Starting phenix.real_space_refine on Sun Sep 29 17:49:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxl_38752/09_2024/8xxl_38752.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxl_38752/09_2024/8xxl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxl_38752/09_2024/8xxl_38752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxl_38752/09_2024/8xxl_38752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxl_38752/09_2024/8xxl_38752.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxl_38752/09_2024/8xxl_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 30.63, per 1000 atoms: 0.40 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: 12.72 Conformation dependent library (CDL) restraints added in 4.4 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: 25.45 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: 60.41 Time building geometry restraints manager: 15.69 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.280 Check model and map are aligned: 0.420 Set scattering table: 0.540 Process input model: 182.850 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.170 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 25 poor density : 772 time to evaluate : 4.439 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: 1.6994 time to fit residues: 1756.6848 Evaluate side-chains 613 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 605 time to evaluate : 4.493 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1138 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 : 7.00 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 fitting. rotamer outliers: 90 poor density : 640 time to evaluate : 4.389 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: 0.6694 (pm20) cc_final: 0.6380 (pm20) REVERT: SE 19 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7450 (mpp) REVERT: SK 3 MET cc_start: 0.7651 (tmm) cc_final: 0.7391 (ttp) REVERT: SR 1 MET cc_start: 0.5015 (mpp) cc_final: 0.3673 (tpt) REVERT: SR 67 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.4922 (mtt-85) REVERT: SR 104 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: ST 35 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: Sc 55 VAL cc_start: 0.8320 (p) cc_final: 0.8054 (m) REVERT: SC 117 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.5997 (mtm-85) outliers start: 90 outliers final: 45 residues processed: 684 average time/residue: 1.6360 time to fit residues: 1481.3068 Evaluate side-chains 639 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 589 time to evaluate : 4.408 ------------------------------------------------------------------------------- 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 330 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 495 optimal weight: 7.9990 chunk 405 optimal weight: 1.9990 chunk 164 optimal weight: 50.0000 chunk 595 optimal weight: 6.9990 chunk 643 optimal weight: 1.9990 chunk 530 optimal weight: 8.9990 chunk 590 optimal weight: 0.0370 chunk 203 optimal weight: 6.9990 chunk 478 optimal weight: 10.0000 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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 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 Sg 226 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 81191 Z= 0.272 Angle : 0.633 11.479 117768 Z= 0.325 Chirality : 0.040 0.285 14526 Planarity : 0.005 0.060 8600 Dihedral : 22.984 179.991 32307 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.10 % Favored : 93.70 % Rotamer: Outliers : 3.11 % Allowed : 14.17 % 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: -1.23 (0.12), residues: 4903 helix: 0.08 (0.13), residues: 1612 sheet: -0.89 (0.17), residues: 903 loop : -1.37 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 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 0.010 0.001 ARGST 16 *********************** 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 758 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 625 time to evaluate : 4.469 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: 0.6586 (pm20) cc_final: 0.6352 (pm20) REVERT: SE 19 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7683 (mpp) REVERT: SF 102 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8002 (mm) REVERT: SI 167 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: SK 3 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7230 (ttp) REVERT: SR 1 MET cc_start: 0.5164 (mpp) cc_final: 0.3910 (tpt) REVERT: SR 104 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: ST 35 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: Sc 55 VAL cc_start: 0.8363 (p) cc_final: 0.8123 (m) REVERT: SC 117 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6168 (mtm-85) REVERT: SC 273 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7754 (mp) REVERT: SG 126 ASP cc_start: 0.6750 (p0) cc_final: 0.6498 (p0) outliers start: 133 outliers final: 64 residues processed: 698 average time/residue: 1.6526 time to fit residues: 1527.1874 Evaluate side-chains 656 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 584 time to evaluate : 4.421 ------------------------------------------------------------------------------- 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 102 LEU 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 3 MET 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 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 SS residue 117 ILE Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 35 ASP 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 588 optimal weight: 3.9990 chunk 448 optimal weight: 0.5980 chunk 309 