Starting phenix.real_space_refine on Sun Jan 26 13:47:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xp3_38549/01_2025/8xp3_38549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xp3_38549/01_2025/8xp3_38549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xp3_38549/01_2025/8xp3_38549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xp3_38549/01_2025/8xp3_38549.map" model { file = "/net/cci-nas-00/data/ceres_data/8xp3_38549/01_2025/8xp3_38549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xp3_38549/01_2025/8xp3_38549.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 1739 5.49 5 S 201 5.16 5 C 43943 2.51 5 N 14775 2.21 5 O 19773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 80435 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: 36896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1740, 36896 Classifications: {'DNA': 15, 'RNA': 1725} Modifications used: {'5*END': 1, 'rna2p_pur': 155, 'rna2p_pyr': 129, 'rna3p_pur': 751, 'rna3p_pyr': 687} Link IDs: {'rna2p': 283, 'rna3p': 1456} Chain breaks: 4 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {' G:plan2': 3, ' A:plan': 1, ' C:plan': 11, ' U:plan': 3, ' G:plan': 3, ' C:plan2': 11, ' A:plan2': 1} Unresolved non-hydrogen planarities: 203 Chain: "SA" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1747 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "SB" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1738 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "SD" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "SE" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "SF" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "SH" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1497 Classifications: {'peptide': 186} Link IDs: {'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: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1182 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "SP" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1045 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "SQ" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SR" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1090 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "SS" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1198 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "ST" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "SU" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "SV" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "SX" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Sa" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "Sc" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "Sd" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "Sg" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "SC" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "SG" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "SJ" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "SM" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "SN" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SO" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1010 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "SW" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "SY" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1022 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "SZ" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Sb" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "Se" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "Sf" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 497 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "JD" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain breaks: 1 Chain: "JC" Number of atoms: 3941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3941 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Link IDs: {'PCIS': 6, 'PTRANS': 36, 'TRANS': 469} Chain breaks: 2 Chain: "Sa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Sf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 59425 SG CYSSa 23 83.666 174.284 113.396 1.00 57.76 S ATOM 59446 SG CYSSa 26 83.105 173.129 109.849 1.00 56.39 S ATOM 59829 SG CYSSa 74 85.589 171.301 112.172 1.00 52.90 S ATOM 59848 SG CYSSa 77 86.417 174.507 110.519 1.00 51.37 S ATOM 74753 SG CYSSb 37 62.302 157.456 177.959 1.00 89.58 S ATOM 75830 SG CYSSf 121 167.847 163.564 26.821 1.00217.67 S ATOM 75984 SG CYSSf 141 164.308 162.982 27.279 1.00202.34 S ATOM 76003 SG CYSSf 144 165.313 165.556 29.511 1.00204.38 S Time building chain proxies: 31.26, per 1000 atoms: 0.39 Number of scatterers: 80435 At special positions: 0 Unit cell: (202.842, 263.58, 213.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 201 16.00 P 1739 15.00 O 19773 8.00 N 14775 7.00 C 43943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.34 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNSa 201 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 26 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 74 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 77 " pdb="ZN ZNSa 201 " - pdb=" SG CYSSa 23 " pdb=" ZNSb 101 " pdb="ZN ZNSb 101 " - pdb=" SG CYSSb 37 " pdb=" ZNSf 200 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 144 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 121 " pdb="ZN ZNSf 200 " - pdb=" SG CYSSf 141 " Number of angles added : 6 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10148 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 61 sheets defined 35.9% alpha, 19.0% beta 533 base pairs and 884 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 removed outlier: 3.923A pdb=" N LEUSA 16 " --> pdb=" O GLUSA 12 " (cutoff:3.500A) 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 50 through 68 removed outlier: 3.536A pdb=" N ILESA 65 " --> pdb=" O ALASA 61 " (cutoff:3.500A) Processing helix chain 'SA' and resid 70 through 72 No H-bonds generated for 'chain 'SA' and resid 70 through 72' Processing helix chain 'SA' and resid 83 through 95 removed outlier: 3.556A pdb=" N LEUSA 88 " --> pdb=" O GLNSA 84 " (cutoff:3.500A) Processing