Starting phenix.real_space_refine on Fri Jan 24 21:22:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxl_38752/01_2025/8xxl_38752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxl_38752/01_2025/8xxl_38752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxl_38752/01_2025/8xxl_38752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxl_38752/01_2025/8xxl_38752.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxl_38752/01_2025/8xxl_38752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxl_38752/01_2025/8xxl_38752.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1723 5.49 5 Mg 22 5.21 5 S 184 5.16 5 C 41350 2.51 5 N 14016 2.21 5 O 18942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 76240 Number of models: 1 Model: "" Number of chains: 41 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: 36538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1723, 36538 Classifications: {'DNA': 15, 'RNA': 1708} Modifications used: {'rna2p_pur': 147, 'rna2p_pyr': 129, 'rna3p_pur': 752, 'rna3p_pyr': 677} Link IDs: {'rna2p': 275, 'rna3p': 1447} Chain breaks: 3 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: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1741 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} 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: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "SH" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1497 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, '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: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1247 Classifications: {'peptide': 153} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 144} Chain: "SP" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} 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: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} 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: {'CIS': 1, 'PTRANS': 12, 'TRANS': 208} 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: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1049 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 131} 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: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1065 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} 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: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "CD" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 346 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "S2" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Unusual residues: {' MG': 21} Classifications: {'undetermined': 21} Link IDs: {None: 20} 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: "SG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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 59100 SG CYSSa 23 88.457 171.327 112.389 1.00 9.58 S ATOM 59121 SG CYSSa 26 87.720 170.177 108.866 1.00 11.06 S ATOM 59504 SG CYSSa 74 90.129 168.113 111.036 1.00 7.35 S ATOM 59523 SG CYSSa 77 91.153 171.336 109.592 1.00 7.90 S ATOM 60415 SG CYSSd 21 152.048 164.998 73.567 1.00 12.75 S ATOM 60439 SG CYSSd 24 149.027 163.104 72.263 1.00 17.79 S ATOM 60560 SG CYSSd 39 148.573 165.908 75.155 1.00 7.59 S ATOM 60586 SG CYSSd 42 149.918 163.016 76.290 1.00 11.52 S ATOM 75638 SG CYSSf 121 170.506 160.241 25.069 1.00 49.95 S ATOM 75674 SG CYSSf 126 171.630 157.782 27.874 1.00 49.61 S ATOM 75792 SG CYSSf 141 167.577 158.389 26.335 1.00 57.52 S Time building chain proxies: 31.34, per 1000 atoms: 0.41 Number of scatterers: 76240 At special positions: 0 Unit cell: (206.416, 256.424, 207.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 184 16.00 P 1723 15.00 Mg 22 11.99 O 18942 8.00 N 14016 7.00 C 41350 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: 14.22 Conformation dependent library (CDL) restraints added in 4.3 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=" ZNSd 101 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 24 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 39 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 21 " pdb="ZN ZNSd 101 " - pdb=" SG CYSSd 42 " pdb=" ZNSf 200 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 121 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 126 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 141 " Number of angles added : 12 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9206 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 56 sheets defined 34.9% alpha, 17.2% beta 530 base pairs and 895 stacking pairs defined. Time for finding SS restraints: 25.29 Creating SS restraints... Processing helix chain 'Ln' and resid 2 through 24 Processing helix chain 'SA' and resid 11 through 22 Processing helix chain 'SA' and resid 34 through 36 No H-bonds generated for 'chain 'SA' and resid 34 through 36' Processing helix chain 'SA' and resid 52 through 67 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 137 Processing helix chain 'SA' and resid 167 through 187 removed outlier: 3.541A pdb=" N GLYSA 172 " --> pdb=" O ALASA 168 " (cutoff:3.500A) Processing helix chain 'SA' and resid 198 through 203 Processing helix chain 'SA' and resid 206 through 223 removed outlier: 3.945A pdb=" N LYSSA 212 " --> pdb=" O GLUSA 208 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLUSA 214 " --> pdb=" O ILESA 210 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLNSA 215 " --> pdb=" O GLUSA 211 " (cutoff:3.500A) Processing helix chain 'SB' and resid 71 through 76 Processing helix chain 'SB' and resid 106 through 114 removed outlier: 3.769A pdb=" N VALSB 114 " --> pdb=" O METSB 110 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 178 removed outlier: 3.666A pdb=" N VALSB 176 " --> pdb=" O METSB 172 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THRSB 178 " --> pdb=" O ARGSB 174 " (cutoff:3.500A) Processing helix chain 'SB' and resid 180 through 186 removed outlier: 3.720A pdb=" N VALSB 185 " --> pdb=" O LEUSB 181 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASNSB 186 " --> pdb=" O LYSSB 182 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 Processing helix chain 'SB' and resid 202 through 204 No H-bonds generated for 'chain 'SB' and resid 202 through 204' Processing helix chain 'SB' and resid 225 through 233 removed outlier: 3.749A pdb=" N GLUSB 230 " --> pdb=" O GLYSB 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEUSB 231 " --> pdb=" O LYSSB 227 " (cutoff:3.500A) Processing helix chain 'SD' and resid 6 through 29 removed outlier: 3.532A pdb=" N VALSD 12 " --> pdb=" O LYSSD 8 " (cutoff:3.500A) Processing helix chain 'SD' and resid 54 through 60 Processing helix chain 'SD' and resid 63 through 78 Processing helix chain 'SD' and resid 93 through 96 Processing helix chain 'SD' and resid 97 through 112 Processing helix chain 'SD' and resid 114 through 129 Processing helix chain 'SD' and resid 163 through 167 Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 43 through 50 Processing helix chain 'SE' and resid 57 through 66 Processing helix chain 'SE' and resid 117 through 119 No H-bonds generated for 'chain 'SE' and resid 117 through 119' Processing helix chain 'SE' and resid 133 through 135 No H-bonds generated for 'chain 'SE' and resid 133 through 135' Processing helix chain 'SE' and resid 247 through 263 Processing helix chain 'SF' and resid 18 through 22 Processing helix chain 'SF' and resid 32 through 37 removed outlier: 4.113A pdb=" N ASPSF 37 " --> pdb=" O ILESF 33 " (cutoff:3.500A) Processing helix chain 'SF' and resid 42 through 46 Processing helix chain 'SF' and resid 67 through 77 removed outlier: 3.914A pdb=" N METSF 77 " --> pdb=" O THRSF 73 " (cutoff:3.500A) Processing helix chain 'SF' and resid 85 through 104 removed outlier: 4.113A pdb=" N ARGSF 91 " --> pdb=" O LEUSF 87 " (cutoff:3.500A) Processing helix chain 'SF' and resid 107 through 120 Processing helix chain 'SF' and resid 142 through 162 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 31 removed outlier: 3.864A pdb=" N GLUSH 29 " --> pdb=" O GLNSH 25 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEUSH 30 " --> pdb=" O ALASH 26 " (cutoff:3.500A) Processing helix chain 'SH' and resid 34 through 39 removed outlier: 3.515A pdb=" N ALASH 38 " --> pdb=" O ASPSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 68 through 75 removed outlier: 3.804A pdb=" N ILESH 75 " --> pdb=" O SERSH 71 " (cutoff:3.500A) Processing helix chain 'SH' and resid 76 through 87 removed outlier: 3.507A pdb=" N ARGSH 81 " --> pdb=" O VALSH 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLUSH 82 " --> pdb=" O ARGSH 78 " (cutoff:3.500A) Processing helix chain 'SH' and resid 117 through 120 Processing helix chain 'SH' and resid 121 through 132 removed outlier: 3.797A pdb=" N LEUSH 130 " --> pdb=" O HISSH 126 " (cutoff:3.500A) Processing helix chain 'SH' and resid 162 through 166 removed outlier: 3.609A pdb=" N ASNSH 165 " --> pdb=" O GLNSH 162 " (cutoff:3.500A) Processing helix chain 'SH' and resid 169 through 181 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 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 88 through 93 Processing helix chain 'SI' and resid 106 through 117 removed outlier: 3.607A pdb=" N GLUSI 114 " --> pdb=" O ARGSI 110 " (cutoff:3.500A) Processing helix chain 'SI' and resid 129 through 137 removed outlier: 3.960A pdb=" N GLUSI 134 " --> pdb=" O THRSI 130 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLUSI 135 " --> pdb=" O PROSI 131 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILESI 136 " --> pdb=" O GLUSI 132 " (cutoff:3.500A) Processing helix chain 'SI' and resid 142 through 155 removed outlier: 4.007A pdb=" N GLUSI 151 " --> pdb=" O LYSSI 147 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARGSI 152 " --> pdb=" O LYSSI 148 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYSSI 154 " --> pdb=" O ASPSI 150 " (cutoff:3.500A) Processing helix chain 'SI' and resid 160 through 169 Processing helix chain 'SI' and resid 178 through 183 Processing helix chain 'SI' and resid 192 through 206 Processing helix chain 'SK' and resid 4 through 18 removed outlier: 3.549A pdb=" N ALASK 10 " --> pdb=" O LYSSK 6 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLUSK 18 " --> pdb=" O LEUSK 14 " (cutoff:3.500A) Processing helix chain 'SK' and resid 41 through 55 Processing helix chain 'SK' and resid 72 through 83 removed outlier: 3.667A pdb=" N GLNSK 77 " --> pdb=" O ASNSK 73 " (cutoff:3.500A) Processing helix chain 'SL' and resid 47 through 52 Processing helix chain 'SP' and resid 21 through 27 removed outlier: 3.515A pdb=" N LEUSP 25 " --> pdb=" O ASPSP 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASPSP 27 " --> pdb=" O ASPSP 23 " (cutoff:3.500A) Processing helix chain 'SP' and resid 29 through 35 removed outlier: 4.245A pdb=" N GLNSP 35 " --> pdb=" O GLUSP 31 " (cutoff:3.500A) Processing helix chain 'SP' and resid 38 through 47 Processing helix chain 'SP' and resid 50 through 66 Processing helix chain 'SP' and resid 86 through 90 Processing helix chain 'SP' and resid 115 through 120 removed outlier: 3.686A pdb=" N PHESP 119 " --> pdb=" O LEUSP 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SERSP 120 " --> pdb=" O GLYSP 117 " (cutoff:3.500A) 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: 4.078A pdb=" N LEUSQ 51 " --> pdb=" O LEUSQ 47 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 57 removed outlier: 3.760A pdb=" N LEUSQ 