optimal weight: 1.9990 chunk 65 optimal weight: 40.0000 chunk 284 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 chunk 598 optimal weight: 8.9990 chunk 633 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 566 optimal weight: 40.0000 chunk 170 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 SH 186 ASN SK 73 ASN SP 35 GLN ** SP 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 24 HIS SS 97 GLN ST 12 GLN ST 126 GLN SV 35 ASN SX 77 ASN Sa 25 ASN SC 267 GLN SG 202 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 81191 Z= 0.264 Angle : 0.622 9.883 117768 Z= 0.319 Chirality : 0.040 0.310 14526 Planarity : 0.005 0.068 8600 Dihedral : 22.942 179.603 32301 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.08 % Favored : 93.72 % Rotamer: Outliers : 3.58 % Allowed : 15.83 % Favored : 80.59 % 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: -1.02 (0.12), residues: 4903 helix: 0.41 (0.13), residues: 1612 sheet: -0.86 (0.17), residues: 891 loop : -1.34 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPSg 177 HIS 0.005 0.001 HISSI 22 PHE 0.018 0.002 PHESW 50 TYR 0.024 0.002 TYRSK 78 ARG 0.013 0.001 ARGSR 80 *********************** 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 756 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 603 time to evaluate : 4.458 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: SA 52 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7431 (ptmm) REVERT: SE 19 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7699 (mpp) REVERT: SI 167 GLN cc_start: 0.7652 (mp10) cc_final: 0.7423 (mp10) REVERT: SK 3 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7192 (ttp) REVERT: SK 34 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: SK 47 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7910 (mptt) REVERT: SR 104 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: SC 117 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6264 (mtm-85) REVERT: SC 273 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7764 (mp) REVERT: SO 88 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8052 (tt) REVERT: Sf 94 LYS cc_start: 0.5083 (tttt) cc_final: 0.4878 (tptt) REVERT: Sf 97 LYS cc_start: 0.3437 (mmtm) cc_final: 0.2903 (mtpt) REVERT: Sf 104 LYS cc_start: 0.3784 (mmpt) cc_final: 0.3473 (mmpt) outliers start: 153 outliers final: 83 residues processed: 696 average time/residue: 1.5951 time to fit residues: 1479.0690 Evaluate side-chains 673 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 581 time to evaluate : 4.392 ------------------------------------------------------------------------------- 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 75 SER 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 SE residue 19 MET Chi-restraints excluded: chain SE residue 38 LEU 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 93 VAL Chi-restraints excluded: chain SF residue 102 LEU Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 119 SER 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 3 MET 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 87 VAL Chi-restraints excluded: chain SP residue 76 VAL Chi-restraints excluded: chain SP residue 122 THR 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 70 VAL 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 88 VAL Chi-restraints excluded: chain SR residue 104 GLU 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 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 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 19 THR Chi-restraints excluded: chain Sg residue 69 VAL Chi-restraints excluded: chain Sg residue 303 THR Chi-restraints excluded: chain SC residue 117 ARG 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 SJ residue 152 ASP Chi-restraints excluded: chain SM residue 72 HIS 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 56 VAL Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 88 LEU 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 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 Sb residue 53 VAL 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 527 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 471 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 540 optimal weight: 9.9990 chunk 437 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 568 optimal weight: 0.0170 chunk 159 optimal weight: 20.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- 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 SE 197 ASN SF 51 HIS ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SK 73 ASN SP 35 GLN SP 128 HIS SR 93 GLN SS 10 GLN SS 97 GLN ST 12 GLN ST 126 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sg 191 HIS SC 113 GLN SG 70 HIS SG 202 ASN SO 13 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 81191 Z= 0.375 Angle : 0.678 15.352 117768 Z= 0.346 Chirality : 0.043 0.332 14526 Planarity : 0.006 0.075 8600 Dihedral : 22.934 179.223 32301 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.67 % Favored : 93.15 % Rotamer: Outliers : 4.21 % Allowed : 16.86 % Favored : 78.93 % 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: -0.99 (0.12), residues: 4903 helix: 0.48 (0.13), residues: 1614 sheet: -0.84 (0.17), residues: 891 loop : -1.35 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPSg 177 HIS 0.019 0.001 HISSG 70 PHE 0.022 0.002 PHESJ 147 TYR 0.027 0.002 TYRSK 78 ARG 0.010 0.001 ARGST 16 *********************** 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 796 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 616 time to evaluate : 4.447 