helix chain 'SA' and resid 130 through 138 removed outlier: 3.664A pdb=" N LEUSA 134 " --> pdb=" O ASPSA 130 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SERSA 138 " --> pdb=" O LEUSA 134 " (cutoff:3.500A) Processing helix chain 'SA' and resid 167 through 187 removed outlier: 3.659A pdb=" N VALSA 171 " --> pdb=" O GLYSA 167 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLYSA 172 " --> pdb=" O ALASA 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALASA 179 " --> pdb=" O TRPSA 175 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARGSA 184 " --> pdb=" O ARGSA 180 " (cutoff:3.500A) Processing helix chain 'SA' and resid 198 through 203 Processing helix chain 'SA' and resid 206 through 223 removed outlier: 4.391A pdb=" N GLUSA 211 " --> pdb=" O PROSA 207 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYSSA 212 " --> pdb=" O GLUSA 208 " (cutoff:3.500A) Processing helix chain 'SB' and resid 23 through 27 removed outlier: 3.982A pdb=" N LYSSB 27 " --> pdb=" O ASPSB 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 23 through 27' Processing helix chain 'SB' and resid 57 through 63 Processing helix chain 'SB' and resid 106 through 114 removed outlier: 3.588A pdb=" N VALSB 114 " --> pdb=" O METSB 110 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 179 removed outlier: 3.708A pdb=" N VALSB 176 " --> pdb=" O METSB 172 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASNSB 179 " --> pdb=" O GLUSB 175 " (cutoff:3.500A) Processing helix chain 'SB' and resid 180 through 189 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 224 through 233 removed outlier: 4.496A pdb=" N LEUSB 228 " --> pdb=" O GLUSB 224 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N METSB 229 " --> pdb=" O LEUSB 225 " (cutoff:3.500A) Processing helix chain 'SD' and resid 6 through 29 removed outlier: 3.979A pdb=" N VALSD 12 " --> pdb=" O LYSSD 8 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLUSD 23 " --> pdb=" O ALASD 19 " (cutoff:3.500A) Processing helix chain 'SD' and resid 30 through 32 No H-bonds generated for 'chain 'SD' and resid 30 through 32' Processing helix chain 'SD' and resid 54 through 60 Processing helix chain 'SD' and resid 61 through 63 No H-bonds generated for 'chain 'SD' and resid 61 through 63' Processing helix chain 'SD' and resid 64 through 78 removed outlier: 3.556A pdb=" N VALSD 72 " --> pdb=" O GLUSD 68 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VALSD 73 " --> pdb=" O LEUSD 69 " (cutoff:3.500A) Processing helix chain 'SD' and resid 97 through 111 removed outlier: 4.302A pdb=" N GLNSD 101 " --> pdb=" O CYSSD 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALASD 102 " --> pdb=" O ALASD 98 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARGSD 106 " --> pdb=" O ALASD 102 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYRSD 107 " --> pdb=" O GLUSD 103 " (cutoff:3.500A) Processing helix chain 'SD' and resid 114 through 130 removed outlier: 3.685A pdb=" N TYRSD 120 " --> pdb=" O ARGSD 116 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHESD 125 " --> pdb=" O GLYSD 121 " (cutoff:3.500A) Processing helix chain 'SD' and resid 162 through 167 removed outlier: 3.991A pdb=" N TYRSD 166 " --> pdb=" O ASPSD 162 " (cutoff:3.500A) Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 37 through 41 removed outlier: 3.729A pdb=" N CYSSE 41 " --> pdb=" O LEUSE 38 " (cutoff:3.500A) 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 247 through 263 Processing helix chain 'SF' and resid 18 through 22 removed outlier: 3.601A pdb=" N GLYSF 21 " --> pdb=" O LYSSF 18 " (cutoff:3.500A) Processing helix chain 'SF' and resid 35 through 39 removed outlier: 4.022A pdb=" N ILESF 39 " --> pdb=" O GLNSF 36 " (cutoff:3.500A) Processing helix chain 'SF' and resid 42 through 46 removed outlier: 3.849A pdb=" N ALASF 46 " --> pdb=" O GLUSF 43 " (cutoff:3.500A) Processing helix chain 'SF' and resid 61 through 65 removed outlier: 3.675A pdb=" N ALASF 64 " --> pdb=" O PHESF 61 " (cutoff:3.500A) Processing helix chain 'SF' and resid 67 through 75 Processing helix chain 'SF' and resid 79 through 83 Processing helix chain 'SF' and resid 85 through 105 removed outlier: 3.575A pdb=" N PHESF 97 " --> pdb=" O VALSF 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLUSF 98 " --> pdb=" O LYSSF 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HISSF 101 " --> pdb=" O PHESF 97 " (cutoff:3.500A) Processing helix chain 'SF' and resid 107 through 118 Processing helix chain 'SF' and resid 142 through 162 removed outlier: 3.744A pdb=" N LEUSF 154 " --> pdb=" O ALASF 150 " (cutoff:3.500A) Processing helix chain 'SF' and resid 168 through 183 Processing helix chain 'SF' and resid 187 through 203 removed outlier: 3.933A pdb=" N LYSSF 191 " --> pdb=" O SERSF 187 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYSSF 192 " --> pdb=" O TYRSF 188 " (cutoff:3.500A) Processing helix chain 'SH' and resid 17 through 33 removed outlier: 3.759A pdb=" N SERSH 21 " --> pdb=" O ASPSH 17 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLYSH 22 " --> pdb=" O GLUSH 18 " (cutoff:3.500A) Processing helix chain 'SH' and resid 65 through 87 removed outlier: 3.520A pdb=" N LEUSH 69 " --> pdb=" O PROSH 65 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYSSH 70 " --> pdb=" O VALSH 66 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SERSH 71 " --> pdb=" O PROSH 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILESH 75 " --> pdb=" O SERSH 71 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VALSH 77 " --> pdb=" O GLNSH 73 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARGSH 78 " --> pdb=" O LYSSH 74 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARGSH 81 " --> pdb=" O VALSH 77 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLUSH 82 " --> pdb=" O ARGSH 78 " (cutoff:3.500A) Processing helix chain 'SH' and resid 121 through 134 removed outlier: 4.123A pdb=" N VALSH 134 " --> pdb=" O LEUSH 130 " (cutoff:3.500A) Processing helix chain 'SH' and resid 162 through 167 removed outlier: 3.501A pdb=" N VALSH 166 " --> 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 