232 ASN cc_start: 0.9050 (t0) cc_final: 0.8808 (t0) REVERT: SF 32 ASP cc_start: 0.9067 (t0) cc_final: 0.8846 (t0) REVERT: SF 73 THR cc_start: 0.9451 (m) cc_final: 0.9250 (p) REVERT: SH 39 GLN cc_start: 0.8219 (mp-120) cc_final: 0.7880 (mp10) REVERT: SI 88 ASN cc_start: 0.9232 (m-40) cc_final: 0.8756 (t0) REVERT: SI 132 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: SK 9 ILE cc_start: 0.9371 (mm) cc_final: 0.9055 (mm) REVERT: SK 13 GLU cc_start: 0.8750 (pt0) cc_final: 0.8047 (pt0) REVERT: SK 17 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8631 (mmtt) REVERT: SK 26 ASP cc_start: 0.8788 (t0) cc_final: 0.8343 (t0) REVERT: SK 31 LYS cc_start: 0.9312 (mmmm) cc_final: 0.8900 (tptt) REVERT: SK 39 ASN cc_start: 0.8933 (t0) cc_final: 0.8561 (t0) REVERT: SK 80 ARG cc_start: 0.8958 (ttm-80) cc_final: 0.8704 (tpp-160) REVERT: SL 3 ASP cc_start: 0.8300 (t0) cc_final: 0.7865 (t0) REVERT: SL 7 GLU cc_start: 0.8221 (pt0) cc_final: 0.7830 (pt0) REVERT: SL 11 GLN cc_start: 0.8067 (mm110) cc_final: 0.7760 (mm-40) REVERT: SL 49 GLU cc_start: 0.8805 (mp0) cc_final: 0.8588 (mt-10) REVERT: SP 103 ASN cc_start: 0.8793 (m110) cc_final: 0.8543 (m-40) REVERT: SP 118 GLU cc_start: 0.8551 (mp0) cc_final: 0.8336 (mp0) REVERT: SQ 80 GLN cc_start: 0.8919 (mt0) cc_final: 0.8642 (mt0) REVERT: SQ 114 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8648 (tm-30) REVERT: SR 74 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: SS 58 GLU cc_start: 0.8128 (pm20) cc_final: 0.7700 (pm20) REVERT: SS 63 GLU cc_start: 0.8699 (pt0) cc_final: 0.8002 (pm20) REVERT: SS 89 ASP cc_start: 0.8000 (t0) cc_final: 0.7632 (t0) REVERT: SS 91 LYS cc_start: 0.9397 (ttmm) cc_final: 0.8813 (tmtt) REVERT: SS 101 ASN cc_start: 0.8835 (p0) cc_final: 0.8463 (t0) REVERT: ST 10 ASN cc_start: 0.9033 (t0) cc_final: 0.8694 (t0) REVERT: ST 49 ASP cc_start: 0.8837 (t0) cc_final: 0.8449 (t70) REVERT: ST 126 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7497 (tm-30) REVERT: ST 130 ASP cc_start: 0.9265 (p0) cc_final: 0.8912 (p0) REVERT: SU 18 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8400 (t-90) REVERT: SV 1 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6672 (ppp) REVERT: SX 127 ASN cc_start: 0.9026 (t0) cc_final: 0.8729 (t0) REVERT: Sa 25 ASN cc_start: 0.9236 (t0) cc_final: 0.8830 (t0) REVERT: Sc 31 ARG cc_start: 0.8703 (ttm-80) cc_final: 0.8441 (ttm-80) REVERT: Sd 34 TYR cc_start: 0.9043 (m-80) cc_final: 0.8624 (m-80) REVERT: Sg 5 MET cc_start: 0.8533 (mmp) cc_final: 0.7983 (mmm) REVERT: SC 72 ASP cc_start: 0.9266 (m-30) cc_final: 0.9043 (m-30) REVERT: SC 105 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8190 (tm-30) REVERT: SC 221 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8531 (m-30) REVERT: SC 248 TYR cc_start: 0.9415 (OUTLIER) cc_final: 0.8801 (m-80) REVERT: SG 57 ASP cc_start: 0.8909 (t0) cc_final: 0.8670 (t0) REVERT: SG 110 ASN cc_start: 0.8300 (t160) cc_final: 0.7784 (t0) REVERT: SG 146 ASN cc_start: 0.9053 (t0) cc_final: 0.8754 (t0) REVERT: SG 162 LEU cc_start: 0.8127 (tp) cc_final: 0.7688 (pp) REVERT: SJ 28 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8831 (mt-10) REVERT: SJ 59 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8461 (tm-30) REVERT: SJ 107 GLU cc_start: 0.9185 (tp30) cc_final: 0.8781 (tp30) REVERT: SM 31 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6513 (pp) REVERT: SM 48 HIS cc_start: 0.8325 (m170) cc_final: 0.7724 (m-70) REVERT: SM 108 CYS cc_start: 0.7980 (t) cc_final: 0.7700 (p) REVERT: SN 144 SER cc_start: 0.9094 (m) cc_final: 0.8805 (p) REVERT: SW 85 ASP cc_start: 0.8575 (t0) cc_final: 0.8232 (t0) REVERT: SW 114 GLU cc_start: 0.8853 (tp30) cc_final: 0.8480 (tm-30) REVERT: SY 42 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8687 (tp30) REVERT: SZ 50 PHE cc_start: 0.8936 (m-80) cc_final: 0.8656 (m-80) REVERT: SZ 60 LYS cc_start: 0.9299 (tppt) cc_final: 0.9088 (tppt) REVERT: SZ 66 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8271 (mtpt) REVERT: SZ 89 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: Sb 15 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8171 (mm-30) REVERT: Sb 51 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8862 (mt0) REVERT: Sf 132 MET cc_start: 0.7944 (ttt) cc_final: 0.7424 (tpp) REVERT: JD 610 GLU cc_start: 0.7738 (tt0) cc_final: 0.7514 (tt0) REVERT: JD 611 GLN cc_start: 0.9118 (mt0) cc_final: 0.8851 (mt0) REVERT: JD 638 ILE cc_start: 0.8590 (tp) cc_final: 0.8382 (tp) outliers start: 134 outliers final: 96 residues processed: 1020 average time/residue: 0.7135 time to fit residues: 1257.3214 Evaluate side-chains 1011 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 904 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 20 MET Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 152 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SD residue 160 SER Chi-restraints excluded: chain SD residue 162 ASP Chi-restraints excluded: chain SD residue 223 ILE Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SF residue 31 ASN Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SF residue 172 CYS Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 88 SER Chi-restraints excluded: chain SH residue 180 LEU Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 48 VAL Chi-restraints excluded: chain SI residue 72 CYS Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 132 GLU Chi-restraints excluded: chain SI residue 155 ASN Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 45 VAL Chi-restraints excluded: chain SK residue 71 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SR residue 20 TYR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 74 GLN Chi-restraints excluded: chain SS residue 18 THR Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain ST residue 51 ASN Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 81 GLN Chi-restraints excluded: chain SU residue 97 ILE Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 9 VAL Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 79 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain Sa residue 45 