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: SA 52 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7432 (ptmm) REVERT: SE 19 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7836 (mpp) REVERT: SE 66 MET cc_start: 0.8851 (mmm) cc_final: 0.8575 (tpp) REVERT: SK 3 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7261 (ttp) REVERT: SK 34 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: SK 47 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7911 (mptt) REVERT: SR 104 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: SC 117 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6341 (mtm-85) REVERT: SO 88 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8085 (tt) REVERT: SW 85 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7463 (p0) REVERT: Sf 94 LYS cc_start: 0.5278 (tttt) cc_final: 0.5040 (tptt) REVERT: Sf 97 LYS cc_start: 0.3467 (mmtm) cc_final: 0.2952 (mtpt) outliers start: 180 outliers final: 103 residues processed: 727 average time/residue: 1.5684 time to fit residues: 1519.8190 Evaluate side-chains 704 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 592 time to evaluate : 4.388 ------------------------------------------------------------------------------- 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 170 SER 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 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 102 LEU Chi-restraints excluded: chain SF residue 133 THR Chi-restraints excluded: chain SH residue 51 ILE Chi-restraints excluded: chain SH residue 119 SER 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 3 MET 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 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 SP residue 122 THR 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 77 GLU 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 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 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 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 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 46 VAL 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 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 176 ILE 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 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 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 CD residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 213 optimal weight: 0.9990 chunk 570 optimal weight: 50.0000 chunk 125 optimal weight: 3.9990 chunk 371 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 633 optimal weight: 4.9990 chunk 526 optimal weight: 4.9990 chunk 293 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 332 optimal weight: 0.0010 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 51 HIS ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** SV 21 ASN Sa 25 ASN Sd 37 ASN SG 202 ASN Se 37 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 81191 Z= 0.162 Angle : 0.584 12.938 117768 Z= 0.300 Chirality : 0.037 0.346 14526 Planarity : 0.005 0.058 8600 Dihedral : 22.909 179.608 32301 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 2.95 % Allowed : 18.92 % Favored : 78.14 % 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: -0.75 (0.12), residues: 4903 helix: 0.79 (0.13), residues: 1605 sheet: -0.72 (0.18), residues: 873 loop : -1.28 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRPSg 177 HIS 0.005 0.001 HISSP 79 PHE 0.019 0.001 PHESW 50 TYR 0.028 0.001 TYRSK 78 ARG 0.014 0.000 ARGST 16 *********************** 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 737 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 611 time to evaluate : 4.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SA 52 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7391 (ptmm) REVERT: SE 19 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7839 (mpp) REVERT: SE 66 MET cc_start: 0.8832 (mmm) cc_final: 0.8458 (tpp) REVERT: SH 57 ARG cc_start: 0.5822 (tmt90) cc_final: 0.5609 (ttp-170) REVERT: SK 3 MET cc_start: 0.7573 (tmm) cc_final: 0.7207 (ttp) REVERT: SK 34 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: SK 47 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7805 (mptt) REVERT: SR 104 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: SC 273 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7848 (mp) REVERT: SG 125 THR cc_start: 0.8511 (p) cc_final: 0.8309 (m) REVERT: SO 84 ARG cc_start: 0.8070 (tpt170) cc_final: 0.7844 (tpt170) REVERT: SO 88 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7994 (tt) REVERT: SY 74 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7569 (mtp) outliers start: 126 outliers final: 60 residues processed: 692 average time/residue: 1.5640 time to fit residues: 1449.0816 Evaluate side-chains 651 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 583 time to evaluate : 4.453 ------------------------------------------------------------------------------- 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 SF residue 102 LEU 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 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 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 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 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 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 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 SX residue 64 SER Chi-restraints excluded: chain SX residue 105 PHE 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 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 221 LEU 