87 through 94 removed outlier: 3.896A pdb=" N VALSI 91 " --> pdb=" O ASNSI 87 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 118 removed outlier: 3.633A pdb=" N GLUSI 114 " --> pdb=" O ARGSI 110 " (cutoff:3.500A) Processing helix chain 'SI' and resid 129 through 139 removed outlier: 3.889A pdb=" N GLUSI 135 " --> pdb=" O PROSI 131 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILESI 136 " --> pdb=" O GLUSI 132 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUSI 137 " --> pdb=" O GLUSI 133 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASNSI 138 " --> pdb=" O GLUSI 134 " (cutoff:3.500A) Processing helix chain 'SI' and resid 142 through 155 removed outlier: 4.196A pdb=" N GLUSI 151 " --> pdb=" O LYSSI 147 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARGSI 152 " --> pdb=" O LYSSI 148 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYSSI 154 " --> pdb=" O ASPSI 150 " (cutoff:3.500A) Processing helix chain 'SI' and resid 159 through 169 removed outlier: 3.881A pdb=" N GLNSI 165 " --> pdb=" O LEUSI 161 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHESI 166 " --> pdb=" O LEUSI 162 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLNSI 167 " --> pdb=" O GLUSI 163 " (cutoff:3.500A) Processing helix chain 'SI' and resid 192 through 207 removed outlier: 3.901A pdb=" N ARGSI 200 " --> pdb=" O GLUSI 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYSSI 201 " --> pdb=" O PHESI 197 " (cutoff:3.500A) Processing helix chain 'SK' and resid 7 through 18 removed outlier: 3.522A pdb=" N LEUSK 14 " --> pdb=" O ALASK 10 " (cutoff:3.500A) Processing helix chain 'SK' and resid 41 through 56 removed outlier: 3.574A pdb=" N LYSSK 47 " --> pdb=" O LEUSK 43 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALASK 48 " --> pdb=" O HISSK 44 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUSK 52 " --> pdb=" O ALASK 48 " (cutoff:3.500A) Processing helix chain 'SK' and resid 72 through 84 removed outlier: 3.746A pdb=" N GLNSK 77 " --> pdb=" O ASNSK 73 " (cutoff:3.500A) Processing helix chain 'SL' and resid 48 through 53 Processing helix chain 'SP' and resid 21 through 28 removed outlier: 3.777A pdb=" N LEUSP 26 " --> pdb=" O LEUSP 22 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASPSP 27 " --> pdb=" O ASPSP 23 " (cutoff:3.500A) Processing helix chain 'SP' and resid 29 through 36 removed outlier: 4.265A pdb=" N GLNSP 35 " --> pdb=" O GLUSP 31 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEUSP 36 " --> pdb=" O GLNSP 32 " (cutoff:3.500A) Processing helix chain 'SP' and resid 38 through 47 Processing helix chain 'SP' and resid 50 through 64 Processing helix chain 'SP' and resid 86 through 90 Processing helix chain 'SP' and resid 108 through 112 removed outlier: 3.951A pdb=" N ILESP 112 " --> pdb=" O PROSP 109 " (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 Processing helix chain 'SQ' and resid 52 through 57 Processing helix chain 'SQ' and resid 76 through 100 removed outlier: 3.508A pdb=" N LYSSQ 98 " --> pdb=" O ALASQ 94 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 102 through 115 removed outlier: 3.623A pdb=" N LYSSQ 106 " --> pdb=" O GLUSQ 102 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLUSQ 107 " --> pdb=" O ALASQ 103 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILESQ 108 " --> pdb=" O SERSQ 104 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILESQ 111 " --> pdb=" O GLUSQ 107 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 116 through 120 Processing helix chain 'SR' and resid 6 through 19 removed outlier: 3.501A pdb=" N ALASR 12 " --> pdb=" O THRSR 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALASR 13 " --> pdb=" O VALSR 9 " (cutoff:3.500A) Processing helix chain 'SR' and resid 27 through 38 removed outlier: 3.781A pdb=" N VALSR 34 " --> pdb=" O THRSR 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYSSR 35 " --> pdb=" O ASNSR 31 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUSR 36 " --> pdb=" O LYSSR 32 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLUSR 37 " --> pdb=" O ARGSR 33 " (cutoff:3.500A) Processing helix chain 'SR' and resid 43 through 64 removed outlier: 3.540A pdb=" N ARGSR 63 " --> pdb=" O LYSSR 59 " (cutoff:3.500A) Processing helix chain 'SR' and resid 71 through 82 removed outlier: 3.640A pdb=" N GLUSR 77 " --> pdb=" O LEUSR 73 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLUSR 79 " --> pdb=" O GLUSR 75 " (cutoff:3.500A) Processing helix chain 'SR' and resid 99 through 109 Processing helix chain 'SS' and resid 25 through 30 removed outlier: 4.091A 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 39 through 49 removed outlier: 3.567A pdb=" N VALSS 44 " --> pdb=" O TYRSS 40 " (cutoff:3.500A) Processing helix chain 'SS' and resid 60 through 73 removed outlier: 3.756A pdb=" N VALSS 64 " --> pdb=" O THRSS 60 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLUSS 65 " --> pdb=" O GLUSS 61 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARGSS 66 " --> pdb=" O ASPSS 62 " (cutoff:3.500A) Processing helix chain 'SS' and resid 74 through 78 Processing helix chain 'SS' and resid 80 through 84 Processing helix chain 'SS' and resid 99 through 116 removed outlier: 4.053A pdb=" N GLUSS 109 " --> pdb=" O ASNSS 105 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUSS 114 " --> pdb=" O ASPSS 110 " (cutoff:3.500A) Processing helix chain 'SS' and resid 119 through 127 Processing helix chain 'SS' and resid 140 through 145 removed outlier: 3.617A pdb=" N ARGSS 144 " --> pdb=" O GLYSS 140 " (cutoff:3.500A) Processing helix chain 'ST' and resid 5 through 9 Processing helix chain 'ST' and resid 10 through 25 removed outlier: 3.552A pdb=" N ARGST 16 " --> pdb=" O GLNST 12 " (cutoff:3.500A) Processing helix chain 'ST' and resid 51 through 67 removed outlier: 3.957A pdb=" N ARGST 62 " --> pdb=" O ALAST 58 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYRST 65 " --> pdb=" O ALAST 61 " (cutoff:3.500A) Processing helix chain 'ST' and resid 71 through 79 Processing helix chain 'ST' and resid 97 through 110 Processing helix