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 177 TRP Chi-restraints excluded: chain SC residue 86 LEU Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 225 GLN Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 46 VAL Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 35 ILE Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 24 THR Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SO residue 48 SER Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 45 ASN Chi-restraints excluded: chain SZ residue 83 LEU Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 51 GLN Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Se residue 40 ARG Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 598 LEU Chi-restraints excluded: chain JD residue 603 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 534 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 275 optimal weight: 0.8980 chunk 346 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 484 optimal weight: 6.9990 chunk 551 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SD 22 ASN ** SF 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SI 165 GLN SK 44 HIS SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 83 GLN SU 81 GLN ** SU 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sd 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sd 45 GLN SM 55 ASN SN 5 HIS SW 70 ASN SW 92 ASN SZ 46 ASN SZ 112 ASN Sb 9 HIS JD 587 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.046907 restraints weight = 258270.410| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.08 r_work: 0.2644 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 81503 Z= 0.316 Angle : 0.631 11.286 118265 Z= 0.324 Chirality : 0.039 0.297 14599 Planarity : 0.005 0.094 8596 Dihedral : 22.837 178.493 32555 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 3.26 % Allowed : 20.56 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.48 (0.12), residues: 4879 helix: 0.69 (0.13), residues: 1621 sheet: -0.57 (0.18), residues: 878 loop : -0.87 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPSG 45 HIS 0.008 0.001 HISSS 125 PHE 0.020 0.002 PHESN 65 TYR 0.019 0.002 TYRSD 34 ARG 0.013 0.001 ARGSZ 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 899 time to evaluate : 4.862 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: Ln 1 MET cc_start: 0.6691 (ttm) cc_final: 0.6288 (ttt) REVERT: Ln 2 ARG cc_start: 0.8363 (ttt180) cc_final: 0.7484 (ttt-90) REVERT: SA 11 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8957 (mmtp) REVERT: SB 76 ASN cc_start: 0.8420 (p0) cc_final: 0.8016 (p0) REVERT: SB 103 MET cc_start: 0.9106 (tmm) cc_final: 0.8896 (tmm) REVERT: SD 87 TYR cc_start: 0.8767 (m-10) cc_final: 0.8487 (m-10) REVERT: SD 223 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7900 (mp) REVERT: SD 226 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8255 (mm-40) REVERT: SE 232 ASN cc_start: 0.9075 (t0) cc_final: 0.8779 (t0) REVERT: SF 32 ASP cc_start: 0.9049 (t0) cc_final: 0.8813 (t0) REVERT: SF 38 TYR cc_start: 0.8924 (m-10) cc_final: 0.8717 (m-10) REVERT: SF 194 ASP cc_start: 0.9116 (m-30) cc_final: 0.8866 (p0) REVERT: SH 39 GLN cc_start: 0.8238 (mp-120) cc_final: 0.7900 (mp10) REVERT: SI 88 ASN cc_start: 0.9196 (m-40) cc_final: 0.8758 (t0) REVERT: SI 132 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8752 (pm20) REVERT: SK 9 ILE cc_start: 0.9409 (mm) cc_final: 0.9063 (mm) REVERT: SK 13 GLU cc_start: 0.8787 (pt0) cc_final: 0.8074 (pt0) REVERT: SK 17 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8677 (mmtt) REVERT: SK 26 ASP cc_start: 0.8828 (t0) cc_final: 0.8394 (t0) REVERT: SK 31 LYS cc_start: 0.9348 (mmmm) cc_final: 0.9080 (tttp) REVERT: SK 39 ASN cc_start: 0.8974 (t0) cc_final: 0.8480 (t0) REVERT: SK 80 ARG cc_start: 0.8970 (ttm-80) cc_final: 0.8677 (tpp-160) REVERT: SL 3 ASP cc_start: 0.8386 (t0) cc_final: 0.7911 (t70) REVERT: SL 7 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: SL 119 ASP cc_start: 0.8089 (p0) cc_final: 0.7643 (p0) REVERT: SP 34 MET cc_start: 0.9264 (mmm) cc_final: 0.8518 (mmt) REVERT: SP 103 ASN cc_start: 0.8759 (m110) cc_final: 0.8468 (m-40) REVERT: SP 104 GLN cc_start: 0.8674 (tp40) cc_final: 0.8330 (tp-100) REVERT: SP 118 GLU cc_start: 0.8623 (mp0) cc_final: 0.8338 (mp0) REVERT: SQ 48 GLN cc_start: 0.8801 (tp40) cc_final: 0.8469 (tp40) REVERT: SQ 114 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8687 (tm-30) REVERT: SR 1 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5548 (mpp) REVERT: SR 74 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: SS 1 MET cc_start: 0.7535 (tmm) cc_final: 0.7091 (ppp) REVERT: SS 21 ASP cc_start: 0.8977 (t0) cc_final: 0.8762 (t0) REVERT: SS 58 GLU cc_start: 0.7950 (pm20) cc_final: 0.7466 (pm20) REVERT: SS 63 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: SS 83 PHE cc_start: 0.9037 (t80) cc_final: 0.8527 (t80) REVERT: SS 91 LYS cc_start: 0.9432 (ttmm) cc_final: 0.8809 (tmtt) REVERT: ST 10 ASN cc_start: 0.9112 (t0) cc_final: 0.8798 (t0) REVERT: ST 49 ASP cc_start: 0.8966 (t0) cc_final: 0.8667 (t70) REVERT: ST 126 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7561 (tm-30) REVERT: ST 130 ASP cc_start: 0.9218 (p0) cc_final: 0.8944 (p0) REVERT: SU 18 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.8438 (t-90) REVERT: SU 113 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8339 (tm-30) REVERT: SV 1 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6822 (ppp) REVERT: SX 127 ASN cc_start: 0.9076 (t0) cc_final: 0.8832 (t0) REVERT: Sa 25 ASN cc_start: 0.9257 (t0) cc_final: 0.8848 (t0) REVERT: Sd 12 ARG cc_start: 0.8545 (mmt-90) cc_final: 0.8208 (mmt-90) REVERT: Sg 5 MET cc_start: 0.8603 (mmp) cc_final: 0.7995 (mmp) REVERT: Sg 173 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8853 (tp) REVERT: SC 72 ASP cc_start: 0.9277 (m-30) cc_final: 0.9035 (m-30) REVERT: SC 105 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8203 (tm-30) REVERT: SG 57 ASP cc_start: 0.8962 (t0) cc_final: 0.8739 (t0) REVERT: SG 105 ASN cc_start: 0.8929 (p0) cc_final: 0.8691 (p0) REVERT: SG 110 ASN cc_start: 0.8413 (t160) cc_final: 0.7888 (t0) REVERT: SG 146 ASN cc_start: 0.9181 (t0) cc_final: 0.8880 (t0) REVERT: SJ 28 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8885 (mt-10) REVERT: SJ 59 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8508 (tm-30) REVERT: SJ 107 GLU cc_start: 0.9219 (tp30) cc_final: 0.8789 (tp30) REVERT: SM 31 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6650 (pp) REVERT: SM 48 HIS cc_start: 0.8337 (m170) cc_final: 0.7714 (m-70) REVERT: SM 108 CYS cc_start: 0.7953 (t) cc_final: 0.7661 (p) REVERT: SN 144 SER cc_start: 0.9127 (m) cc_final: 0.8858 (p) REVERT: SW 85 ASP cc_start: 0.8656 (t0) cc_final: 0.8343 (t0) REVERT: SW 114 GLU cc_start: 0.8880 (tp30) cc_final: 0.8490 (tm-30) REVERT: SZ 46 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7599 (t0) REVERT: SZ 50 PHE cc_start: 0.8974 (m-80) cc_final: 0.8684 (m-80) REVERT: SZ 89 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: SZ 98 LYS cc_start: 0.8526 (mttt) cc_final: 0.7997 (mttm) REVERT: Sb 6 ASP cc_start: 0.9125 (t0) cc_final: 0.8887 (t0) REVERT: Sb 15 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8373 (mm-30) REVERT: Sb 51 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8937 (mt0) REVERT: Sf 132 MET cc_start: 0.7891 (ttt) cc_final: 0.7216 (tpp) REVERT: JD 611 GLN cc_start: 0.9138 (mt0) cc_final: 0.8870 (mt0) outliers start: 139 outliers final: 104 residues processed: 974 average time/residue: 0.7116 time to fit residues: 1203.9507 Evaluate side-chains 994 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 876 time to evaluate : 4.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 20 MET Chi-restraints excluded: chain SA residue 38 ILE Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 190 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SD residue 126 ILE Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SD residue 160 SER Chi-restraints excluded: chain SD residue 162 ASP Chi-restraints excluded: chain SD residue 223 ILE Chi-restraints excluded: chain SD residue 224 SER Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SF residue 25 THR Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SF residue 172 CYS Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 88 SER Chi-restraints excluded: chain SH residue 180 LEU Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 72 CYS Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 132 GLU Chi-restraints excluded: chain SI residue 155 ASN Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 45 VAL Chi-restraints excluded: chain SK residue 71 LEU Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 7 GLU Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SR residue 1 MET Chi-restraints excluded: chain SR residue 20 TYR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 72 LYS Chi-restraints excluded: chain SR residue 74 GLN Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 53 THR Chi-restraints excluded: chain SS residue 63 GLU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 87 GLN Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 51 ASN Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 68 THR Chi-restraints excluded: chain SU residue 97 ILE Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 9 VAL Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 68 SER Chi-restraints excluded: chain SV residue 79 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain Sa residue 88 SER Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain Sg residue 173 LEU Chi-restraints excluded: chain SC residue 63 VAL Chi-restraints excluded: chain SC residue 86 LEU Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SG residue 89 THR Chi-restraints excluded: chain SG residue 151 ASP Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SG residue 192 ILE Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 46 VAL Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 35 ILE Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 24 THR Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SN residue 52 VAL Chi-restraints excluded: chain SN residue 60 VAL Chi-restraints excluded: chain SO residue 48 SER Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 96 LEU Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 46 ASN Chi-restraints excluded: chain SZ residue 83 LEU Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 51 GLN Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Se residue 53 LYS Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 598 LEU Chi-restraints excluded: chain JD residue 603 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 305 optimal weight: 0.5980 chunk 407 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 554 optimal weight: 0.9990 chunk 584 optimal weight: 1.9990 chunk 609 optimal weight: 1.9990 chunk 557 optimal weight: 0.8980 chunk 293 optimal weight: 8.9990 chunk 530 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 365 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SD 22 ASN SF 36 GLN ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 39 GLN SI 165 GLN SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SU 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sd 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sd 45 GLN SC 113 GLN SM 55 ASN SW 70 ASN SW 92 ASN JD 587 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048755 restraints weight = 257184.036| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.06 r_work: 0.2696 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 81503 Z= 0.168 Angle : 0.588 12.283 118265 Z= 0.303 Chirality : 0.036 0.310 14599 Planarity : 0.004 0.091 8596 Dihedral : 22.859 178.831 32555 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 2.83 % Allowed : 21.36 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.34 (0.12), residues: 4879 helix: 0.80 (0.13), residues: 1610 sheet: -0.45 (0.18), residues: 853 loop : -0.79 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPSG 45 HIS 0.008 0.001 HISSd 3 PHE 0.023 0.001 PHESN 65 TYR 0.021 0.001 TYRSg 140 ARG 0.014 0.000 ARGSZ 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 930 time to