57 " --> pdb=" O GLUSQ 53 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 59 through 63 removed outlier: 3.688A pdb=" N ARGSQ 62 " --> pdb=" O GLYSQ 59 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 76 through 100 removed outlier: 3.578A pdb=" N ILESQ 81 " --> pdb=" O HISSQ 77 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SERSQ 89 " --> pdb=" O ARGSQ 85 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VALSQ 100 " --> pdb=" O TYRSQ 96 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 101 through 115 removed outlier: 3.598A pdb=" N LYSSQ 105 " --> pdb=" O ASPSQ 101 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLUSQ 107 " --> pdb=" O ALASQ 103 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILESQ 108 " --> pdb=" O SERSQ 104 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEUSQ 112 " --> pdb=" O ILESQ 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILESQ 113 " --> pdb=" O LYSSQ 109 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 116 through 120 Processing helix chain 'SR' and resid 6 through 21 removed outlier: 3.550A pdb=" N ALASR 12 " --> pdb=" O THRSR 8 " (cutoff:3.500A) Processing helix chain 'SR' and resid 27 through 38 removed outlier: 3.758A pdb=" N GLUSR 37 " --> pdb=" O ARGSR 33 " (cutoff:3.500A) Processing helix chain 'SR' and resid 43 through 63 removed outlier: 3.828A pdb=" N ARGSR 63 " --> pdb=" O LYSSR 59 " (cutoff:3.500A) Processing helix chain 'SR' and resid 70 through 82 Processing helix chain 'SR' and resid 99 through 108 Processing helix chain 'SS' and resid 25 through 30 removed outlier: 3.713A 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 48 removed outlier: 3.619A pdb=" N VALSS 43 " --> pdb=" O ARGSS 39 " (cutoff:3.500A) Processing helix chain 'SS' and resid 55 through 59 removed outlier: 3.788A pdb=" N GLUSS 58 " --> pdb=" O ARGSS 55 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEUSS 59 " --> pdb=" O ALASS 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 55 through 59' Processing helix chain 'SS' and resid 60 through 70 Processing helix chain 'SS' and resid 80 through 84 removed outlier: 3.892A pdb=" N LEUSS 84 " --> pdb=" O ASPSS 81 " (cutoff:3.500A) Processing helix chain 'SS' and resid 100 through 117 removed outlier: 3.807A pdb=" N ASPSS 104 " --> pdb=" O ALASS 100 " (cutoff:3.500A) Processing helix chain 'SS' and resid 119 through 127 Processing helix chain 'ST' and resid 10 through 25 Processing helix chain 'ST' and resid 51 through 67 Processing helix chain 'ST' and resid 71 through 79 removed outlier: 3.645A pdb=" N LYSST 77 " --> pdb=" O GLYST 73 " (cutoff:3.500A) Processing helix chain 'ST' and resid 96 through 110 Processing helix chain 'ST' and resid 124 through 144 removed outlier: 3.645A pdb=" N LEUST 131 " --> pdb=" O GLYST 127 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLNST 137 " --> pdb=" O ARGST 133 " (cutoff:3.500A) Processing helix chain 'SU' and resid 28 through 45 Processing helix chain 'SU' and resid 94 through 102 removed outlier: 3.983A pdb=" N VALSU 98 " --> pdb=" O PROSU 94 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYSSU 99 " --> pdb=" O SERSU 95 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLNSU 100 " --> pdb=" O GLUSU 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILESU 101 " --> pdb=" O ILESU 97 " (cutoff:3.500A) Processing helix chain 'SV' and resid 58 through 63 Processing helix chain 'SV' and resid 64 through 76 removed outlier: 3.550A pdb=" N ASPSV 76 " --> pdb=" O LEUSV 72 " (cutoff:3.500A) Processing helix chain 'SX' and resid 9 through 21 Processing helix chain 'SX' and resid 24 through 33 removed outlier: 4.355A pdb=" N GLYSX 33 " --> pdb=" O LYSSX 29 " (cutoff:3.500A) Processing helix chain 'SX' and resid 33 through 39 Processing helix chain 'SX' and resid 129 through 135 Processing helix chain 'Sa' and resid 46 through 49 Processing helix chain 'Sa' and resid 50 through 57 removed outlier: 3.515A pdb=" N GLUSa 55 " --> pdb=" O ARGSa 51 " (cutoff:3.500A) Processing helix chain 'Sa' and resid 74 through 81 Processing helix chain 'Sa' and resid 90 through 94 Processing helix chain 'Sd' and resid 3 through 8 removed outlier: 4.103A 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 51 removed outlier: 3.696A pdb=" N GLNSd 45 " --> pdb=" O GLNSd 41 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYSSd 48 " --> pdb=" O ARGSd 44 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASPSd 49 " --> pdb=" O GLNSd 45 " (cutoff:3.500A) Processing helix chain 'SC' and resid 64 through 72 removed outlier: 3.555A pdb=" N ASPSC 72 " --> pdb=" O ARGSC 68 " (cutoff:3.500A) Processing helix chain 'SC' and resid 78 through 84 removed outlier: 3.947A pdb=" N PHESC 84 " --> pdb=" O GLUSC 80 " (cutoff:3.500A) Processing helix chain 'SC' and resid 90 through 98 removed outlier: 4.218A pdb=" N ILESC 94 " --> pdb=" O GLUSC 90 " (cutoff:3.500A) Processing helix chain 'SC' and resid 146 through 161 removed outlier: 3.517A pdb=" N ILESC 156 " --> pdb=" O ARGSC 152 " (cutoff:3.500A) Processing helix chain 'SC' and resid 207 through 216 removed outlier: 3.637A pdb=" N LEUSC 213 " --> pdb=" O VALSC 209 " (cutoff:3.500A) Processing helix chain 'SC' and resid 232 through 246 Processing helix chain 'SC' and resid 252 through 256 Processing helix chain 'SC' and resid 264 through 269 Processing helix chain 'SC' and resid 269 through 277 removed outlier: 3.791A pdb=" N VALSC 274 " --> pdb=" O THRSC 270 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYSSC 275 " --> pdb=" O ASPSC 271 " (cutoff:3.500A) Processing helix chain 'SG' and resid 20 through 28 removed outlier: 3.740A pdb=" N LEUSG 24 " --> pdb=" O ASPSG 20 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THRSG 26 " --> pdb=" O ARGSG 22 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHESG 27 " --> pdb=" O LYSSG 23 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 145 Processing helix chain 'SG' and resid 181 through 216 Processing helix chain 'SG' and resid 218 through 234 removed outlier: 3.589A pdb=" N LEUSG 234 " --> pdb=" O LYSSG 230 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 21 through 34 Processing helix chain 'SJ' and resid 40 through 62 removed outlier: 3.553A pdb=" N VALSJ 46 " --> pdb=" O GLUSJ 42 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 67 through 84 Processing helix chain 'SJ' and resid 93 through 98 removed outlier: 3.711A pdb=" N ILESJ 97 " --> pdb=" O LYSSJ 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEUSJ 98 " --> pdb=" O LEUSJ 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'SJ' and resid 93 through 98' Processing helix chain 'SJ' and resid 101 through 107 removed outlier: 3.883A pdb=" N PHESJ 105 " --> pdb=" O LYSSJ 101 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 109 through 117 removed outlier: 3.520A pdb=" N PHESJ 115 " --> pdb=" O GLNSJ 111 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 122 through 132 removed outlier: 3.588A pdb=" N VALSJ 128 " --> pdb=" O HISSJ 124 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 171 through 184 Processing helix chain 'SM' and resid 12 through 29 removed outlier: 3.607A pdb=" N THRSM 16 " --> pdb=" O METSM 12 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALASM 17 " --> pdb=" O ASPSM 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEUSM 22 " --> pdb=" O LEUSM 18 " (cutoff:3.500A) Processing helix chain 'SM' and resid 34 through 44 Processing helix chain 'SM' and resid 58 through 72 removed outlier: 3.722A pdb=" N LEUSM 64 " --> pdb=" O METSM 60 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALSM 65 " --> pdb=" O TYRSM 61 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALASM 67 " --> pdb=" O LYSSM 63 " (cutoff:3.500A) Processing helix chain 'SM' and resid 81 through 90 removed outlier: 4.100A pdb=" N LEUSM 85 " --> pdb=" O ASPSM 81 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLYSM 86 " --> pdb=" O ASNSM 82 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLUSM 87 " --> pdb=" O LYSSM 83 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLYSM 90 " --> pdb=" O GLYSM 86 " (cutoff:3.500A) Processing helix chain 'SM' and resid 119 through 132 removed outlier: 3.675A pdb=" N LYSSM 132 " --> pdb=" O PHESM 128 " (cutoff:3.500A) Processing helix chain 'SN' and resid 29 through 43 removed outlier: 3.607A pdb=" N LYSSN 43 " --> pdb=" O LYSSN 39 " (cutoff:3.500A) Processing helix chain 'SN' and resid 46 through 57 Processing helix chain 'SN' and resid 62 through 68 Processing helix chain 'SN' and resid 70 through 79 Processing helix chain 'SN' and resid 85 through 105 removed outlier: 3.524A pdb=" N LEUSN 91 " --> pdb=" O ASPSN 87 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARGSN 104 " --> pdb=" O LYSSN 100 " (cutoff:3.500A) Processing helix chain 'SN' and resid 108 through 132 Processing helix chain 'SN' and resid 145 through 150 Processing helix chain 'SO' and resid 59 through 61 No H-bonds generated for 'chain 'SO' and resid 59 through 61' Processing helix chain 'SO' and resid 70 through 89 Processing helix chain 'SO' and resid 111 through 122 removed outlier: 3.505A pdb=" N LEUSO 119 " --> pdb=" O ALASO 115 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 20 Processing helix chain 'SW' and resid 31 through 44 removed outlier: 3.517A pdb=" N HISSW 44 " --> pdb=" O VALSW 40 " (cutoff:3.500A) Processing helix chain 'SW' and resid 85 through 94 removed outlier: 3.854A pdb=" N TRPSW 89 " --> pdb=" O ASPSW 85 " (cutoff:3.500A) Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SY' and resid 36 through 49 Processing helix chain 'SY' and resid 78 through 85 Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 103 through 116 removed outlier: 3.736A pdb=" N LYSSY 116 " --> pdb=" O ASNSY 112 " (cutoff:3.500A) Processing helix chain 'SY' and resid 120 through 125 Processing helix chain 'SZ' and resid 51 through 60 removed outlier: 3.586A pdb=" N LYSSZ 60 " --> pdb=" O ASPSZ 56 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 61 through 65 removed outlier: 3.891A pdb=" N TYRSZ 65 " --> pdb=" O VALSZ 62 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 69 through 77 removed outlier: 3.761A pdb=" N GLUSZ 75 " --> pdb=" O ALASZ 71 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 82 through 95 removed outlier: 3.509A pdb=" N GLYSZ 95 " --> pdb=" O LEUSZ 91 " (cutoff:3.500A) Processing helix chain 'Sb' and resid 11 through 18 Processing helix chain 'Se' and resid 10 through 16 Processing helix chain 'Se' and resid 30 through 43 Processing helix chain 'CD' and resid 113 through 118 removed outlier: 3.620A pdb=" N GLYCD 116 " --> pdb=" O PROCD 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SA' and resid 38 through 41 removed outlier: 6.981A 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: 6.588A pdb=" N VALSA 74 " --> pdb=" O THRSA 97 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILESA 99 " --> pdb=" O VALSA 74 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VALSA 76 " --> pdb=" O ILESA 99 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEUSA 122 " --> pdb=" O ILESA 145 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEUSA 147 " --> pdb=" O LEUSA 122 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VALSA 124 " --> pdb=" O LEUSA 147 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THRSA 144 " --> pdb=" O ILESA 159 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILESA 161 " --> pdb=" O THRSA 144 " (cutoff:3.500A) removed