chain 'ST' and resid 124 through 143 removed outlier: 3.502A pdb=" N LEUST 131 " --> pdb=" O GLYST 127 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYSST 143 " --> pdb=" O ALAST 139 " (cutoff:3.500A) Processing helix chain 'SU' and resid 28 through 46 removed outlier: 3.728A pdb=" N LYSSU 34 " --> pdb=" O LYSSU 30 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VALSU 35 " --> pdb=" O SERSU 31 " (cutoff:3.500A) Processing helix chain 'SU' and resid 96 through 105 removed outlier: 3.568A pdb=" N GLNSU 100 " --> pdb=" O GLUSU 96 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SERSU 105 " --> pdb=" O ILESU 101 " (cutoff:3.500A) Processing helix chain 'SV' and resid 56 through 63 removed outlier: 3.524A pdb=" N ARGSV 60 " --> pdb=" O CYSSV 56 " (cutoff:3.500A) Processing helix chain 'SV' and resid 64 through 77 Processing helix chain 'SX' and resid 9 through 22 removed outlier: 3.567A pdb=" N TRPSX 22 " --> pdb=" O ARGSX 18 " (cutoff:3.500A) Processing helix chain 'SX' and resid 24 through 32 removed outlier: 3.514A pdb=" N LYSSX 28 " --> pdb=" O ASPSX 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALASX 30 " --> pdb=" O GLNSX 26 " (cutoff:3.500A) Processing helix chain 'SX' and resid 33 through 39 removed outlier: 3.513A pdb=" N LYSSX 37 " --> pdb=" O GLYSX 33 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALASX 38 " --> pdb=" O THRSX 34 " (cutoff:3.500A) Processing helix chain 'SX' and resid 129 through 135 removed outlier: 3.876A pdb=" N LYSSX 135 " --> pdb=" O LEUSX 131 " (cutoff:3.500A) Processing helix chain 'Sa' and resid 46 through 56 removed outlier: 4.316A pdb=" N ARGSa 51 " --> pdb=" O ALASa 47 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASPSa 52 " --> pdb=" O ALASa 48 " (cutoff:3.500A) Processing helix chain 'Sa' and resid 74 through 81 Processing helix chain 'Sa' and resid 88 through 93 removed outlier: 3.924A pdb=" N LYSSa 93 " --> pdb=" O ARGSa 89 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 32 through 36 removed outlier: 3.649A pdb=" N LEUSd 36 " --> pdb=" O LYSSd 33 " (cutoff:3.500A) Processing helix chain 'Sd' and resid 40 through 46 Processing helix chain 'Sd' and resid 46 through 51 removed outlier: 3.524A pdb=" N ILESd 50 " --> pdb=" O TYRSd 46 " (cutoff:3.500A) Processing helix chain 'SC' and resid 64 through 72 Processing helix chain 'SC' and resid 77 through 84 removed outlier: 4.180A pdb=" N ILESC 81 " --> pdb=" O SERSC 77 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHESC 84 " --> pdb=" O GLUSC 80 " (cutoff:3.500A) Processing helix chain 'SC' and resid 91 through 98 Processing helix chain 'SC' and resid 146 through 161 Processing helix chain 'SC' and resid 207 through 217 removed outlier: 3.995A pdb=" N METSC 216 " --> pdb=" O LYSSC 212 " (cutoff:3.500A) Processing helix chain 'SC' and resid 232 through 249 removed outlier: 3.903A pdb=" N THRSC 240 " --> pdb=" O PHESC 236 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYRSC 248 " --> pdb=" O ILESC 244 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SERSC 249 " --> pdb=" O SERSC 245 " (cutoff:3.500A) 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 Processing helix chain 'SG' and resid 21 through 26 removed outlier: 4.060A pdb=" N THRSG 26 " --> pdb=" O ARGSG 22 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 152 through 157 removed outlier: 3.729A pdb=" N VALSG 157 " --> pdb=" O ARGSG 154 " (cutoff:3.500A) Processing helix chain 'SG' and resid 181 through 237 Processing helix chain 'SJ' and resid 21 through 36 removed outlier: 3.523A pdb=" N LYSSJ 30 " --> pdb=" O ASPSJ 26 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEUSJ 31 " --> pdb=" O GLNSJ 27 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 40 through 63 removed outlier: 3.581A pdb=" N ILESJ 53 " --> pdb=" O THRSJ 49 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEUSJ 63 " --> pdb=" O GLUSJ 59 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 67 through 84 removed outlier: 3.554A pdb=" N ASNSJ 75 " --> pdb=" O LEUSJ 71 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 94 through 99 removed outlier: 3.913A pdb=" N LEUSJ 98 " --> pdb=" O LEUSJ 94 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 101 through 107 removed outlier: 4.149A pdb=" N PHESJ 105 " --> pdb=" O LYSSJ 101 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUSJ 106 " --> pdb=" O ILESJ 102 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 109 through 117 removed outlier: 3.844A pdb=" N PHESJ 115 " --> pdb=" O GLNSJ 111 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 122 through 132 Processing helix chain 'SJ' and resid 171 through 185 Processing helix chain 'SM' and resid 14 through 29 removed outlier: 3.550A pdb=" N GLNSM 19 " --> pdb=" O ASNSM 15 " (cutoff:3.500A) Processing helix chain 'SM' and resid 34 through 44 removed outlier: 3.797A pdb=" N LYSSM 40 " --> pdb=" O ARGSM 36 " (cutoff:3.500A) Processing helix chain 'SM' and resid 58 through 72 removed outlier: 3.644A pdb=" N LYSSM 63 " --> pdb=" O PROSM 59 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEUSM 64 " --> pdb=" O METSM 60 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HISSM 72 " --> pdb=" O LEUSM 68 " (cutoff:3.500A) Processing helix chain 'SM' and resid 81 through 89 Processing helix chain 'SM' and resid 119 through 132 Processing helix chain 'SN' and resid 29 through 43 removed outlier: 3.616A pdb=" N LYSSN 34 " --> pdb=" O SERSN 30 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILESN 37 " --> pdb=" O VALSN 33 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYSSN 43 " --> pdb=" O LYSSN 39 " (cutoff:3.500A) Processing helix chain 'SN' and resid 49 through 59 Processing helix chain 'SN' and resid 62 through 68 removed outlier: 3.587A pdb=" N VALSN 66 " --> pdb=" O GLNSN 62 " (cutoff:3.500A) Processing helix chain 'SN' and resid 70 through 79 Processing helix chain 'SN' and resid 85 through 105 removed outlier: 3.511A pdb=" N ILESN 92 " --> pdb=" O LEUSN 88 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HISSN 101 " --> pdb=" O ALASN 97 " (cutoff:3.500A) Processing