evaluate : 4.698 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: Ln 1 MET cc_start: 0.6655 (ttm) cc_final: 0.6370 (ttt) REVERT: Ln 2 ARG cc_start: 0.8358 (ttt180) cc_final: 0.7500 (ttt-90) REVERT: SA 10 MET cc_start: 0.9085 (mmm) cc_final: 0.8852 (mmm) REVERT: SA 40 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8627 (ttpt) REVERT: SA 84 GLN cc_start: 0.9115 (mt0) cc_final: 0.8830 (mp10) REVERT: SB 38 MET cc_start: 0.9159 (mpp) cc_final: 0.8957 (mpp) REVERT: SB 76 ASN cc_start: 0.8401 (p0) cc_final: 0.7959 (p0) REVERT: SB 103 MET cc_start: 0.9107 (tmm) cc_final: 0.8871 (tmm) REVERT: SB 211 PHE cc_start: 0.8632 (m-80) cc_final: 0.8411 (m-80) REVERT: SD 87 TYR cc_start: 0.8735 (m-10) cc_final: 0.8430 (m-10) REVERT: SD 223 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7836 (mp) REVERT: SD 226 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8222 (mm-40) REVERT: SE 199 GLU cc_start: 0.8758 (mp0) cc_final: 0.8375 (mp0) REVERT: SE 232 ASN cc_start: 0.9079 (t0) cc_final: 0.8751 (t0) REVERT: SF 73 THR cc_start: 0.9488 (m) cc_final: 0.9265 (p) REVERT: SF 194 ASP cc_start: 0.9083 (m-30) cc_final: 0.8872 (p0) REVERT: SI 88 ASN cc_start: 0.9206 (m-40) cc_final: 0.8784 (t0) REVERT: SI 132 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8751 (pm20) REVERT: SI 168 GLN cc_start: 0.9275 (mm110) cc_final: 0.8951 (mm-40) REVERT: SK 9 ILE cc_start: 0.9380 (mm) cc_final: 0.9031 (mm) REVERT: SK 13 GLU cc_start: 0.8740 (pt0) cc_final: 0.8431 (pt0) REVERT: SK 26 ASP cc_start: 0.8821 (t0) cc_final: 0.8370 (t0) REVERT: SK 31 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8981 (tttp) REVERT: SK 39 ASN cc_start: 0.8964 (t0) cc_final: 0.8454 (t0) REVERT: SK 80 ARG cc_start: 0.8985 (ttm-80) cc_final: 0.8694 (tpp-160) REVERT: SL 3 ASP cc_start: 0.8350 (t0) cc_final: 0.7932 (t0) REVERT: SL 7 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: SL 91 ASP cc_start: 0.9191 (m-30) cc_final: 0.8931 (m-30) REVERT: SP 34 MET cc_start: 0.9194 (mmm) cc_final: 0.8470 (mmt) REVERT: SP 41 GLN cc_start: 0.9120 (mp10) cc_final: 0.8594 (mp10) REVERT: SP 103 ASN cc_start: 0.8759 (m110) cc_final: 0.8492 (m-40) REVERT: SP 104 GLN cc_start: 0.8647 (tp40) cc_final: 0.8357 (tp-100) REVERT: SP 118 GLU cc_start: 0.8598 (mp0) cc_final: 0.8241 (mp0) REVERT: SQ 114 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8672 (tm-30) REVERT: SR 1 MET cc_start: 0.5952 (ttm) cc_final: 0.5622 (mpp) REVERT: SR 69 ILE cc_start: 0.9550 (mp) cc_final: 0.9336 (mm) REVERT: SR 74 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: SS 1 MET cc_start: 0.7426 (tmm) cc_final: 0.6947 (ppp) REVERT: SS 49 ASP cc_start: 0.9112 (t0) cc_final: 0.8759 (t0) REVERT: SS 58 GLU cc_start: 0.8077 (pm20) cc_final: 0.7589 (pm20) REVERT: SS 63 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: SS 83 PHE cc_start: 0.9010 (t80) cc_final: 0.8476 (t80) REVERT: SS 89 ASP cc_start: 0.8037 (t0) cc_final: 0.7683 (t70) REVERT: SS 91 LYS cc_start: 0.9398 (ttmm) cc_final: 0.8885 (tmtt) REVERT: SS 101 ASN cc_start: 0.8824 (p0) cc_final: 0.8505 (t0) REVERT: ST 10 ASN cc_start: 0.9072 (t0) cc_final: 0.8752 (t0) REVERT: ST 49 ASP cc_start: 0.8847 (t0) cc_final: 0.8538 (t70) REVERT: ST 54 TYR cc_start: 0.9335 (m-80) cc_final: 0.9060 (m-80) REVERT: ST 126 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7166 (tm-30) REVERT: ST 130 ASP cc_start: 0.9247 (p0) cc_final: 0.8641 (p0) REVERT: SU 18 HIS cc_start: 0.8937 (OUTLIER) cc_final: 0.8474 (t-90) REVERT: SU 113 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8423 (tm-30) REVERT: SV 1 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6672 (ppp) REVERT: Sa 25 ASN cc_start: 0.9267 (t0) cc_final: 0.8832 (t0) REVERT: Sc 31 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8477 (ttm-80) REVERT: Sc 35 MET cc_start: 0.7499 (ptp) cc_final: 0.6942 (ptp) REVERT: Sc 40 ARG cc_start: 0.7232 (ttp-170) cc_final: 0.6696 (ttp-170) REVERT: Sd 12 ARG cc_start: 0.8441 (mmt-90) cc_final: 0.8125 (mmt-90) REVERT: Sg 5 MET cc_start: 0.8659 (mmp) cc_final: 0.8193 (mmp) REVERT: SC 72 ASP cc_start: 0.9256 (m-30) cc_final: 0.9014 (m-30) REVERT: SC 105 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8257 (tm-30) REVERT: SC 216 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8629 (mtm) REVERT: SG 57 ASP cc_start: 0.8962 (t0) cc_final: 0.8727 (t0) REVERT: SG 105 ASN cc_start: 0.8898 (p0) cc_final: 0.8507 (p0) REVERT: SG 110 ASN cc_start: 0.8369 (t160) cc_final: 0.7796 (t0) REVERT: SG 146 ASN cc_start: 0.9001 (t0) cc_final: 0.8694 (t0) REVERT: SJ 28 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8869 (mt-10) REVERT: SJ 59 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8462 (tm-30) REVERT: SJ 107 GLU cc_start: 0.9206 (tp30) cc_final: 0.8804 (tp30) REVERT: SM 31 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6708 (pp) REVERT: SM 48 HIS cc_start: 0.8332 (m170) cc_final: 0.7703 (m-70) REVERT: SM 108 CYS cc_start: 0.7885 (t) cc_final: 0.7623 (p) REVERT: SN 144 SER cc_start: 0.9101 (m) cc_final: 0.8833 (p) REVERT: SW 85 ASP cc_start: 0.8584 (t0) cc_final: 0.8261 (t0) REVERT: SW 114 GLU cc_start: 0.8866 (tp30) cc_final: 0.8518 (tm-30) REVERT: SW 115 GLU cc_start: 0.9095 (pt0) cc_final: 0.8755 (pt0) REVERT: SZ 50 PHE cc_start: 0.8932 (m-80) cc_final: 0.8704 (m-80) REVERT: SZ 66 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8028 (tttm) REVERT: SZ 89 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: SZ 90 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8494 (tm-30) REVERT: SZ 98 LYS cc_start: 0.8559 (mttt) cc_final: 0.8089 (mttm) REVERT: SZ 106 GLN cc_start: 0.9399 (tp40) cc_final: 0.9111 (tp40) REVERT: Sb 15 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8377 (mm-30) REVERT: Sb 51 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8877 (mt0) REVERT: Sf 132 MET cc_start: 0.7910 (ttt) cc_final: 0.7325 (tpp) REVERT: JD 610 GLU cc_start: 0.7666 (tt0) cc_final: 0.7409 (tt0) REVERT: JD 611 GLN cc_start: 0.9117 (mt0) cc_final: 0.8843 (mt0) REVERT: JD 633 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7844 (mmtp) outliers start: 121 outliers final: 88 residues