outlier: 6.604A 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: 3.789A pdb=" N GLYSB 45 " --> pdb=" O VALSB 33 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASPSB 90 " --> pdb=" O LEUSB 97 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASNSB 99 " --> pdb=" O THRSB 88 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THRSB 88 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SB' and resid 69 through 70 removed outlier: 8.779A pdb=" N ARGSB 213 " --> pdb=" O LEUSB 105 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VALSB 212 " --> pdb=" O VALSB 140 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VALSB 140 " --> pdb=" O VALSB 212 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEUSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'SD' and resid 37 through 42 removed outlier: 3.629A pdb=" N THRSD 42 " --> pdb=" O ARGSD 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARGSD 45 " --> pdb=" O THRSD 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SD' and resid 148 through 155 removed outlier: 3.662A pdb=" N GLYSD 133 " --> pdb=" O METSD 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'SD' and resid 209 through 210 removed outlier: 3.897A pdb=" N SERSD 209 " --> pdb=" O ILESR 40 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILESR 40 " --> pdb=" O SERSD 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'SE' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'SE' and resid 102 through 103 removed outlier: 4.379A pdb=" N ILESE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SE' and resid 121 through 125 removed outlier: 6.194A pdb=" N ASPSE 163 " --> pdb=" O ILESE 169 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILESE 169 " --> pdb=" O ASPSE 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'SE' and resid 128 through 132 removed outlier: 3.503A pdb=" N ILESE 136 " --> pdb=" O GLYSE 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SE' and resid 217 through 221 removed outlier: 6.532A pdb=" N VALSE 207 " --> pdb=" O ARGSE 198 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARGSE 198 " --> pdb=" O VALSE 207 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HISSE 209 " --> pdb=" O THRSE 196 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEUSE 180 " --> pdb=" O ILESE 228 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSSE 230 " --> pdb=" O LYSSE 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSSE 233 " --> pdb=" O LYSSE 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SF' and resid 123 through 125 removed outlier: 8.042A pdb=" N ALASF 138 " --> pdb=" O ASNSc 45 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LYSSc 47 " --> pdb=" O ALASF 138 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASPSF 140 " --> pdb=" O LYSSc 47 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYSSc 27 " --> pdb=" O ARGSc 20 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARGSc 20 " --> pdb=" O CYSSc 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SH' and resid 47 through 52 removed outlier: 3.533A pdb=" N ALASH 47 " --> pdb=" O PHESH 63 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HISSH 91 " --> pdb=" O LYSSH 58 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VALSH 93 " --> pdb=" O ILESH 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILESH 62 " --> pdb=" O VALSH 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SH' and resid 185 through 188 removed outlier: 6.382A pdb=" N ILESH 154 " --> pdb=" O ASNSH 186 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLUSH 188 " --> pdb=" O ILESH 154 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VALSH 156 " --> pdb=" O GLUSH 188 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYSSH 142 " --> pdb=" O ASPSW 54 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHESW 50 " --> pdb=" O VALSH 146 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLUSW 49 " --> pdb=" O ASNSW 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SI' and resid 3 through 4 removed outlier: 4.178A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SI' and resid 37 through 38 removed outlier: 6.505A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SI' and resid 62 through 67 removed outlier: 6.311A pdb=" N LEUSI 103 " --> pdb=" O ILESI 79 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VALSI 81 " --> pdb=" O ILESI 101 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILESI 101 " --> pdb=" O VALSI 81 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYSSI 100 " --> pdb=" O ILESI 175 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLYSI 187 " --> pdb=" O VALSI 62 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 187 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VALSI 189 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SERSI 66 " --> pdb=" O VALSI 189 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SK' and resid 20 through 24 removed outlier: 3.674A pdb=" N METSK 21 " --> pdb=" O TRPSK 69 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRPSK 69 " --> pdb=" O METSK 21 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SL' and resid 72 through 79 removed outlier: 18.276A pdb=" N ILESL 72 " --> pdb=" O LEUSL 93 " (cutoff:3.500A) removed outlier: 15.167A pdb=" N LEUSL 93 " --> pdb=" O ILESL 72 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SERSL 74 " --> pdb=" O ASPSL 91 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASPSL 91 " --> pdb=" O SERSL 74 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VALSL 87 " --> pdb=" O THRSL 78 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHESL 140 " --> pdb=" O ASNSL 108 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SERSL 110 " --> pdb=" O PHESL 140 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VALSL 142 " --> pdb=" O SERSL 110 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HISSL 112 " --> pdb=" O VALSL 142 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N LYSSL 144 " --> pdb=" O HISSL 112 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THRSL 127 " --> pdb=" O LEUSL 143 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VALSL 145 " --> pdb=" O ILESL 125 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILESL 125 " --> pdb=" O VALSL 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SP' and resid 76 through 78 removed outlier: 3.657A pdb=" N VALSP 94 " --> pdb=" O VALSP 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SQ' and resid 9 through 16 Processing sheet with id=AC5, first strand: chain 'SR' and resid 96 through 98 removed outlier: 5.830A pdb=" N ILESR 96 " --> pdb=" O GLNSR 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'SS' and resid 12 through 14 Processing sheet with id=AC7, first strand: chain 'ST' and resid 81 through 83 Processing sheet with id=AC8, first strand: chain 'ST' and resid 113 through 115 Processing sheet with id=AC9, first strand: chain 'SU' and resid 50 through 65 removed outlier: 8.346A pdb=" N ASPSU 90 " --> pdb=" O PROSU 53 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARGSU 55 " --> pdb=" O LEUSU 88 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEUSU 88 " --> pdb=" O ARGSU 55 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYSSU 86 " --> pdb=" O PROSU 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLUSU 113 " --> pdb=" O THRSU 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THRSU 25 " --> pdb=" O GLUSU 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'SU' and resid 50 through 65 removed outlier: 8.346A pdb=" N ASPSU 90 " --> pdb=" O PROSU 53 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARGSU 55 " --> pdb=" O LEUSU 88 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEUSU 88 " --> pdb=" O ARGSU 55 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYSSU 86 " --> pdb=" O PROSU 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'SV' and resid 32 through 39 removed outlier: 5.770A pdb=" N GLNSV 49 " --> pdb=" O GLUSV 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'SX' and resid 46 through 58 removed outlier: 6.767A pdb=" N ARGSX 71 " --> pdb=" O LEUSX 52 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYSSX 54 " --> pdb=" O CYSSX 69 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N CYSSX 69 " --> pdb=" O LYSSX 54 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLYSX 56 " --> pdb=" O ARGSX 67 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARGSX 67 " --> pdb=" O GLYSX 56 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N PHESX 120 " --> pdb=" O LYSSX 80 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THRSX 82 " --> pdb=" O PHESX 120 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VALSX 122 " --> pdb=" O THRSX 82 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHESX 84 " --> pdb=" O VALSX 122 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LYSSX 124 " --> pdb=" O PHESX 84 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VALSX 125 " --> pdb=" O GLUSX 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLUSX 99 " --> pdb=" O VALSX 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Sa' and resid 20 through 22 Processing sheet with id=AD5, first strand: chain 'Sa' and resid 36 through 43 Processing sheet with id=AD6, first strand: chain 'Sc' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'Sd' and resid 30 through 31 Processing sheet with id=AD8, first strand: chain 'Sg' and resid 4 through 11 removed outlier: 4.977A pdb=" N METSg 5 " --> pdb=" O THRSg 313 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THRSg 313 " --> pdb=" O METSg 5 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEUSg 7 " --> pdb=" O GLNSg 311 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLNSg 311 " --> pdb=" O LEUSg 7 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLYSg 9 " --> pdb=" O VALSg 309 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VALSg 309 " --> pdb=" O GLYSg 9 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Sg' and resid 18 through 22 removed outlier: 3.721A pdb=" N LEUSg 32 " --> pdb=" O ALASg 22 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THRSg 39 " --> pdb=" O SERSg 35 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYSSg 44 " --> pdb=" O PROSg 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Sg' and resid 66 through 71 removed outlier: 6.684A pdb=" N GLYSg 81 " --> pdb=" O SERSg 67 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VALSg 69 " --> pdb=" O LEUSg 79 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEUSg 79 " --> pdb=" O VALSg 69 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILESg 71 " --> pdb=" O PHESg 77 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHESg 77 " --> pdb=" O ILESg 71 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THRSg 86 " --> pdb=" O SERSg 82 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASPSg 91 " --> pdb=" O THRSg 97 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N THRSg 97 " --> pdb=" O ASPSg 91 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Sg' and resid 108 through 113 removed outlier: 6.970A pdb=" N GLYSg 123 " --> pdb=" O LEUSg 109 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VALSg 111 " --> pdb=" O VALSg 121 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VALSg 121 " --> pdb=" O VALSg 111 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Sg' and resid 151 through 156 removed outlier: 4.861A pdb=" N CYSSg 153 " --> pdb=" O CYSSg 168 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYSSg 168 " --> pdb=" O CYSSg 153 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASNSg 178 " --> pdb=" O LEUSg 184 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEUSg 184 " --> pdb=" O ASNSg 178 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Sg' and resid 195 through 200 removed outlier: 3.537A pdb=" N THRSg 197 " --> pdb=" O GLYSg 210 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLYSg 211 " --> pdb=" O GLNSg 215 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLNSg 215 " --> pdb=" O GLYSg 211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Sg' and resid 236 through 240 removed outlier: 3.864A pdb=" N ALASg 238 " --> pdb=" O ALASg 251 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'SC' and resid 103 through 115 removed outlier: 6.692A pdb=" N PHESC 127 " --> pdb=" O LEUSC 107 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILESC 109 " --> pdb=" O LYSSC 125 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYSSC 125 " --> pdb=" O ILESC 109 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARGSC 123 " --> pdb=" O PROSC 111 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLNSC 113 " --> pdb=" O ARGSC 121 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARGSC 121 " --> pdb=" O GLNSC 113 " (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: 6.863A pdb=" N LYSSG 2 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEUSG 111 " --> pdb=" O LYSSG 2 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASNSG 4 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILESG 113 " --> pdb=" O ASNSG 4 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SERSG 6 " --> pdb=" O ILESG 113 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYSSG 115 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VALSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILESG 52 " --> pdb=" O VALSG 112 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VALSG 114 " --> pdb=" O VALSG 50 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VALSG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'SG' and resid 30 through 31 removed outlier: 3.871A pdb=" N LYSSG 30 " --> pdb=" O VALSG 102 " (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 Processing sheet with id=AF3, first strand: chain 'SJ' and resid 140 through 141 Processing sheet with id=AF4, first strand: chain 'SM' and resid 32 through 33 Processing sheet with id=AF5, first strand: chain 'SO' and resid 52 through 57 removed outlier: 7.114A pdb=" N VALSO 44 " --> pdb=" O ILESO 53 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARGSO 55 " --> pdb=" O VALSO 42 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VALSO 42 " --> pdb=" O ARGSO 55 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THRSO 57 " --> pdb=" O THRSO 40 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THRSO 40 " --> pdb=" O THRSO 57 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEUSO 93 " --> pdb=" O GLYSO 127 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILESO 129 " --> pdb=" O LEUSO 93 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILESO 95 " --> pdb=" O ILESO 129 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASPSO 131 " --> pdb=" O ILESO 95 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEUSO 97 " --> pdb=" O ASPSO 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'SW' and resid 80 through 81 removed outlier: 5.540A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'SY' and resid 6 through 15 removed outlier: 4.464A pdb=" N PHESY 12 " --> pdb=" O GLNSY 22 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLNSY 22 " --> pdb=" O PHESY 12 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N THRSY 14 " --> pdb=" O ARGSY 20 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARGSY 20 " --> pdb=" O THRSY 14 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLYSY 67 " --> pdb=" O HISSY 29 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THRSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHESY 60 " --> pdb=" O THRSY 70 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'SZ' and resid 97 through 99 Processing sheet with id=AF9, first strand: chain 'Sb' and resid 33 through 34 removed outlier: 3.925A pdb=" N ARGSb 80 " --> pdb=" O ASPSb 34 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Sb' and resid 54 through 55 removed outlier: 6.858A pdb=" N VALSb 54 " --> pdb=" O LEUSb 63 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Sf' and resid 138 through 141 removed outlier: 3.991A pdb=" N CYSSf 141 " --> pdb=" O LEUSf 146 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEUSf 146 " --> pdb=" O CYSSf 141 " (cutoff:3.500A) 1481 hydrogen bonds defined for protein. 4185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1307 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 530 basepair parallelities 895 stacking parallelities Total time for adding SS restraints: 59.36 Time building geometry restraints manager: 17.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10749 1.33 - 1.45: 30365 1.45 - 1.57: 36353 1.57 - 1.70: 3442 1.70 - 1.82: 282 Bond restraints: 81191 Sorted by residual: bond pdb=" CA SERSZ 82 " pdb=" CB SERSZ 82 " ideal model delta sigma weight residual 1.534 1.475 0.058 1.58e-02 4.01e+03 1.36e+01 bond pdb=" C VALSX 100 " pdb=" O VALSX 100 " ideal model delta sigma weight residual 1.236 1.201 0.035 9.90e-03 1.02e+04 1.24e+01 bond pdb=" N LYSSX 124 " pdb=" CA LYSSX 124 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.21e+01 bond pdb=" CA SERSd 25 " pdb=" CB SERSd 25 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.43e-02 4.89e+03 1.12e+01 bond pdb=" N LYSSA 11 " pdb=" CA LYSSA 11 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 ... (remaining 81186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 116172 2.92 - 5.83: 1402 5.83 - 8.75: 169 8.75 - 11.67: 22 11.67 - 14.59: 3 Bond angle restraints: 117768 Sorted by residual: angle pdb=" N ILESB 150 " pdb=" CA ILESB 150 " pdb=" C ILESB 150 " ideal model delta sigma weight residual 110.05 102.96 7.09 1.09e+00 8.42e-01 4.23e+01 angle pdb=" C ILESB 150 " pdb=" N ARGSB 151 " pdb=" CA ARGSB 151 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" CA VALSO 14 " pdb=" C VALSO 14 " pdb=" N ILESO 15 " ideal model delta sigma weight residual 117.37 121.42 -4.05 7.40e-01 1.83e+00 3.00e+01 angle pdb=" C VALSO 14 " pdb=" N ILESO 15 " pdb=" CA ILESO 15 " ideal model delta sigma weight residual 121.70 131.29 -9.59 1.80e+00 3.09e-01 2.84e+01 angle pdb=" C3' US2 688 " pdb=" O3' US2 688 " pdb=" P US2 689 " ideal model delta sigma weight residual 120.20 128.16 -7.96 1.50e+00 4.44e-01 2.81e+01 ... (remaining 117763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 46852 35.95 - 71.91: 4402 71.91 - 107.86: 490 107.86 - 143.82: 10 143.82 - 179.77: 17 Dihedral angle restraints: 51771 sinusoidal: 37490 harmonic: 14281 Sorted by residual: dihedral pdb=" O4' CS21139 " pdb=" C1' CS21139 " pdb=" N1 CS21139 " pdb=" C2 CS21139 " ideal model delta sinusoidal sigma weight residual 200.00 21.35 178.65 1 1.50e+01 4.44e-03 8.53e+01 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 22.89 177.11 1 1.50e+01 4.44e-03 8.53e+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 42.53 157.47 1 1.50e+01 4.44e-03 8.21e+01 ... (remaining 51768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 13503 0.088 - 0.176: 940 0.176 - 0.263: 72 0.263 - 0.351: 9 0.351 - 0.439: 2 Chirality restraints: 14526 Sorted by residual: chirality pdb=" CA VALSX 123 " pdb=" N VALSX 123 " pdb=" C VALSX 123 " pdb=" CB VALSX 123 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CB VALSX 123 " pdb=" CA VALSX 123 " pdb=" CG1 VALSX 123 " pdb=" CG2 VALSX 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA VALSZ 48 " pdb=" N VALSZ 48 " pdb=" C VALSZ 48 " pdb=" CB VALSZ 48 " both_signs ideal model delta sigma weight residual False 2.44 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 14523 not shown) Planarity restraints: 8600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASNSd 37 " 0.029 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" C ASNSd 37 " -0.100 2.00e-02 2.50e+03 pdb=" O ASNSd 37 " 0.038 2.00e-02 2.50e+03 pdb=" N METSd 38 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CS21756 " 0.003 2.00e-02 2.50e+03 3.32e-02 2.48e+01 pdb=" N1 CS21756 " -0.007 2.00e-02 2.50e+03 pdb=" C2 CS21756 " 0.078 2.00e-02 2.50e+03 pdb=" O2 CS21756 " -0.058 2.00e-02 2.50e+03 pdb=" N3 CS21756 " 0.011 2.00e-02 2.50e+03 pdb=" C4 CS21756 " 0.001 2.00e-02 2.50e+03 pdb=" N4 CS21756 " -0.008 2.00e-02 2.50e+03 pdb=" C5 CS21756 " -0.017 2.00e-02 2.50e+03 pdb=" C6 CS21756 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYSSM 99 " 0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PROSM 100 " -0.165 5.00e-02 4.00e+02 pdb=" CA PROSM 100 " 0.050 5.00e-02 4.00e+02 pdb=" CD PROSM 100 " 0.052 5.00e-02 4.00e+02 ... (remaining 8597 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1655 2.64 - 3.20: 60768 3.20 - 3.77: 144710 3.77 - 4.33: 196696 4.33 - 4.90: 275043 Nonbonded interactions: 678872 Sorted by model distance: nonbonded pdb=" OP2 AS2 449 " pdb="MG MGS21907 " model vdw 2.070 2.170 nonbonded pdb=" OP1 GS21837 " pdb="MG MGS21916 " model vdw 2.099 2.170 nonbonded pdb=" OP2 US21839 " pdb="MG MGS21918 " model vdw 2.122 2.170 nonbonded pdb=" OP1 GS2 684 " pdb="MG MGS21911 " model vdw 2.125 2.170 nonbonded pdb=" OP1 US21072 " pdb="MG MGS21919 " model vdw 2.136 2.170 ... (remaining 678867 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.500 Check model and map are aligned: 0.470 Set scattering table: 0.560 Process input model: 184.080 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.005 0.066 81191 Z= 0.286 Angle : 0.824 14.586 117768 Z= 0.439 Chirality : 0.046 0.439 14526 Planarity : 0.006 0.096 8600 Dihedral : 21.862 179.772 42565 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.16 % Favored : 93.39 % Rotamer: Outliers : 0.58 % Allowed : 0.98 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -2.86 (0.10), residues: 4903 helix: -2.74 (0.09), residues: 1552 sheet: -0.95 (0.17), residues: 887 loop : -1.58 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPSN 25 HIS 0.011 0.001 HISSP 79 PHE 0.040 0.002 PHESX 105 TYR 0.052 0.002 TYRST 79 ARG 0.011 0.001 ARGSX 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 772 time to evaluate : 4.616 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: SR 1 MET cc_start: 0.4641 (mpp) cc_final: 0.3162 (tpt) REVERT: SR 15 VAL cc_start: 0.8763 (t) cc_final: 0.8558 (t) REVERT: SG 126 ASP cc_start: 0.6730 (p0) cc_final: 0.6458 (p0) REVERT: SW 18 GLU cc_start: 0.7919 (tp30) cc_final: 0.7518 (mm-30) REVERT: SW 55 ASP cc_start: 0.7508 (p0) cc_final: 0.7263 (p0) outliers start: 25 outliers final: 8 residues processed: 790 average time/residue: 1.6669 time to fit residues: 1722.7612 Evaluate side-chains 613 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 605 time to evaluate : 4.