helix chain 'SN' and resid 108 through 132 removed outlier: 3.876A pdb=" N ILESN 116 " --> pdb=" O LYSSN 112 " (cutoff:3.500A) Processing helix chain 'SN' and resid 145 through 150 removed outlier: 3.597A pdb=" N VALSN 150 " --> pdb=" O ALASN 146 " (cutoff:3.500A) 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 removed outlier: 3.564A pdb=" N ALASO 78 " --> pdb=" O ALASO 74 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLNSO 79 " --> pdb=" O METSO 75 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASPSO 80 " --> pdb=" O LEUSO 76 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VALSO 81 " --> pdb=" O ALASO 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLYSO 89 " --> pdb=" O CYSSO 85 " (cutoff:3.500A) Processing helix chain 'SO' and resid 110 through 123 removed outlier: 4.110A pdb=" N SERSO 114 " --> pdb=" O PROSO 110 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 21 removed outlier: 3.505A pdb=" N ASPSW 9 " --> pdb=" O ASNSW 5 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 44 removed outlier: 3.511A pdb=" N HISSW 44 " --> pdb=" O VALSW 40 " (cutoff:3.500A) Processing helix chain 'SW' and resid 85 through 94 removed outlier: 3.668A pdb=" N TRPSW 89 " --> pdb=" O ASPSW 85 " (cutoff:3.500A) Processing helix chain 'SW' and resid 112 through 119 Processing helix chain 'SY' and resid 36 through 48 Processing helix chain 'SY' and resid 51 through 53 No H-bonds generated for 'chain 'SY' and resid 51 through 53' Processing helix chain 'SY' and resid 80 through 85 removed outlier: 3.614A pdb=" N LYSSY 84 " --> pdb=" O ASPSY 80 " (cutoff:3.500A) Processing helix chain 'SY' and resid 87 through 94 removed outlier: 3.776A pdb=" N HISSY 94 " --> pdb=" O ARGSY 90 " (cutoff:3.500A) Processing helix chain 'SY' and resid 103 through 115 removed outlier: 3.522A pdb=" N ARGSY 107 " --> pdb=" O SERSY 103 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYSSY 115 " --> pdb=" O LYSSY 111 " (cutoff:3.500A) Processing helix chain 'SY' and resid 121 through 126 Processing helix chain 'SZ' and resid 51 through 62 Processing helix chain 'SZ' and resid 63 through 65 No H-bonds generated for 'chain 'SZ' and resid 63 through 65' Processing helix chain 'SZ' and resid 69 through 78 removed outlier: 3.604A pdb=" N LEUSZ 77 " --> pdb=" O VALSZ 73 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSSZ 78 " --> pdb=" O SERSZ 74 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 81 through 95 removed outlier: 3.640A pdb=" N ALASZ 86 " --> pdb=" O SERSZ 82 " (cutoff:3.500A) Processing helix chain 'Sb' and resid 11 through 18 Processing helix chain 'Se' and resid 5 through 9 removed outlier: 4.011A pdb=" N ARGSe 8 " --> pdb=" O SERSe 5 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALASe 9 " --> pdb=" O LEUSe 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Se' and resid 5 through 9' Processing helix chain 'Se' and resid 30 through 43 removed outlier: 3.599A pdb=" N ARGSe 34 " --> pdb=" O GLYSe 30 " (cutoff:3.500A) Processing helix chain 'Sf' and resid 100 through 105 removed outlier: 3.910A pdb=" N LYSSf 104 " --> pdb=" O LEUSf 100 " (cutoff:3.500A) Processing helix chain 'JD' and resid 590 through 614 removed outlier: 3.726A pdb=" N GLUJD 610 " --> pdb=" O LEUJD 606 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLNJD 611 " --> pdb=" O PHEJD 607 " (cutoff:3.500A) Processing helix chain 'JD' and resid 639 through 647 Processing helix chain 'JC' and resid 10 through 19 Processing helix chain 'JC' and resid 28 through 38 removed outlier: 3.834A pdb=" N GLUJC 32 " --> pdb=" O GLYJC 28 " (cutoff:3.500A) Processing helix chain 'JC' and resid 43 through 47 Processing helix chain 'JC' and resid 69 through 74 removed outlier: 3.585A pdb=" N LEUJC 74 " --> pdb=" O LEUJC 70 " (cutoff:3.500A) Processing helix chain 'JC' and resid 147 through 152 Processing helix chain 'JC' and resid 169 through 174 removed outlier: 3.619A pdb=" N ARGJC 174 " --> pdb=" O GLUJC 171 " (cutoff:3.500A) Processing helix chain 'JC' and resid 195 through 201 removed outlier: 3.920A pdb=" N ALAJC 199 " --> pdb=" O PROJC 196 " (cutoff:3.500A) Processing helix chain 'JC' and resid 218 through 224 Processing helix chain 'JC' and resid 239 through 249 removed outlier: 3.751A pdb=" N LYSJC 244 " --> pdb=" O LYSJC 240 " (cutoff:3.500A) Processing helix chain 'JC' and resid 250 through 261 removed outlier: 3.676A pdb=" N ILEJC 254 " --> pdb=" O GLNJC 250 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYRJC 257 " --> pdb=" O SERJC 253 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEUJC 258 " --> pdb=" O ILEJC 254 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALJC 260 " --> pdb=" O GLUJC 256 " (cutoff:3.500A) Processing helix chain 'JC' and resid 327 through 332 removed outlier: 3.766A pdb=" N ASPJC 331 " --> pdb=" O GLUJC 328 " (cutoff:3.500A) Processing helix chain 'JC' and resid 351 through 366 Processing helix chain 'JC' and resid 409 through 427 removed outlier: 3.652A pdb=" N ARGJC 414 " --> pdb=" O LYSJC 410 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLNJC 415 " --> pdb=" O GLUJC 411 " (cutoff:3.500A) Processing helix chain 'JC' and resid 489 through 517 removed outlier: 3.701A pdb=" N GLUJC 505 " --> pdb=" O LEUJC 501 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N METJC 506 " --> pdb=" O LYSJC 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SA' and resid 38 through 41 removed outlier: 6.775A 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: 6.738A pdb=" N VALSA 74 " --> pdb=" O THRSA 97 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILESA 99 " --> pdb=" O VALSA 74 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VALSA 76 " --> pdb=" O ILESA 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SB' and resid 43 through 50 removed outlier: 4.024A pdb=" N GLYSB 45 " --> pdb=" O VALSB 33 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYSSB 96 " --> pdb=" O VALSB 91 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VALSB 91 " --> pdb=" O CYSSB 96 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THRSB 98 " --> pdb=" O