processed: 995 average time/residue: 0.7051 time to fit residues: 1220.5512 Evaluate side-chains 1001 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 901 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 20 MET Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SD residue 160 SER Chi-restraints excluded: chain SD residue 162 ASP Chi-restraints excluded: chain SD residue 223 ILE Chi-restraints excluded: chain SD residue 224 SER Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 98 ASN Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SF residue 172 CYS Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 88 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 132 GLU Chi-restraints excluded: chain SI residue 155 ASN Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 7 GLU Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 20 TYR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 74 GLN Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 18 THR Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 60 THR Chi-restraints excluded: chain SS residue 63 GLU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain ST residue 51 ASN Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 112 MET Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 68 THR Chi-restraints excluded: chain SU residue 97 ILE Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 9 VAL Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 79 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 24 THR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain SC residue 86 LEU Chi-restraints excluded: chain SC residue 101 SER Chi-restraints excluded: chain SC residue 216 MET Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 46 VAL Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 35 ILE Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 96 LEU Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 83 LEU Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 51 GLN Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 598 LEU Chi-restraints excluded: chain JD residue 603 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 245 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 320 optimal weight: 0.3980 chunk 604 optimal weight: 0.0670 chunk 350 optimal weight: 3.9990 chunk 530 optimal weight: 6.9990 chunk 332 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 165 GLN SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 62 GLN ST 83 GLN ** SU 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sd 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sd 45 GLN SM 55 ASN SW 70 ASN SW 92 ASN SZ 46 ASN JD 587 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049345 restraints weight = 256464.664| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.06 r_work: 0.2713 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 81503 Z= 0.167 Angle : 0.586 12.456 118265 Z= 0.302 Chirality : 0.036 0.320 14599 Planarity : 0.004 0.091 8596 Dihedral : 22.814 178.945 32555 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.79 % Allowed : 21.83 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4879 helix: 0.82 (0.13), residues: 1619 sheet: -0.43 (0.18), residues: 855 loop : -0.77 (0.13), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPSG 45 HIS 0.008 0.001 HISSd 3 PHE 0.026 0.001 PHEST 53 TYR 0.024 0.001 TYRSD 34 ARG 0.007 0.000 ARGSZ 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 936 time to evaluate : 4.602 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: Ln 1 MET cc_start: 0.6651 (ttm) cc_final: 0.6411 (ttt) REVERT: Ln 2 ARG cc_start: 0.8342 (ttt180) cc_final: 0.7517 (ttt-90) REVERT: SA 84 GLN cc_start: 0.9061 (mt0) cc_final: 0.8818 (mp10) REVERT: SB 38 MET cc_start: 0.9147 (mpp) cc_final: 0.8938 (mpp) REVERT: SB 76 ASN cc_start: 0.8416 (p0) cc_final: 0.7980 (p0) REVERT: SB 103 MET cc_start: 0.9066 (tmm) cc_final: 0.8844 (tmm) REVERT: SB 211 PHE cc_start: 0.8606 (m-80) cc_final: 0.8382 (m-80) REVERT: SD 68 GLU cc_start: 0.8723 (pp20) cc_final: 0.8204 (pp20) REVERT: SD 87 TYR cc_start: 0.8745 (m-10) cc_final: 0.8496 (m-10) REVERT: SD 169 ASP cc_start: 0.8450 (t0) cc_final: 0.8165 (t0) REVERT: SD 223 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7906 (mp) REVERT: SD 226 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8222 (mm-40) REVERT: SE 199 GLU cc_start: 0.8744 (mp0) cc_final: 0.8346 (mp0) REVERT: SE 232 ASN cc_start: 0.9080 (t0) cc_final: 0.8755 (t0) REVERT: SF 36 GLN cc_start: 0.8396 (pt0) cc_final: 0.8155 (pm20) REVERT: SF 38 TYR cc_start: 0.8871 (m-10) cc_final: 0.8605 (m-10) REVERT: SF 73 THR cc_start: 0.9467 (m) cc_final: 0.9265 (p) REVERT: SH 39 GLN cc_start: 0.8250 (mp10) cc_final: 0.8046 (mp10) REVERT: SI 88 ASN cc_start: 0.9220 (m-40) cc_final: 0.8806 (t0) REVERT: SI 132 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: SK 9 ILE cc_start: 0.9347 (mm) cc_final: 0.8986 (mm) REVERT: SK 13 GLU cc_start: 0.8738 (pt0) cc_final: 0.7979 (pt0) REVERT: SK 17 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8702 (mmtt) REVERT: SK 26 ASP cc_start: 0.8802 (t0) cc_final: 0.8359 (t0) REVERT: SK 31 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8982 (tttp) REVERT: SK 39 ASN cc_start: 0.8945 (t0) cc_final: 0.8449 (t0) REVERT: SK 80 ARG cc_start: 0.8991 (ttm-80) cc_final: 0.8699 (tpp-160) REVERT: SK 95 ARG cc_start: 0.8708 (tpm170) cc_final: 0.7859 (tpm170) REVERT: SL 3 ASP cc_start: 0.8309 (t0) cc_final: 0.7900 (t0) REVERT: SL 7 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: SL 91 ASP cc_start: 0.9176 (m-30) cc_final: 0.8923 (m-30) REVERT: SP 34 MET cc_start: 0.9192 (mmm) cc_final: 0.8468 (mmt) REVERT: SP 41 GLN cc_start: 0.9123 (mp10) cc_final: 0.8595 (mp10) REVERT: SP 53 GLN cc_start: 0.8897 (mp10) cc_final: 0.8300 (pm20) REVERT: SP 103 ASN cc_start: 0.8761 (m110) cc_final: 0.8522 (m-40) REVERT: SP 104 GLN cc_start: 0.8612 (tp40) cc_final: 0.8317 (tp-100) REVERT: SP 118 GLU cc_start: 0.8589 (mp0) cc_final: 0.8227 (mp0) REVERT: SQ 114 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8632 (tm-30) REVERT: SR 1 