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SH residue 41 ARG Chi-restraints excluded: chain SH residue 43 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SX residue 123 VAL Chi-restraints excluded: chain SZ residue 44 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 553 optimal weight: 0.9990 chunk 496 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 265 optimal weight: 0.7980 chunk 513 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 594 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 169 HIS SB 208 HIS SD 74 GLN SF 186 ASN SH 12 ASN SH 114 GLN SI 84 ASN SI 167 GLN SK 42 ASN SL 65 ASN SL 112 HIS ** SP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SP 46 ASN SP 53 GLN ** SP 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 8 GLN SQ 11 GLN SR 31 ASN ** SS 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 87 GLN SS 97 GLN ST 12 GLN ST 51 ASN Sd 3 HIS Sd 26 ASN SC 115 GLN SC 178 HIS SG 65 GLN SN 36 GLN SW 120 HIS SZ 45 ASN Sb 49 HIS Se 22 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101308 restraints weight = 113785.843| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 0.70 r_work: 0.2983 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 81191 Z= 0.295 Angle : 0.666 12.813 117768 Z= 0.343 Chirality : 0.042 0.271 14526 Planarity : 0.006 0.071 8600 Dihedral : 23.060 179.559 32311 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.75 % Favored : 94.02 % Rotamer: Outliers : 2.10 % Allowed : 11.46 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.11), residues: 4903 helix: -0.66 (0.12), residues: 1599 sheet: -0.92 (0.17), residues: 909 loop : -1.49 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPSg 177 HIS 0.007 0.001 HISSP 79 PHE 0.027 0.002 PHESZ 50 TYR 0.018 0.002 TYRSR 21 ARG 0.009 0.001 ARGSO 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 640 time to evaluate : 4.584 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: SD 4 GLN cc_start: 0.6816 (pm20) cc_final: 0.6495 (pm20) REVERT: SE 19 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: SR 1 MET cc_start: 0.5376 (mpp) cc_final: 0.3751 (tpt) REVERT: SR 67 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.4929 (mtt-85) REVERT: SR 104 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: ST 35 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: ST 114 GLU cc_start: 0.8197 (pp20) cc_final: 0.7995 (pp20) REVERT: Sc 55 VAL cc_start: 0.8538 (p) cc_final: 0.8222 (m) REVERT: SC 117 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.5991 (mtm-85) REVERT: SW 55 ASP cc_start: 0.7856 (p0) cc_final: 0.7613 (p0) outliers start: 90 outliers final: 45 residues processed: 684 average time/residue: 1.5820 time to fit residues: 1432.9076 Evaluate side-chains 639 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 589 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SF residue 199 VAL Chi-restraints excluded: chain SH residue 27 LEU Chi-restraints excluded: chain SH residue 41 ARG Chi-restraints excluded: chain SH residue 119 SER Chi-restraints excluded: chain SH residue 137 SER Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SK residue 51 SER Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 67 ARG Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain ST residue 35 ASP Chi-restraints excluded: chain ST residue 98 SER Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 11 LEU Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SX residue 64 SER Chi-restraints excluded: chain SX residue 123 VAL Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 132 TRP Chi-restraints excluded: chain SC residue 117 ARG Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 56 VAL Chi-restraints excluded: chain SW residue 66 THR Chi-restraints excluded: chain SW residue 80 ASP Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Se residue 36 MET Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 558 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 615 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 486 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 406 optimal weight: 6.9990 chunk 645 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 57 ASN SD 74 GLN SH 97 GLN SH 114 GLN SH 162 GLN SH 163 GLN SI 9 HIS SI 167 GLN SP 32 GLN ** SP 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 86 GLN SR 26 ASN SS 17 ASN SS 97 GLN ST 12 GLN SU 81 GLN ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sd 3 HIS Sg 147 HIS ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 70 HIS SG 202 ASN SN 105 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101618 restraints weight = 113743.104| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.67 r_work: 0.2992 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 81191 Z= 0.284 Angle : 0.638 11.608 117768 Z= 0.328 Chirality : 0.041 0.284 14526 Planarity : 0.005 0.060 8600 Dihedral : 22.988 179.794 32307 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.12 % Favored : 93.68 % Rotamer: Outliers : 3.06 % Allowed : 14.22 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4903 helix: 0.07 (0.13), residues: 1611 sheet: -0.90 (0.17), residues: 903 loop : -1.38 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPSg 177 HIS 0.018 0.001 HISSG 70 PHE 0.020 0.002 PHESJ 147 TYR 0.022 0.002 TYRSK 78 ARG 0.018 0.001 ARGSZ 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 622 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 4 GLN cc_start: 0.6783 (pm20) cc_final: 0.6514 (pm20) REVERT: SE 19 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.7945 (mpp) REVERT: SI 167 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: SR 1 MET cc_start: 0.5588 (mpp) cc_final: 0.4034 (tpt) REVERT: SR 104 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: ST 35 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: ST 114 GLU cc_start: 0.8285 (pp20) cc_final: 0.8072 (pp20) REVERT: ST 126 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7684 (tp-100) REVERT: Sc 55 VAL cc_start: 0.8605 (p) cc_final: 0.8308 (m) REVERT: SC 117 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6197 (mtm-85) REVERT: SC 273 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7849 (mp) REVERT: SG 126 ASP cc_start: 0.7146 (p0) cc_final: 0.6906 (p0) REVERT: SN 87 ASP cc_start: 0.8537 (m-30) cc_final: 0.8337 (m-30) REVERT: SW 55 ASP cc_start: 0.7946 (p0) cc_final: 0.7721 (p0) outliers start: 131 outliers final: 65 residues processed: 692 average time/residue: 1.6272 time to fit residues: 1491.1494 Evaluate side-chains 653 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 582 time to evaluate : 4.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 40 LYS Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 78 MET Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SF residue 199 VAL Chi-restraints excluded: chain SH residue 27 LEU Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 137 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 167 GLN Chi-restraints excluded: chain SK residue 51 SER Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 92 SER Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 52 LEU Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 60 LYS Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SR residue 73 LEU Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 88 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 35 ASP Chi-restraints excluded: chain ST residue 98 SER Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 11 LEU Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SV residue 74 LYS Chi-restraints excluded: chain SX residue 64 SER Chi-restraints excluded: chain SX residue 123 VAL Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 27 CYS Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 46 VAL Chi-restraints excluded: chain Sg residue 42 MET Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain SC residue 117 ARG Chi-restraints excluded: chain SC residue 260 VAL Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 125 THR Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SW residue 66 THR Chi-restraints excluded: chain SW residue 80 ASP Chi-restraints excluded: chain SY residue 6 THR Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 248 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 629 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 440 optimal weight: 4.9990 chunk 490 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 433 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 149 GLN SD 57 ASN SD 74 GLN SH 97 GLN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SP 35 GLN ** SP 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 24 HIS SS 97 GLN ST 12 GLN ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sd 37 ASN ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 202 ASN Se 37 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103797 restraints weight = 114284.888| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 0.58 r_work: 0.2913 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 81191 Z= 0.180 Angle : 0.584 9.925 117768 Z= 0.300 Chirality : 0.037 0.308 14526 Planarity : 0.005 0.070 8600 Dihedral : 22.930 179.346 32301 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.77 % Favored : 94.02 % Rotamer: Outliers : 3.04 % Allowed : 16.25 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4903 helix: 0.48 (0.13), residues: 1607 sheet: -0.79 (0.17), residues: 888 loop : -1.31 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPSg 177 HIS 0.005 0.001 HISSP 79 PHE 0.017 0.001 PHESW 50 TYR 0.022 0.001 TYRSK 78 ARG 0.009 0.000 ARGSD 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 613 time to evaluate : 4.715 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: SA 52 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8131 (ptmm) REVERT: SB 175 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8437 (mm-30) REVERT: SE 19 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8020 (mpp) REVERT: SE 66 MET cc_start: 0.9024 (mmm) cc_final: 0.8685 (tpp) REVERT: SI 167 GLN cc_start: 0.8290 (mp10) cc_final: 0.8016 (mp10) REVERT: SK 34 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: SK 47 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.7968 (mptt) REVERT: SR 1 MET cc_start: 0.5814 (mpp) cc_final: 0.4089 (tpt) REVERT: SR 104 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: ST 114 GLU cc_start: 0.8505 (pp20) cc_final: 0.8102 (pp20) REVERT: ST 126 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7860 (tp-100) REVERT: SC 95 ASP cc_start: 0.8016 (m-30) cc_final: 0.7779 (m-30) REVERT: SC 273 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7655 (mp) REVERT: SN 87 ASP cc_start: 0.8500 (m-30) cc_final: 0.8277 (m-30) REVERT: SO 88 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8599 (tt) REVERT: SW 55 ASP cc_start: 0.8000 (p0) cc_final: 0.7776 (p0) REVERT: Sb 17 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8232 (ttm-80) REVERT: Sb 80 ARG cc_start: 0.7152 (ptp-110) cc_final: 0.6937 (ptp90) outliers start: 130 outliers final: 61 residues processed: 685 average time/residue: 1.5840 time to fit residues: 1447.6236 Evaluate side-chains 653 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 585 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 40 LYS Chi-restraints excluded: chain SA residue 52 LYS Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SB residue 225 LEU Chi-restraints excluded: chain SD residue 35 SER Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 137 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 174 CYS Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 47 LYS Chi-restraints excluded: chain SK residue 51 SER Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 45 LYS Chi-restraints excluded: chain SP residue 122 THR Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 60 LYS Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 106 LYS Chi-restraints excluded: chain SR residue 73 LEU Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SV