GLUSB 89 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLUSB 89 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHESB 100 " --> pdb=" O ILESB 87 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILESB 87 " --> pdb=" O PHESB 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SB' and resid 43 through 50 removed outlier: 4.024A pdb=" N GLYSB 45 " --> pdb=" O VALSB 33 " (cutoff:3.500A) removed outlier: 12.621A pdb=" N ASNSB 99 " --> pdb=" O LYSSB 219 " (cutoff:3.500A) removed outlier: 12.791A pdb=" N LYSSB 219 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N HISSB 101 " --> pdb=" O METSB 217 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N METSB 217 " --> pdb=" O HISSB 101 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ARGSB 213 " --> pdb=" O LEUSB 105 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHESB 138 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VALSB 215 " --> pdb=" O ARGSB 136 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARGSB 136 " --> pdb=" O VALSB 215 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N METSB 217 " --> pdb=" O LEUSB 134 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEUSB 134 " --> pdb=" O METSB 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUSB 137 " --> pdb=" O VALSB 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'SD' and resid 34 through 40 removed outlier: 6.771A pdb=" N THRSD 46 " --> pdb=" O GLUSD 85 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYRSD 87 " --> pdb=" O THRSD 46 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILESD 48 " --> pdb=" O TYRSD 87 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLUSD 89 " --> pdb=" O ILESD 48 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILESD 50 " --> pdb=" O GLUSD 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SD' and resid 148 through 155 removed outlier: 3.561A pdb=" N GLYSD 133 " --> pdb=" O METSD 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'SR' and resid 39 through 40 removed outlier: 3.739A pdb=" N SERSD 209 " --> pdb=" O ILESR 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'SD' and resid 223 through 224 removed outlier: 3.551A pdb=" N ILESD 223 " --> pdb=" O ILESg 189 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILESg 189 " --> pdb=" O ILESD 223 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEUSg 184 " --> pdb=" O ASNSg 178 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASNSg 178 " --> pdb=" O LEUSg 184 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THRSg 186 " --> pdb=" O VALSg 176 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEUSg 173 " --> pdb=" O GLYSg 169 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N CYSSg 168 " --> pdb=" O SERSg 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SE' and resid 75 through 76 removed outlier: 4.135A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SE' and resid 102 through 103 removed outlier: 4.728A pdb=" N ILESE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALASE 110 " --> pdb=" O ILESE 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'SE' and resid 146 through 148 removed outlier: 3.564A pdb=" N ILESE 136 " --> pdb=" O GLYSE 132 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THRSE 159 " --> pdb=" O ILESE 173 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASPSE 163 " --> pdb=" O ILESE 169 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILESE 169 " --> pdb=" O ASPSE 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SE' and resid 217 through 221 removed outlier: 6.848A pdb=" N VALSE 207 " --> pdb=" O ARGSE 198 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARGSE 198 " --> pdb=" O VALSE 207 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HISSE 209 " --> pdb=" O THRSE 196 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEUSE 180 " --> pdb=" O ILESE 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SF' and resid 123 through 125 removed outlier: 8.288A pdb=" N ALASF 138 " --> pdb=" O ASNSc 45 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LYSSc 47 " --> pdb=" O ALASF 138 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASPSF 140 " --> pdb=" O LYSSc 47 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N CYSSc 27 " --> pdb=" O GLYSc 19 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLYSc 19 " --> pdb=" O CYSSc 27 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLNSc 29 " --> pdb=" O VALSc 17 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VALSc 17 " --> pdb=" O GLNSc 29 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARGSc 31 " --> pdb=" O THRSc 15 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SH' and resid 47 through 53 removed outlier: 3.613A pdb=" N VALSH 53 " --> pdb=" O ARGSH 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARGSH 57 " --> pdb=" O VALSH 53 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYSSH 58 " --> pdb=" O HISSH 91 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VALSH 93 " --> pdb=" O LYSSH 58 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILESH 60 " --> pdb=" O VALSH 93 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILESH 95 " --> pdb=" O ILESH 60 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILESH 62 " --> pdb=" O ILESH 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SH' and resid 185 through 188 removed outlier: 8.168A pdb=" N ASNSH 186 " --> pdb=" O ARGSH 152 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILESH 154 " --> pdb=" O ASNSH 186 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLUSH 188 " --> pdb=" O ILESH 154 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VALSH 156 " --> pdb=" O GLUSH 188 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLYSH 141 " --> pdb=" O HISSH 157 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHESW 50 " --> pdb=" O VALSH 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SI' and resid 3 through 4 removed outlier: 3.748A 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: 6.478A 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: 5.037A pdb=" N ARGSI 77 