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5494 (mpp) REVERT: SR 74 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8284 (tm-30) REVERT: SS 1 MET cc_start: 0.7414 (tmm) cc_final: 0.6925 (ppp) REVERT: SS 49 ASP cc_start: 0.9101 (t0) cc_final: 0.8715 (t0) REVERT: SS 58 GLU cc_start: 0.8059 (pm20) cc_final: 0.7578 (pm20) REVERT: SS 63 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: SS 83 PHE cc_start: 0.8999 (t80) cc_final: 0.8473 (t80) REVERT: SS 89 ASP cc_start: 0.7981 (t0) cc_final: 0.7620 (t0) REVERT: SS 91 LYS cc_start: 0.9398 (ttmm) cc_final: 0.8828 (tmtt) REVERT: SS 101 ASN cc_start: 0.8800 (p0) cc_final: 0.8433 (t0) REVERT: ST 10 ASN cc_start: 0.9078 (t0) cc_final: 0.8755 (t0) REVERT: ST 49 ASP cc_start: 0.8867 (t0) cc_final: 0.8529 (t70) REVERT: ST 54 TYR cc_start: 0.9356 (m-80) cc_final: 0.9125 (m-80) REVERT: ST 126 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7138 (tm-30) REVERT: ST 130 ASP cc_start: 0.9244 (p0) cc_final: 0.8628 (p0) REVERT: SU 18 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8510 (t-90) REVERT: SV 1 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6880 (pmm) REVERT: Sa 25 ASN cc_start: 0.9271 (t0) cc_final: 0.8837 (t0) REVERT: Sc 31 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8453 (ttm-80) REVERT: Sc 35 MET cc_start: 0.7455 (ptp) cc_final: 0.6905 (ptp) REVERT: Sc 40 ARG cc_start: 0.7137 (ttp-170) cc_final: 0.6594 (ttp-170) REVERT: Sg 5 MET cc_start: 0.8657 (mmp) cc_final: 0.8177 (mmp) REVERT: Sg 49 GLU cc_start: 0.8532 (pm20) cc_final: 0.8276 (tp30) REVERT: SC 72 ASP cc_start: 0.9260 (m-30) cc_final: 0.9043 (m-30) REVERT: SC 105 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8266 (tm-30) REVERT: SC 115 GLN cc_start: 0.8326 (tp40) cc_final: 0.8109 (tp40) REVERT: SC 216 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8611 (mtm) REVERT: SC 221 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: SG 57 ASP cc_start: 0.8953 (t0) cc_final: 0.8744 (t0) REVERT: SG 105 ASN cc_start: 0.8822 (p0) cc_final: 0.8391 (p0) REVERT: SG 110 ASN cc_start: 0.8342 (t160) cc_final: 0.7968 (t0) REVERT: SG 146 ASN cc_start: 0.9001 (t0) cc_final: 0.8684 (t0) REVERT: SJ 28 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8833 (mt-10) REVERT: SJ 59 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8440 (tm-30) REVERT: SJ 107 GLU cc_start: 0.9188 (tp30) cc_final: 0.8784 (tp30) REVERT: SM 31 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6702 (pp) REVERT: SM 48 HIS cc_start: 0.8340 (m170) cc_final: 0.7746 (m-70) REVERT: SW 85 ASP cc_start: 0.8555 (t0) cc_final: 0.8223 (t0) REVERT: SW 114 GLU cc_start: 0.8859 (tp30) cc_final: 0.8494 (tm-30) REVERT: SW 115 GLU cc_start: 0.9213 (pt0) cc_final: 0.8819 (pt0) REVERT: SZ 46 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.7546 (t0) REVERT: SZ 66 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8037 (tttm) REVERT: SZ 89 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: SZ 98 LYS cc_start: 0.8547 (mttt) cc_final: 0.8108 (mttm) REVERT: SZ 106 GLN cc_start: 0.9391 (tp40) cc_final: 0.9103 (tp40) REVERT: Sb 15 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8391 (mm-30) REVERT: Sb 51 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8852 (mt0) REVERT: Sf 132 MET cc_start: 0.7916 (ttt) cc_final: 0.7384 (tpp) REVERT: JD 610 GLU cc_start: 0.7761 (tt0) cc_final: 0.7495 (tt0) REVERT: JD 611 GLN cc_start: 0.9112 (mt0) cc_final: 0.8832 (mt0) REVERT: JD 633 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7633 (mmtm) outliers start: 119 outliers final: 89 residues processed: 997 average time/residue: 0.6958 time to fit residues: 1211.3265 Evaluate side-chains 1006 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 902 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 20 MET Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 190 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SD residue 160 SER Chi-restraints excluded: chain SD residue 223 ILE Chi-restraints excluded: chain SD residue 224 SER Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 98 ASN Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SF residue 172 CYS Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 88 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 48 VAL Chi-restraints excluded: chain SI residue 72 CYS Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 132 GLU Chi-restraints excluded: chain SI residue 155 ASN Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 62 PHE Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 7 GLU Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 1 MET Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 74 GLN Chi-restraints excluded: chain SR residue 106 LEU Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 18 THR Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 60 THR Chi-restraints excluded: chain SS residue 63 GLU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 112 MET Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 68 THR Chi-restraints excluded: chain SU residue 97 ILE Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 9 VAL Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 79 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 24 THR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain SC residue 86 LEU Chi-restraints excluded: chain SC residue 216 MET Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 46 VAL Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SO residue 48 SER Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 96 LEU Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 46 ASN Chi-restraints excluded: chain SZ residue 83 LEU Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 51 GLN Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 598 LEU Chi-restraints excluded: chain JD residue 603 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 646 optimal weight: 10.0000 chunk 480 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 517 optimal weight: 6.9990 chunk 379 optimal weight: 7.9990 chunk 522 optimal weight: 0.0470 chunk 518 optimal weight: 4.9990 chunk 629 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 377 optimal weight: 0.