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 SJ residue 3 VAL Chi-restraints excluded: chain SJ residue 23 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SO residue 27 VAL 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 74 MET Chi-restraints excluded: chain SZ residue 44 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 611 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 361 optimal weight: 4.9990 chunk 462 optimal weight: 0.9990 chunk 358 optimal weight: 0.9980 chunk 533 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 chunk 631 optimal weight: 6.9990 chunk 395 optimal weight: 8.9990 chunk 384 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 141 ASN SB 208 HIS SD 57 ASN SD 74 GLN SH 33 ASN ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 114 GLN SH 162 GLN SH 163 GLN SI 7 ASN SK 73 ASN SP 32 GLN SP 35 GLN SP 98 ASN SS 97 GLN ST 12 GLN ST 85 ASN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sd 37 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 81191 Z= 0.350 Angle : 0.660 12.099 117768 Z= 0.337 Chirality : 0.042 0.358 14526 Planarity : 0.005 0.064 8600 Dihedral : 22.870 178.715 32300 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.61 % Favored : 93.25 % Rotamer: Outliers : 3.62 % Allowed : 19.29 % Favored : 77.09 % 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: -0.79 (0.12), residues: 4903 helix: 0.72 (0.13), residues: 1612 sheet: -0.77 (0.18), residues: 871 loop : -1.27 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPSg 177 HIS 0.009 0.001 HISSM 72 PHE 0.021 0.002 PHESJ 147 TYR 0.030 0.002 TYRSK 78 ARG 0.014 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 760 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 605 time to evaluate : 4.459 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: 0.7031 (tpp) cc_final: 0.6725 (tpp) REVERT: SA 52 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7412 (ptmm) REVERT: SE 19 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7944 (mpp) REVERT: SK 3 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7331 (ttp) REVERT: SK 34 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: SK 47 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7963 (mptt) REVERT: SR 104 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: Sg 191 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6775 (m-70) REVERT: SJ 37 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8801 (mp) REVERT: SO 51 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: SO 84 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7862 (tpt170) REVERT: SO 88 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8043 (tt) REVERT: SY 46 LYS cc_start: 0.8095 (mppt) cc_final: 0.7759 (mptt) REVERT: Sf 94 LYS cc_start: 0.5402 (tttt) cc_final: 0.5104 (tptt) REVERT: Sf 97 LYS cc_start: 0.3267 (mmtm) cc_final: 0.2863 (mtpt) outliers start: 155 outliers final: 96 residues processed: 699 average time/residue: 1.5707 time to fit residues: 1470.4092 Evaluate side-chains 690 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 584 time to evaluate : 4.426 ------------------------------------------------------------------------------- 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 118 GLU Chi-restraints excluded: chain SA residue 144 THR Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SB residue 113 MET 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 82 ASN Chi-restraints excluded: chain SF residue 98 GLU Chi-restraints excluded: chain SF residue 102 LEU 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 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 3 MET 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 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 57 LEU 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 61 ILE Chi-restraints excluded: chain SR residue 73 LEU 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 81 ASP 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 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 SX residue 64 SER 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 SC residue 280 VAL 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 37 LEU 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 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 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 390 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 377 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 430 optimal weight: 0.9990 chunk 312 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 496 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SD 57 ASN ** SH 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 114 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** Sa 25 ASN Sd 37 ASN Sg 62 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 81191 Z= 0.224 Angle : 0.612 11.763 117768 Z= 0.314 Chirality : 0.039 0.368 14526 Planarity : 0.005 0.063 8600 Dihedral : 22.880 179.503 32300 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.87 % Favored : 93.96 % Rotamer: Outliers : 3.11 % Allowed : 20.08 % Favored : 76.81 % 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: -0.73 (0.12), residues: 4903 helix: 0.80 (0.13), residues: 1613 sheet: -0.74 (0.18), residues: 870 loop : -1.25 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRPSg 177 HIS 0.012 0.001 HISSg 62 PHE 0.020 0.001 PHESW 50 TYR 0.029 0.001 TYRSK 78 ARG 0.014 0.000 ARGSc 13 *********************** 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 725 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 592 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 