residue 74 LYS Chi-restraints excluded: chain SX residue 64 SER Chi-restraints excluded: chain SX residue 123 VAL Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sg residue 19 THR Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 56 VAL Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 88 LEU Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 44 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 473 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 208 HIS SD 57 ASN SD 74 GLN SE 197 ASN SF 51 HIS ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 97 GLN SH 114 GLN SH 162 GLN SH 163 GLN SI 7 ASN SK 73 ASN SP 35 GLN SP 128 HIS SQ 24 HIS SR 93 GLN SS 10 GLN SS 97 GLN ST 12 GLN ST 85 ASN ** SV 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SX 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sc 29 GLN Sd 5 GLN ** Sd 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sd 37 ASN Sg 191 HIS SC 113 GLN ** SC 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 13 GLN SZ 112 ASN Se 37 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.097741 restraints weight = 113955.848| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.83 r_work: 0.2885 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.115 81191 Z= 0.649 Angle : 0.851 16.626 117768 Z= 0.426 Chirality : 0.054 0.337 14526 Planarity : 0.007 0.124 8600 Dihedral : 23.026 179.682 32301 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.18 % Favored : 92.64 % Rotamer: Outliers : 4.33 % Allowed : 17.30 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -1.19 (0.12), residues: 4903 helix: 0.22 (0.13), residues: 1609 sheet: -0.99 (0.17), residues: 907 loop : -1.38 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRPSg 177 HIS 0.012 0.002 HISSV 29 PHE 0.029 0.003 PHESJ 147 TYR 0.029 0.003 TYRSK 78 ARG 0.013 0.001 ARGSJ 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 621 time to evaluate : 4.652 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: SA 52 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7974 (ptmm) REVERT: SE 19 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8029 (mpp) REVERT: SE 66 MET cc_start: 0.9094 (mmm) cc_final: 0.8879 (mmm) REVERT: SK 34 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: SK 47 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8029 (mptt) REVERT: SR 104 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: ST 126 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7677 (tp-100) REVERT: SC 95 ASP cc_start: 0.7988 (m-30) cc_final: 0.7787 (m-30) REVERT: SC 105 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: SC 117 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6404 (mtm-85) REVERT: SJ 37 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8731 (mp) REVERT: SO 88 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8336 (tt) REVERT: SW 85 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7598 (p0) REVERT: SY 74 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7981 (mtp) REVERT: Sf 94 LYS cc_start: 0.5416 (tttt) cc_final: 0.5124 (tptt) REVERT: Sf 97 LYS cc_start: 0.3587 (mmtm) cc_final: 0.3152 (mtpt) REVERT: Sf 104 LYS cc_start: 0.4260 (mmpt) cc_final: 0.3819 (mmpt) outliers start: 185 outliers final: 104 residues processed: 739 average time/residue: 1.5799 time to fit residues: 1558.1837 Evaluate side-chains 715 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 600 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 29 ASN Chi-restraints excluded: chain SA residue 52 LYS Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 144 THR Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SB residue 98 THR Chi-restraints excluded: chain SB residue 113 MET Chi-restraints excluded: chain SD residue 35 SER Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 211 VAL Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 76 VAL Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 98 GLU Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 137 SER Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 107 THR Chi-restraints excluded: chain SI residue 174 CYS Chi-restraints excluded: chain SK residue 15 LEU Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 47 LYS Chi-restraints excluded: chain SK residue 51 SER Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 45 LYS Chi-restraints excluded: chain SL residue 66 VAL Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 60 LYS Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 88 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 37 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 98 SER Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SU residue 113 GLU Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 11 LEU Chi-restraints excluded: chain SV residue 43 THR Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SV residue 74 LYS Chi-restraints excluded: chain SX residue 64 SER Chi-restraints excluded: chain SX residue 123 VAL Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 27 CYS Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sg residue 19 THR Chi-restraints excluded: chain Sg residue 42 MET Chi-restraints excluded: chain Sg residue 62 HIS Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain SC residue 76 LYS Chi-restraints excluded: chain SC residue 105 GLU Chi-restraints excluded: chain SC residue 117 ARG Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 192 LEU Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 258 GLU Chi-restraints excluded: chain SC residue 260 VAL Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 125 THR Chi-restraints excluded: chain SG residue 176 ILE Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SJ residue 37 LEU Chi-restraints excluded: chain SJ residue 152 ASP Chi-restraints excluded: chain SO residue 27 VAL Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 88 LEU Chi-restraints excluded: chain SO residue 122 SER Chi-restraints excluded: chain SW residue 66 THR Chi-restraints excluded: chain SW residue 80 ASP Chi-restraints excluded: chain SW residue 85 ASP Chi-restraints excluded: chain SY residue 13 MET Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 44 THR Chi-restraints excluded: chain Sb residue 53 VAL Chi-restraints excluded: chain Sb residue 83 GLN Chi-restraints excluded: chain Se residue 36 MET Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 427 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 622 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 378 optimal weight: 1.9990 chunk 530 optimal weight: 7.9990 chunk 483 optimal weight: 20.0000 chunk 358 optimal weight: 0.9980 chunk 583 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 114 GLN SH 163 GLN SH 186 ASN SI 7 ASN SK 73 ASN SP 32 GLN SP 35 GLN SP 98 ASN SQ 24 HIS ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 35 ASN SX 77 ASN Sa 25 ASN Sd 37 ASN SC 267 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102943 restraints weight = 114406.876| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 0.58 r_work: 0.3016 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 81191 Z= 0.175 Angle : 0.608 13.001 117768 Z= 0.312 Chirality : 0.038 0.350 14526 Planarity : 0.005 0.058 8600 Dihedral : 22.984 179.770 32301 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.11 % Rotamer: Outliers : 3.27 % Allowed : 19.34 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4903 helix: 0.66 (0.13), residues: 1604 sheet: -0.87 (0.17), residues: 886 loop : -1.29 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPSg 177 HIS 0.007 0.001 HISSM 72 PHE 0.019 0.001 PHESW 50 TYR 0.028 0.001 TYRSK 78 ARG 0.013 0.001 ARGSc 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 625 time to evaluate : 4.769 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: Ln 10 MET cc_start: 0.7474 (tpp) cc_final: 0.7163 (tpp) REVERT: SA 52 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7929 (ptmm) REVERT: SB 175 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8163 (mm-30) REVERT: SE 19 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8299 (mpp) REVERT: SK 34 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: SK 47 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.7951 (mptt) REVERT: SP 89 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8549 (ptm) REVERT: SQ 114 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: SR 104 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: ST 114 GLU cc_start: 0.8230 (pp20) cc_final: 0.8029 (pp20) REVERT: ST 126 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7743 (tp-100) REVERT: SC 95 ASP cc_start: 0.7936 (m-30) cc_final: 0.7735 (m-30) REVERT: SO 84 ARG cc_start: 0.8422 (tpt170) cc_final: 0.8194 (tpt170) REVERT: SO 88 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8255 (tt) REVERT: SW 55 ASP cc_start: 0.7942 (p0) cc_final: 0.7709 (p0) REVERT: SY 74 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: Sf 94 LYS cc_start: 0.5411 (tttt) cc_final: 0.5071 (tptt) REVERT: Sf 97 LYS cc_start: 0.3711 (mmtm) cc_final: 0.3160 (mtpt) outliers start: 140 outliers final: 65 residues processed: 714 average time/residue: 1.5896 time to fit residues: 1512.8257 Evaluate side-chains 670 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 596 time to evaluate : 4.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 29 ASN Chi-restraints excluded: chain SA residue 40 LYS Chi-restraints excluded: chain SA residue 52 LYS Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SD residue 35 SER Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 197 ASN Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 92 VAL Chi-restraints excluded: chain SH residue 166 VAL Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 174 CYS Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 47 LYS Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SP residue 89 MET Chi-restraints excluded: chain SP residue 122 THR Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SQ residue 114 GLN Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain SX residue 123 VAL Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 27 CYS Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sg residue 19 THR Chi-restraints excluded: chain Sg residue 43 TRP Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 191 HIS Chi-restraints excluded: chain Sg residue 221 LEU Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 258 GLU Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SO residue 27 VAL Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 88 LEU Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 380 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 472 optimal weight: 0.7980 chunk 447 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 562 optimal weight: 20.0000 chunk 321 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 533 optimal weight: 0.0070 chunk 183 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 57 ASN SD 74 GLN SF 165 ASN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SK 73 ASN SP 32 GLN SP 35 GLN SP 98 ASN SS 97 GLN ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sd 37 ASN ** Sb 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099367 restraints weight = 113743.284| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 0.76 r_work: 0.2938 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 81191 Z= 0.373 Angle : 0.679 11.902 117768 Z= 0.347 Chirality : 0.043 0.361 14526 Planarity : 0.006 