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEUSI 103 " --> pdb=" O ILESI 79 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VALSI 81 " --> pdb=" O ILESI 101 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILESI 101 " --> pdb=" O VALSI 81 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N GLYSI 187 " --> pdb=" O VALSI 62 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 187 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VALSI 189 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 6.800A 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: 3.608A pdb=" N METSK 21 " --> pdb=" O TRPSK 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SL' and resid 72 through 82 removed outlier: 18.128A pdb=" N ILESL 72 " --> pdb=" O LEUSL 93 " (cutoff:3.500A) removed outlier: 15.395A pdb=" N LEUSL 93 " --> pdb=" O ILESL 72 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N SERSL 74 " --> pdb=" O ASPSL 91 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASPSL 91 " --> pdb=" O SERSL 74 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VALSL 87 " --> pdb=" O THRSL 78 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N METSL 80 " --> pdb=" O THRSL 85 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THRSL 85 " --> pdb=" O METSL 80 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARGSL 101 " --> pdb=" O ILESL 96 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N PHESL 140 " --> pdb=" O ASNSL 108 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SERSL 110 " --> pdb=" O PHESL 140 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VALSL 142 " --> pdb=" O SERSL 110 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HISSL 112 " --> pdb=" O VALSL 142 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LYSSL 144 " --> pdb=" O HISSL 112 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VALSL 142 " --> pdb=" O GLYSL 129 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLYSL 129 " --> pdb=" O VALSL 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SP' and resid 76 through 78 removed outlier: 6.490A pdb=" N VALSP 76 " --> pdb=" O GLYSP 95 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYRSP 97 " --> pdb=" O VALSP 76 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THRSP 78 " --> pdb=" O TYRSP 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SQ' and resid 9 through 16 removed outlier: 6.224A pdb=" N LEUSQ 31 " --> pdb=" O ILESQ 68 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VALSQ 70 " --> pdb=" O LEUSQ 31 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYSSQ 33 " --> pdb=" O VALSQ 70 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VALSQ 72 " --> pdb=" O LYSSQ 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'SR' and resid 97 through 98 Processing sheet with id=AC6, first strand: chain 'SS' and resid 12 through 13 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 51 through 55 removed outlier: 3.706A pdb=" N ASPSU 90 " --> pdb=" O LYSSU 51 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEUSU 88 " --> pdb=" O PROSU 53 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARGSU 55 " --> pdb=" O LYSSU 86 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYSSU 86 " --> pdb=" O ARGSU 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'SU' and resid 51 through 55 removed outlier: 3.706A pdb=" N ASPSU 90 " --> pdb=" O LYSSU 51 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEUSU 88 " --> pdb=" O PROSU 53 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARGSU 55 " --> pdb=" O LYSSU 86 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYSSU 86 " --> pdb=" O ARGSU 55 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEUSU 91 " --> pdb=" O ILESU 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILESU 20 " --> pdb=" O LEUSU 91 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'SV' and resid 15 through 16 removed outlier: 4.421A pdb=" N ARGSV 15 " --> pdb=" O ILESV 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'SV' and resid 32 through 39 removed outlier: 4.934A pdb=" N GLNSV 49 " --> pdb=" O GLUSV 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'SX' and resid 46 through 58 removed outlier: 6.544A pdb=" N ARGSX 71 " --> pdb=" O LEUSX 52 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYSSX 54 " --> pdb=" O CYSSX 69 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYSSX 69 " --> pdb=" O LYSSX 54 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLYSX 56 " --> pdb=" O ARGSX 67 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARGSX 67 " --> pdb=" O GLYSX 56 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHESX 120 " --> pdb=" O THRSX 82 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VALSX 125 " --> pdb=" O GLUSX 99 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLUSX 99 " --> pdb=" O VALSX 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Sa' and resid 20 through 22 Processing sheet with id=AD6, first strand: chain 'Sa' and resid 36 through 43 Processing sheet with id=AD7, first strand: chain 'Sd' and resid 30 through 31 removed outlier: 3.686A pdb=" N METSd 38 " --> pdb=" O ILESd 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Sg' and resid 4 through 11 removed outlier: 5.329A pdb=" N METSg 5 " --> pdb=" O THRSg 313 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THRSg 313 " --> pdb=" O METSg 5 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEUSg 7 " --> pdb=" O GLNSg 311 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLNSg 311 " --> pdb=" O LEUSg 7 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALASg 300 " --> pdb=" O ARGSg 308 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Sg' and resid 18 through 23 removed outlier: 6.658A pdb=" N ALASg 34 " --> pdb=" O THRSg 19 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILESg 21 " --> pdb=" O LEUSg 32 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEUSg 32 " --> pdb=" O ILESg 21 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THRSg 23 " --> pdb=" O METSg 30 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N METSg 30 " --> pdb=" O THRSg 23 