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 4 GLN ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SI 22 HIS SI 165 GLN SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sd 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sd 45 GLN ** SC 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 277 HIS SM 55 ASN SW 70 ASN SW 92 ASN SZ 46 ASN JD 587 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.066021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046988 restraints weight = 258668.346| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.07 r_work: 0.2647 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 81503 Z= 0.308 Angle : 0.642 11.614 118265 Z= 0.330 Chirality : 0.039 0.345 14599 Planarity : 0.005 0.092 8596 Dihedral : 22.805 178.631 32555 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 2.55 % Allowed : 22.32 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.36 (0.12), residues: 4879 helix: 0.80 (0.13), residues: 1614 sheet: -0.49 (0.18), residues: 867 loop : -0.80 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPSG 45 HIS 0.007 0.001 HISSS 125 PHE 0.041 0.002 PHESB 223 TYR 0.027 0.002 TYRSF 38 ARG 0.008 0.001 ARGSS 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 902 time to evaluate : 4.635 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: Ln 1 MET cc_start: 0.6706 (ttm) cc_final: 0.6403 (ttt) REVERT: Ln 2 ARG cc_start: 0.8342 (ttt180) cc_final: 0.7480 (ttt-90) REVERT: SA 84 GLN cc_start: 0.9111 (mt0) cc_final: 0.8789 (mp10) REVERT: SB 38 MET cc_start: 0.9158 (mpp) cc_final: 0.8928 (mpp) REVERT: SB 76 ASN cc_start: 0.8348 (p0) cc_final: 0.7927 (p0) REVERT: SB 103 MET cc_start: 0.9108 (tmm) cc_final: 0.8869 (tmm) REVERT: SD 68 GLU cc_start: 0.8743 (pp20) cc_final: 0.8237 (pp20) REVERT: SD 87 TYR cc_start: 0.8769 (m-10) cc_final: 0.8490 (m-10) REVERT: SD 169 ASP cc_start: 0.8490 (t0) cc_final: 0.8176 (t0) REVERT: SD 223 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7819 (mp) REVERT: SD 226 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8291 (mm-40) REVERT: SE 232 ASN cc_start: 0.9131 (t0) cc_final: 0.8811 (t0) REVERT: SI 88 ASN cc_start: 0.9194 (m-40) cc_final: 0.8852 (t0) REVERT: SI 132 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8718 (pm20) REVERT: SK 9 ILE cc_start: 0.9326 (mm) cc_final: 0.8935 (mm) REVERT: SK 13 GLU cc_start: 0.8786 (pt0) cc_final: 0.8472 (pt0) REVERT: SK 26 ASP cc_start: 0.8822 (t0) cc_final: 0.8397 (t0) REVERT: SK 31 LYS cc_start: 0.9285 (mmmm) cc_final: 0.8990 (tttp) REVERT: SK 39 ASN cc_start: 0.8965 (t0) cc_final: 0.8459 (t0) REVERT: SK 80 ARG cc_start: 0.8980 (ttm-80) cc_final: 0.8661 (tpp-160) REVERT: SL 3 ASP cc_start: 0.8373 (t0) cc_final: 0.8039 (t0) REVERT: SL 11 GLN cc_start: 0.8214 (mm110) cc_final: 0.8014 (mm-40) REVERT: SL 49 GLU cc_start: 0.8821 (mp0) cc_final: 0.8543 (mt-10) REVERT: SL 91 ASP cc_start: 0.9183 (m-30) cc_final: 0.8931 (m-30) REVERT: SP 34 MET cc_start: 0.9203 (mmm) cc_final: 0.8904 (mmm) REVERT: SP 53 GLN cc_start: 0.8924 (mp10) cc_final: 0.8319 (pm20) REVERT: SP 82 ASP cc_start: 0.9194 (p0) cc_final: 0.8872 (p0) REVERT: SP 103 ASN cc_start: 0.8825 (m110) cc_final: 0.8492 (m-40) REVERT: SP 104 GLN cc_start: 0.8644 (tp40) cc_final: 0.8331 (tp-100) REVERT: SP 118 GLU cc_start: 0.8688 (mp0) cc_final: 0.8286 (mp0) REVERT: SQ 114 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8617 (tm-30) REVERT: SR 74 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: SS 1 MET cc_start: 0.7662 (tmm) cc_final: 0.7444 (ppp) REVERT: SS 49 ASP cc_start: 0.9142 (t0) cc_final: 0.8761 (t0) REVERT: SS 58 GLU cc_start: 0.7878 (pm20) cc_final: 0.7363 (pm20) REVERT: SS 63 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: SS 83 PHE cc_start: 0.9061 (t80) cc_final: 0.8578 (t80) REVERT: SS 89 ASP cc_start: 0.8170 (t0) cc_final: 0.7785 (t70) REVERT: SS 91 LYS cc_start: 0.9415 (ttmm) cc_final: 0.8898 (tmtt) REVERT: ST 10 ASN cc_start: 0.9118 (t0) cc_final: 0.8808 (t0) REVERT: ST 49 ASP cc_start: 0.8880 (t0) cc_final: 0.8568 (t70) REVERT: ST 54 TYR cc_start: 0.9381 (m-80) cc_final: 0.9103 (m-80) REVERT: ST 126 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7164 (tm-30) REVERT: ST 130 ASP cc_start: 0.9232 (p0) cc_final: 0.8568 (p0) REVERT: SU 18 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8482 (t-90) REVERT: SU 30 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8866 (mmmm) REVERT: SU 51 LYS cc_start: 0.9258 (tppt) cc_final: 0.8942 (tppt) REVERT: SU 113 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8345 (tm-30) REVERT: SV 1 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6814 (ppp) REVERT: Sa 25 ASN cc_start: 0.9286 (t0) cc_final: 0.8877 (t0) REVERT: Sc 31 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.8538 (ttm-80) REVERT: Sd 12 ARG cc_start: 0.8528 (mmt-90) cc_final: 0.8153 (mmt-90) REVERT: Sg 5 MET cc_start: 0.8617 (mmp) cc_final: 0.8024 (mmp) REVERT: Sg 173 LEU cc_start: 0.9170 (mp) cc_final: 0.8826 (tp) REVERT: SC 72 ASP cc_start: 0.9288 (m-30) cc_final: 0.9033 (m-30) REVERT: SC 216 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8701 (mtm) REVERT: SG 57 ASP cc_start: 0.8971 (t0) cc_final: 0.8740 (t0) REVERT: SG 110 ASN cc_start: 0.8432 (t160) cc_final: 0.8053 (t0) REVERT: SG 146 ASN cc_start: 0.9106 (t0) cc_final: 0.8811 (t0) REVERT: SJ 28 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8871 (mt-10) REVERT: SJ 59 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8541 (tm-30) REVERT: SJ 107 GLU cc_start: 0.9219 (tp30) cc_final: 0.8763 (tp30) REVERT: SM 31 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6859 (pp) REVERT: SM 48 HIS cc_start: 0.8397 (m170) cc_final: 0.7797 (m-70) REVERT: SO 34 PHE cc_start: 0.9034 (t80) cc_final: 0.8803 (t80) REVERT: SW 85 ASP cc_start: 0.8668 (t0) cc_final: 0.8345 (t0) REVERT: SW 114 GLU cc_start: 0.8922 (tp30) cc_final: 0.8513 (tm-30) REVERT: SW 115 GLU cc_start: 0.9297 (pt0) cc_final: 0.8891 (pt0) REVERT: SY 47 MET cc_start: 0.9261 (ttp) cc_final: 0.9026 (ttt) REVERT: SZ 46 