10 MET cc_start: 0.6979 (tpp) cc_final: 0.6713 (tpp) REVERT: SA 52 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7395 (ptmm) REVERT: SE 19 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7937 (mpp) REVERT: SK 3 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7309 (ttp) REVERT: SK 34 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: SK 47 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7874 (mptt) REVERT: SR 104 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: SR 119 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.6068 (p) REVERT: SO 51 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: SO 88 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7983 (tt) REVERT: SY 46 LYS cc_start: 0.8029 (mppt) cc_final: 0.7715 (mptt) REVERT: SY 74 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7535 (mtp) REVERT: Sf 94 LYS cc_start: 0.5450 (tttt) cc_final: 0.5171 (tptt) REVERT: Sf 97 LYS cc_start: 0.3216 (mmtm) cc_final: 0.2868 (mtpt) outliers start: 133 outliers final: 82 residues processed: 684 average time/residue: 1.7079 time to fit residues: 1583.7107 Evaluate side-chains 674 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 582 time to evaluate : 4.479 ------------------------------------------------------------------------------- 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 SB residue 105 LEU Chi-restraints excluded: chain SB residue 113 MET 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 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 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 3 MET 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 SP residue 122 THR Chi-restraints excluded: chain SQ residue 7 LEU 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 61 ILE Chi-restraints excluded: chain SR residue 85 VAL Chi-restraints excluded: chain SR residue 104 GLU Chi-restraints excluded: chain SR residue 119 VAL Chi-restraints excluded: chain SR residue 126 MET Chi-restraints excluded: chain SS residue 81 ASP 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 24 LEU Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SX residue 64 SER 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 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 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 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 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 88 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 574 optimal weight: 3.9990 chunk 604 optimal weight: 0.8980 chunk 551 optimal weight: 0.8980 chunk 588 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 461 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 531 optimal weight: 7.9990 chunk 556 optimal weight: 4.9990 chunk 586 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SI 167 GLN SK 73 ASN SP 35 GLN SP 98 ASN SS 97 GLN ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN SO 83 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 81191 Z= 0.231 Angle : 0.611 10.932 117768 Z= 0.313 Chirality : 0.039 0.380 14526 Planarity : 0.005 0.071 8600 Dihedral : 22.839 179.503 32299 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.45 % Rotamer: Outliers : 3.37 % Allowed : 20.20 % Favored : 76.43 % 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: -0.63 (0.12), residues: 4903 helix: 0.91 (0.13), residues: 1601 sheet: -0.65 (0.18), residues: 859 loop : -1.22 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 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 0.020 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 741 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 597 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 10 MET cc_start: 0.6986 (tpp) cc_final: 0.6728 (tpp) REVERT: SA 52 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7391 (ptmm) REVERT: SE 19 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7984 (mpp) REVERT: SK 34 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: SK 47 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7869 (mptt) REVERT: SR 104 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: SO 51 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: SO 88 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8027 (tt) REVERT: SY 74 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7556 (mtp) REVERT: Sf 94 LYS cc_start: 0.5554 (tttt) cc_final: 0.5257 (tptt) REVERT: Sf 97 LYS cc_start: 0.3225 (mmtm) cc_final: 0.2868 (mtpt) outliers start: 144 outliers final: 89 residues processed: 685 average time/residue: 1.5771 time to fit residues: 1440.9607 Evaluate side-chains 686 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 589 time to evaluate : 4.393 ------------------------------------------------------------------------------- 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 SB residue 105 LEU Chi-restraints excluded: chain SB residue 113 MET 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 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 22 VAL 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 45 LYS 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 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 38 ILE Chi-restraints excluded: chain SR residue 40 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 5 ILE Chi-restraints excluded: chain SS residue 81 ASP 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 24 LEU Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 51 LYS Chi-restraints excluded: chain SX residue 64 SER 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 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 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 88 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 386 optimal weight: 5.9990 chunk 622 optimal weight: 0.7980 chunk 379 optimal weight: 0.9980 chunk 295 optimal weight: 0.9980 chunk 432 optimal weight: 0.8980 chunk 652 optimal weight: 0.0670 chunk 600 optimal weight: 0.8980 chunk 519 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 401 optimal weight: 0.0570 chunk 318 optimal weight: 1.