0.078 8600 Dihedral : 22.919 179.357 32301 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.85 % Favored : 92.98 % Rotamer: Outliers : 3.60 % Allowed : 19.64 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 4903 helix: 0.62 (0.13), residues: 1608 sheet: -0.89 (0.17), residues: 896 loop : -1.30 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPSg 177 HIS 0.009 0.001 HISSM 72 PHE 0.021 0.002 PHESJ 147 TYR 0.029 0.002 TYRSK 78 ARG 0.015 0.001 ARGSR 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 617 time to evaluate : 4.639 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: Ln 10 MET cc_start: 0.7563 (tpp) cc_final: 0.7295 (tpp) REVERT: SA 52 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8011 (ptmm) REVERT: SA 117 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8276 (mtt90) REVERT: SE 19 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8278 (mpp) REVERT: SE 66 MET cc_start: 0.8971 (mmm) cc_final: 0.8750 (tpp) REVERT: SK 15 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8827 (tt) REVERT: SK 34 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: SK 47 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8082 (mptt) REVERT: SR 104 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: ST 114 GLU cc_start: 0.8284 (pp20) cc_final: 0.8028 (pp20) REVERT: ST 126 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7745 (tp-100) REVERT: SV 38 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7291 (mt-10) REVERT: SC 95 ASP cc_start: 0.8127 (m-30) cc_final: 0.7881 (m-30) REVERT: SO 51 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: SO 84 ARG cc_start: 0.8513 (tpt170) cc_final: 0.8265 (tpt170) REVERT: SO 88 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8304 (tt) REVERT: SW 55 ASP cc_start: 0.7995 (p0) cc_final: 0.7753 (p0) REVERT: Sf 94 LYS cc_start: 0.5501 (tttt) cc_final: 0.5119 (tptt) REVERT: Sf 97 LYS cc_start: 0.3817 (mmtm) cc_final: 0.3202 (mtpt) REVERT: Sf 104 LYS cc_start: 0.4153 (mmpt) cc_final: 0.3745 (mmpt) outliers start: 154 outliers final: 93 residues processed: 713 average time/residue: 1.5576 time to fit residues: 1480.0820 Evaluate side-chains 706 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 604 time to evaluate : 4.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 29 ASN Chi-restraints excluded: chain SA residue 40 LYS Chi-restraints excluded: chain SA residue 52 LYS Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 117 ARG Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SD residue 35 SER Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 197 ASN Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 78 MET Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 98 GLU Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 92 VAL Chi-restraints excluded: chain SH residue 166 VAL Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 174 CYS Chi-restraints excluded: chain SK residue 15 LEU Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 47 LYS Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 54 THR Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 122 THR Chi-restraints excluded: chain SQ residue 7 LEU Chi-restraints excluded: chain SQ residue 10 VAL Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 52 LEU Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 61 ILE Chi-restraints excluded: chain SR residue 77 GLU Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SR residue 126 MET Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SX residue 123 VAL Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 24 THR Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 27 CYS Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sg residue 19 THR Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 191 HIS Chi-restraints excluded: chain Sg residue 221 LEU Chi-restraints excluded: chain Sg residue 248 LEU Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 192 LEU Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 258 GLU Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 27 VAL Chi-restraints excluded: chain SO residue 45 THR Chi-restraints excluded: chain SO residue 51 GLU Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 88 LEU Chi-restraints excluded: chain SO residue 140 THR Chi-restraints excluded: chain SW residue 80 ASP Chi-restraints excluded: chain SY residue 13 MET Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 371 optimal weight: 0.9980 chunk 528 optimal weight: 0.9990 chunk 376 optimal weight: 0.8980 chunk 330 optimal weight: 0.9990 chunk 469 optimal weight: 6.9990 chunk 308 optimal weight: 0.7980 chunk 443 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 536 optimal weight: 5.9990 chunk 641 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 57 ASN SD 74 GLN SF 186 ASN SH 33 ASN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SI 167 GLN SK 73 ASN SP 32 GLN SP 35 GLN SP 98 ASN SS 97 GLN ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 21 ASN Sa 25 ASN Sd 37 ASN Sg 62 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.125082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102996 restraints weight = 114376.927| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 0.59 r_work: 0.3010 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 81191 Z= 0.181 Angle : 0.601 10.971 117768 Z= 0.308 Chirality : 0.038 0.370 14526 Planarity : 0.005 0.058 8600 Dihedral : 22.900 179.868 32301 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.81 % Favored : 94.06 % Rotamer: Outliers : 2.97 % Allowed : 20.67 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.12), residues: 4903 helix: 0.86 (0.13), residues: 1598 sheet: -0.74 (0.18), residues: 870 loop : -1.25 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRPSg 177 HIS 0.008 0.001 HISSM 72 PHE 0.020 0.001 PHESW 50 TYR 0.029 0.001 TYRSK 78 ARG 0.014 0.000 ARGST 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 611 time to evaluate : 4.721 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: SA 52 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7756 (ptmm) REVERT: SA 117 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8127 (mtt90) REVERT: SE 19 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8186 (mpp) REVERT: SE 66 MET cc_start: 0.8900 (mmm) cc_final: 0.8604 (tpp) REVERT: SK 15 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8650 (tt) REVERT: SK 34 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: SK 47 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8002 (mptt) REVERT: SR 104 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: SC 273 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7801 (mp) REVERT: SO 51 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: SW 55 ASP cc_start: 0.7750 (p0) cc_final: 0.7529 (p0) REVERT: SY 74 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: Sb 6 ASP cc_start: 0.7738 (t0) cc_final: 0.7531 (t0) REVERT: Sf 94 LYS cc_start: 0.5523 (tttt) cc_final: 0.5186 (tptt) REVERT: Sf 97 LYS cc_start: 0.3678 (mmtm) cc_final: 0.3190 (mtpt) outliers start: 127 outliers final: 80 residues processed: 691 average time/residue: 1.6066 time to fit residues: 1474.0175 Evaluate side-chains 684 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 594 time to evaluate : 4.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 29 ASN Chi-restraints excluded: chain SA residue 40 LYS Chi-restraints excluded: chain SA residue 52 LYS Chi-restraints excluded: chain SA residue 117 ARG Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SB residue 105 LEU Chi-restraints excluded: chain SB residue 225 LEU Chi-restraints excluded: chain SD residue 35 SER Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 175 VAL Chi-restraints excluded: chain SD residue 211 VAL Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 197 ASN Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 78 MET Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 92 VAL Chi-restraints excluded: chain SH residue 137 SER Chi-restraints excluded: chain SH residue 166 VAL Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 174 CYS Chi-restraints excluded: chain SK residue 15 LEU Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 47 LYS Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SP residue 122 THR Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SR residue 126 MET Chi-restraints excluded: chain SS residue 81 ASP Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 49 LYS Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SX residue 105 PHE Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 27 CYS Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sg residue 19 THR Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 191 HIS Chi-restraints excluded: chain Sg residue 221 LEU Chi-restraints excluded: chain Sg residue 248 LEU Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 192 LEU Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 258 GLU Chi-restraints excluded: chain SC residue 259 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 102 VAL Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SO residue 27 VAL Chi-restraints excluded: chain SO residue 51 GLU Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 140 THR Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 280 optimal weight: 0.6980 chunk 377 optimal weight: 0.0970 chunk 524 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 609 optimal weight: 2.9990 chunk 491 optimal weight: 0.0040 chunk 51 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 488 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 57 ASN SD 74 GLN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SI 167 GLN SK 73 ASN SP 32 GLN SP 35 GLN SP 98 ASN ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.123940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103117 restraints weight = 114194.768| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 0.57 r_work: 0.2972 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 81191 Z= 0.231 Angle : 0.614 14.554 117768 Z= 0.314 Chirality : 0.039 0.377 14526 Planarity : 0.005 0.065 8600 Dihedral : 22.841 179.908 32299 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 3.13 % Allowed : 20.93 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.12), residues: 4903 helix: 0.91 (0.13), residues: 1597 sheet: -0.71 (0.18), residues: 874 loop : -1.20 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRPSg 177 HIS 0.008 0.001 HISSM 72 PHE 0.018 0.002 PHESW 50 TYR 0.030 0.001 TYRSK 78 ARG 0.017 0.000 ARGSR 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 603 time to evaluate : 4.710 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: SA 52 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8071 (ptmm) REVERT: SA 117 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8240 (mtt90) REVERT: SB 68 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7610 (tp30) REVERT: SE 19 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8341 (mpp) REVERT: SE 66 MET cc_start: 0.8994 (mmm) cc_final: 0.8743 (tpp) REVERT: SK 15 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8728 (tt) REVERT: SK 34 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: SK 47 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.7994 (mptt) REVERT: SR 103 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8340 (ttmt) REVERT: SR 104 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: ST 114 GLU cc_start: 0.8336 (pp20) cc_final: 0.8071 (pp20) REVERT: ST 130 ASP cc_start: 0.7765 (p0) cc_final: 0.7415 (p0) REVERT: SV 74 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8251 (mttp) REVERT: SC 273 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7788 (mp) REVERT: SO 51 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: SW 55 ASP cc_start: 0.7992 (p0) cc_final: 0.7770 (p0) REVERT: SY 46 LYS cc_start: 0.8429 (mppt) cc_final: 0.8119 (mptt) REVERT: SY 74 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8488 (mtp) REVERT: Sf 94 LYS cc_start: 0.5593 (tttt) cc_final: 0.5107 (tptt) REVERT: Sf 97 LYS cc_start: 0.3824 (mmtm) cc_final: 0.3174 (mtpt) outliers start: 134 outliers final: 90 residues processed: 689 average time/residue: 1.5621 time to fit residues: 1437.8659 Evaluate side-chains 689 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 587 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 29 ASN Chi-restraints excluded: chain SA residue 40 LYS Chi-restraints excluded: chain SA residue 52 LYS Chi-restraints excluded: chain SA residue 117 ARG Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SB residue 105 LEU Chi-restraints excluded: chain SB residue 225 LEU Chi-restraints excluded: chain SD residue 35 SER Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 211 VAL Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 197 ASN Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 78 MET Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 92 VAL Chi-restraints excluded: chain SH residue 137 SER Chi-restraints excluded: chain SH residue 166 VAL Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 174 CYS Chi-restraints excluded: chain SK residue 15 LEU Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 47 LYS Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 4 ILE Chi-restraints excluded: chain SP residue 122 THR Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 40 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 103 LYS Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SR residue 126 MET Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 98 SER Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 88 LEU Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SV residue 74 LYS Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 27 CYS Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sg residue 19 THR Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 191 HIS Chi-restraints excluded: chain Sg residue 221 LEU Chi-restraints excluded: chain Sg residue 248 LEU Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 192 LEU Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 258 GLU Chi-restraints excluded: chain SC residue 259 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 102 VAL Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SO residue 27 VAL Chi-restraints excluded: chain SO residue 51 GLU Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 86 LYS Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SO residue 140 THR Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain Sb residue 72 ARG Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 365 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 592 optimal weight: 1.9990 chunk 385 optimal weight: 10.0000 chunk 547 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 475 optimal weight: 5.9990 chunk 633 optimal weight: 0.9990 chunk 632 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 74 GLN SE 197 ASN SF 186 ASN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SK 73 ASN SP 32 GLN SP 35 GLN SP 98 ASN SS 97 GLN ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.124514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102104 restraints weight = 114180.830| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 0.59 r_work: 0.2980 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 81191 Z= 0.210 Angle : 0.614 15.314 117768 Z= 0.313 Chirality : 0.038 0.383 14526 Planarity : 0.005 0.063 8600 Dihedral : 22.832 179.971 32299 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.00 % Favored : 93.88 % Rotamer: Outliers : 2.74 % Allowed : 21.42 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 4903 helix: 0.95 (0.13), residues: 1595 sheet: -0.68 (0.18), residues: 865 loop : -1.20 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRPSg 177 HIS 0.008 0.001 HISSM 72 PHE 0.019 0.001 PHESW 50 TYR 0.030 0.001 TYRSK 78 ARG 0.014 0.000 ARGSD 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9806 Ramachandran restraints generated. 4903 Oldfield, 0 Emsley, 4903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 589 time to evaluate : 4.640 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: SA 52 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8049 (ptmm) REVERT: SA 117 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8267 (mtt90) REVERT: SB 68 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7714 (tp30) REVERT: SE 19 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: SK 34 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: SK 47 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.7953 (mptt) REVERT: SK 80 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7067 (ttm170) REVERT: SR 104 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: ST 114 GLU cc_start: 0.8399 (pp20) cc_final: 0.8110 (pp20) REVERT: SV 74 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8305 (mttp) REVERT: SC 273 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7758 (mp) REVERT: SN 87 ASP cc_start: 0.8603 (m-30) cc_final: 0.8366 (m-30) REVERT: SO 51 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: SW 55 ASP cc_start: 0.8072 (p0) cc_final: 0.7852 (p0) REVERT: SY 46 LYS cc_start: 0.8470 (mppt) cc_final: 0.8167 (mptt) REVERT: SY 74 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: Sb 6 ASP cc_start: 0.7942 (t0) cc_final: 0.7552 (t0) REVERT: Sf 94 LYS cc_start: 0.5649 (tttt) cc_final: 0.5135 (tptt) REVERT: Sf 97 LYS cc_start: 0.3834 (mmtm) cc_final: 0.3229 (mtpt) outliers start: 117 outliers final: 88 residues processed: 665 average time/residue: 1.5462 time to fit residues: 1379.0866 Evaluate side-chains 685 residues out of total 4279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 586 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 8 LEU Chi-restraints excluded: chain SA residue 29 ASN Chi-restraints excluded: chain SA residue 40 LYS Chi-restraints excluded: chain SA residue 52 LYS Chi-restraints excluded: chain SA residue 117 ARG Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SB residue 105 LEU Chi-restraints excluded: chain SB residue 225 LEU Chi-restraints excluded: chain SD residue 35 SER Chi-restraints excluded: chain SD residue 91 VAL Chi-restraints excluded: chain SD residue 142 LEU Chi-restraints excluded: chain SD residue 211 VAL Chi-restraints excluded: chain SE residue 19 MET Chi-restraints excluded: chain SE residue 89 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 208 VAL Chi-restraints excluded: chain SF residue 78 MET Chi-restraints excluded: chain SF residue 82 ASN Chi-restraints excluded: chain SF residue 93 VAL Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 92 VAL Chi-restraints excluded: chain SH residue 119 SER Chi-restraints excluded: chain SH residue 137 SER Chi-restraints excluded: chain SH residue 166 VAL Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 136 ILE Chi-restraints excluded: chain SI residue 174 CYS Chi-restraints excluded: chain SK residue 15 LEU Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 47 LYS Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SK residue 80 ARG Chi-restraints excluded: chain SP residue 122 THR Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 42 ILE Chi-restraints excluded: chain SQ residue 46 THR Chi-restraints excluded: chain SQ residue 57 LEU Chi-restraints excluded: chain SQ residue 70 VAL Chi-restraints excluded: chain SQ residue 100 VAL Chi-restraints excluded: chain SQ residue 104 SER Chi-restraints excluded: chain SR residue 38 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SR residue 126 MET Chi-restraints excluded: chain SS residue 96 SER Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 93 SER Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain ST residue 130 ASP Chi-restraints excluded: chain SU residue 24 LEU Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SV residue 74 LYS Chi-restraints excluded: chain SX residue 125 VAL Chi-restraints excluded: chain Sa residue 30 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sa residue 67 LEU Chi-restraints excluded: chain Sc residue 27 CYS Chi-restraints excluded: chain Sc residue 28 THR Chi-restraints excluded: chain Sc residue 55 VAL Chi-restraints excluded: chain Sg residue 19 THR Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain Sg residue 98 THR Chi-restraints excluded: chain Sg residue 221 LEU Chi-restraints excluded: chain Sg residue 248 LEU Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain SC residue 163 VAL Chi-restraints excluded: chain SC residue 192 LEU Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 258 GLU Chi-restraints excluded: chain SC residue 259 THR Chi-restraints excluded: chain SC residue 270 THR Chi-restraints excluded: chain SC residue 273 LEU Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 89 THR Chi-restraints excluded: chain SG residue 102 VAL Chi-restraints excluded: chain SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 27 VAL Chi-restraints excluded: chain SO residue 51 GLU Chi-restraints excluded: chain SO residue 52 THR Chi-restraints excluded: chain SO residue 86 LYS Chi-restraints excluded: chain SO residue 114 SER Chi-restraints excluded: chain SO residue 140 THR Chi-restraints excluded: chain SY residue 34 THR Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 51 THR Chi-restraints excluded: chain SY residue 74 MET Chi-restraints excluded: chain SZ residue 44 LEU Chi-restraints excluded: chain CD residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 593 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 572 optimal weight: 0.9990 chunk 611 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 592 optimal weight: 0.8980 chunk 410 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 304 optimal weight: 0.8980 chunk 646 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SD 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 74 GLN SE 197 ASN SF 186 ASN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SK 73 ASN SP 98 ASN SS 97 GLN ST 12 GLN ST 126 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sg 191 HIS SO 83 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103507 restraints weight = 114557.796| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 0.58 r_work: 0.2977 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 81191 Z= 0.180 Angle : 0.599 14.737 117768 Z= 0.305 Chirality : 0.038 0.388 14526 Planarity : 0.005 0.079 8600 Dihedral : 22.813 179.733 32299 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 2.67 % Allowed : 21.60 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4903 helix: 1.01 (0.13), residues: 1589 sheet: -0.65 (0.18), residues: 859 loop : -1.17 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRPSg 177 HIS 0.008 0.001 HISSM 72 PHE 0.017 0.001 PHESW 50 TYR 0.029 0.001 TYRSK 78 ARG 0.019 0.000 ARGSR 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41666.71 seconds wall clock time: 715 minutes 7.10 seconds (42907.10 seconds total)