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7051 (t0) REVERT: SZ 66 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8205 (mtpt) REVERT: SZ 89 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: SZ 98 LYS cc_start: 0.8559 (mttt) cc_final: 0.8102 (mttm) REVERT: SZ 106 GLN cc_start: 0.9400 (tp40) cc_final: 0.9104 (tp40) REVERT: Sb 15 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8458 (mm-30) REVERT: Sb 51 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8942 (mt0) REVERT: Sf 132 MET cc_start: 0.7870 (ttt) cc_final: 0.7323 (tpp) REVERT: JD 610 GLU cc_start: 0.7809 (tt0) cc_final: 0.7554 (tt0) REVERT: JD 611 GLN cc_start: 0.9124 (mt0) cc_final: 0.8849 (mt0) outliers start: 109 outliers final: 87 residues processed: 961 average time/residue: 0.7484 time to fit residues: 1247.8895 Evaluate side-chains 982 residues out of total 4272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 883 time to evaluate : 4.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ln residue 20 MET Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 190 SER Chi-restraints excluded: chain SB residue 39 PHE Chi-restraints excluded: chain SD residue 156 LEU Chi-restraints excluded: chain SD residue 160 SER Chi-restraints excluded: chain SD residue 223 ILE Chi-restraints excluded: chain SD residue 224 SER Chi-restraints excluded: chain SE residue 45 ILE Chi-restraints excluded: chain SE residue 98 ASN Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SF residue 160 GLU Chi-restraints excluded: chain SF residue 168 THR Chi-restraints excluded: chain SF residue 172 CYS Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 88 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 72 CYS Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 132 GLU Chi-restraints excluded: chain SI residue 155 ASN Chi-restraints excluded: chain SI residue 177 SER Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 93 THR Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 111 MET Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 41 MET Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 74 GLN Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 44 VAL Chi-restraints excluded: chain SS residue 60 THR Chi-restraints excluded: chain SS residue 63 GLU Chi-restraints excluded: chain SS residue 68 ILE Chi-restraints excluded: chain SS residue 87 GLN Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 116 ASP Chi-restraints excluded: chain SU residue 18 HIS Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 40 ILE Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 68 THR Chi-restraints excluded: chain SU residue 97 ILE Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 42 VAL Chi-restraints excluded: chain SV residue 79 VAL Chi-restraints excluded: chain SX residue 26 GLN Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 24 THR Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 107 ASP Chi-restraints excluded: chain Sg residue 113 PHE Chi-restraints excluded: chain Sg residue 135 LEU Chi-restraints excluded: chain Sg residue 142 VAL Chi-restraints excluded: chain SC residue 86 LEU Chi-restraints excluded: chain SC residue 216 MET Chi-restraints excluded: chain SC residue 221 ASP Chi-restraints excluded: chain SG residue 18 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 78 SER Chi-restraints excluded: chain SG residue 89 THR Chi-restraints excluded: chain SG residue 151 ASP Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SJ residue 28 GLU Chi-restraints excluded: chain SJ residue 29 LEU Chi-restraints excluded: chain SJ residue 46 VAL Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 31 LEU Chi-restraints excluded: chain SM residue 35 ILE Chi-restraints excluded: chain SM residue 55 ASN Chi-restraints excluded: chain SM residue 74 ILE Chi-restraints excluded: chain SN residue 13 GLN Chi-restraints excluded: chain SN residue 30 SER Chi-restraints excluded: chain SO residue 65 ASP Chi-restraints excluded: chain SO residue 103 ASN Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 96 LEU Chi-restraints excluded: chain SY residue 115 LYS Chi-restraints excluded: chain SY residue 117 VAL Chi-restraints excluded: chain SZ residue 46 ASN Chi-restraints excluded: chain SZ residue 83 LEU Chi-restraints excluded: chain SZ residue 89 GLN Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 51 GLN Chi-restraints excluded: chain Sb residue 60 SER Chi-restraints excluded: chain Se residue 25 LYS Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 598 LEU Chi-restraints excluded: chain JD residue 603 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 607 optimal weight: 5.9990 chunk 456 optimal weight: 0.9990 chunk 469 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 chunk 626 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 67 optimal weight: 40.0000 chunk 642 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 22 ASN ** SH 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 11 GLN SQ 142 GLN ** SR 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sd 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SM 55 ASN SO 20 GLN ** SO 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 70 ASN SW 92 ASN JD 587 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.048993 restraints weight = 257546.938| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.07 r_work: 0.2702 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 81503 Z= 0.170 Angle : 0.603 12.316 118265 Z= 0.310 Chirality : 0.036 0.358 14599 Planarity : 0.004 0.090 8596 Dihedral : 22.833 178.961 32555 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 2.46 % Allowed : 22.76 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.28 (0.12), residues: 4879 helix: 0.87 (0.13), residues: 1610 sheet: -0.44 (0.18), residues: 866 loop : -0.76 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPSG 45 HIS 0.006 0.001 HISSd 3 PHE 0.028 0.001 PHESf 136 TYR 0.017 0.001 TYRSK 82 ARG 0.015 0.000 ARGSZ 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42415.97 seconds wall clock time: 728 minutes 1.42 seconds (43681.42 seconds total)