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 SF 165 ASN SH 68 GLN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SI 167 GLN SK 73 ASN SP 35 GLN SP 98 ASN SQ 11 GLN SS 97 GLN ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN SO 83 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 81191 Z= 0.157 Angle : 0.606 17.848 117768 Z= 0.308 Chirality : 0.037 0.420 14526 Planarity : 0.005 0.097 8600 Dihedral : 22.878 179.751 32299 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 2.34 % Allowed : 21.51 % Favored : 76.15 % 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: 0.92 (0.13), residues: 1602 sheet: -0.65 (0.18), residues: 867 loop : -1.19 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRPSg 177 HIS 0.008 0.001 HISSM 72 PHE 0.019 0.001 PHESW 50 TYR 0.032 0.001 TYRSK 78 ARG 0.016 0.000 ARGST 16 ********************** 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 fitting. rotamer outliers: 100 poor density : 606 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SA 52 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7367 (ptmm) REVERT: SE 19 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7983 (mpp) REVERT: SE 126 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8781 (t) REVERT: SK 21 MET cc_start: 0.5988 (ppp) cc_final: 0.5525 (ppp) REVERT: SK 34 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: SP 25 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8403 (mp) REVERT: SR 104 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: SV 74 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8054 (mttp) REVERT: SC 273 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7796 (mp) REVERT: SO 88 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8013 (tt) REVERT: SY 46 LYS cc_start: 0.8049 (mppt) cc_final: 0.7779 (mptt) REVERT: SY 74 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7612 (mtp) REVERT: Sf 94 LYS cc_start: 0.5547 (tttt) cc_final: 0.5243 (tptt) REVERT: Sf 97 LYS cc_start: 0.3177 (mmtm) cc_final: 0.2853 (mtpt) REVERT: CD 103 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7573 (mmm160) outliers start: 100 outliers final: 65 residues processed: 674 average time/residue: 1.5963 time to fit residues: 1430.6985 Evaluate side-chains 661 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 586 time to evaluate : 4.442 ------------------------------------------------------------------------------- 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 SB residue 105 LEU 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 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 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 22 VAL Chi-restraints excluded: chain SK residue 34 GLU Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 4 ILE Chi-restraints excluded: chain SP residue 25 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 SS residue 81 ASP Chi-restraints excluded: chain ST residue 5 THR Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 98 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 74 LYS Chi-restraints excluded: chain SX residue 64 SER 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 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 258 GLU 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 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 52 THR Chi-restraints excluded: chain SO residue 88 LEU Chi-restraints excluded: chain SY residue 34 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 655 random chunks: chunk 412 optimal weight: 1.9990 chunk 553 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 479 optimal weight: 4.9990 chunk 76 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 chunk 520 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 534 optimal weight: 7.9990 chunk 65 optimal weight: 40.0000 chunk 95 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** SD 74 GLN SF 51 HIS SF 165 ASN SF 186 ASN SH 68 GLN SH 114 GLN SH 162 GLN SH 163 GLN SH 186 ASN SI 7 ASN SI 167 GLN SK 73 ASN SP 98 ASN SS 97 GLN ST 12 GLN ** SU 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sa 25 ASN Sd 37 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099484 restraints weight = 113841.375| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 0.75 r_work: 0.2993 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 81191 Z= 0.394 Angle : 0.695 15.546 117768 Z= 0.353 Chirality : 0.044 0.383 14526 Planarity : 0.006 0.075 8600 Dihedral : 22.829 178.557 32299 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.93 % Favored : 92.90 % Rotamer: Outliers : 2.57 % Allowed : 21.51 % Favored : 75.92 % 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: -0.72 (0.12), residues: 4903 helix: 0.75 (0.13), residues: 1620 sheet: -0.63 (0.18), residues: 851 loop : -1.26 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRPSN 25 HIS 0.007 0.001 HISSX 46 PHE 0.023 0.002 PHESJ 147 TYR 0.029 0.002 TYRSK 78 ARG 0.018 0.001 ARGSR 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22488.57 seconds wall clock time: 387 minutes 43.71 seconds (23263.71 seconds total)