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILESg 31 " --> pdb=" O TRPSg 43 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THRSg 39 " --> pdb=" O SERSg 35 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILESg 40 " --> pdb=" O ALASg 58 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALASg 58 " --> pdb=" O ILESg 40 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N METSg 42 " --> pdb=" O GLNSg 56 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Sg' and resid 66 through 71 removed outlier: 3.950A pdb=" N ARGSg 99 " --> pdb=" O LEUSg 89 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASPSg 91 " --> pdb=" O THRSg 97 " (cutoff:3.500A) removed outlier: 5.890A 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 Processing sheet with id=AE3, first strand: chain 'Sg' and resid 195 through 200 removed outlier: 3.855A pdb=" N THRSg 197 " --> pdb=" O GLYSg 210 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLYSg 211 " --> pdb=" O GLNSg 215 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLNSg 215 " --> pdb=" O GLYSg 211 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALASg 216 " --> pdb=" O THRSg 229 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THRSg 229 " --> pdb=" O ALASg 216 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEUSg 218 " --> pdb=" O LEUSg 227 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Sg' and resid 236 through 241 removed outlier: 4.293A pdb=" N ALASg 238 " --> pdb=" O ALASg 251 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUSg 248 " --> pdb=" O TRPSg 259 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASPSg 260 " --> pdb=" O ILESg 266 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILESg 266 " --> pdb=" O ASPSg 260 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'SC' and resid 103 through 115 removed outlier: 5.265A pdb=" N ASPSC 104 " --> pdb=" O GLYSC 131 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLYSC 131 " --> pdb=" O ASPSC 104 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VALSC 106 " --> pdb=" O ALASC 129 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALASC 129 " --> pdb=" O VALSC 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VALSC 137 " --> pdb=" O VALSC 163 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'SC' and resid 184 through 188 Processing sheet with id=AE7, first strand: chain 'SG' and resid 11 through 17 removed outlier: 4.812A pdb=" N CYSSG 12 " --> pdb=" O PHESG 7 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHESG 7 " --> pdb=" O CYSSG 12 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYSSG 2 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEUSG 111 " --> pdb=" O LYSSG 2 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASNSG 4 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILESG 113 " --> pdb=" O ASNSG 4 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SERSG 6 " --> pdb=" O ILESG 113 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LYSSG 115 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLYSG 54 " --> pdb=" O ASNSG 110 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VALSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILESG 52 " --> pdb=" O VALSG 112 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VALSG 114 " --> pdb=" O VALSG 50 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VALSG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'SG' and resid 11 through 17 removed outlier: 4.812A pdb=" N CYSSG 12 " --> pdb=" O PHESG 7 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHESG 7 " --> pdb=" O CYSSG 12 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYSSG 2 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEUSG 111 " --> pdb=" O LYSSG 2 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASNSG 4 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILESG 113 " --> pdb=" O ASNSG 4 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SERSG 6 " --> pdb=" O ILESG 113 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LYSSG 115 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLYSG 54 " --> pdb=" O ASNSG 110 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VALSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILESG 52 " --> pdb=" O VALSG 112 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VALSG 114 " --> pdb=" O VALSG 50 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VALSG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLYSG 55 " --> pdb=" O PROSG 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLYSG 60 " --> pdb=" O ASPSG 57 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'SG' and resid 72 through 77 removed outlier: 3.523A pdb=" N LYSSG 93 " --> pdb=" O LEUSG 77 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'SG' and resid 160 through 162 removed outlier: 3.533A pdb=" N LYSSG 172 " --> pdb=" O LYSSG 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARGSG 170 " --> pdb=" O LEUSG 162 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'SJ' and resid 140 through 141 Processing sheet with id=AF3, first strand: chain 'SM' and resid 32 through 33 removed outlier: 3.515A pdb=" N LEUSM 49 " --> pdb=" O VALSM 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'SO' and resid 52 through 57 removed outlier: 6.844A pdb=" N VALSO 44 " --> pdb=" O ILESO 53 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARGSO 55 " --> pdb=" O VALSO 42 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VALSO 42 " --> pdb=" O ARGSO 55 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THRSO 57 " --> pdb=" O THRSO 40 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THRSO 40 " --> pdb=" O THRSO 57 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEUSO 93 " --> pdb=" O ARGSO 128 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLUSO 130 " --> pdb=" O LEUSO 93 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILESO 95 " --> pdb=" O GLUSO 130 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'SW' and resid 72 through 73 Processing sheet with id=AF6, first strand: chain 'SW' and resid 72 through 73 removed outlier: 6.542A pdb=" N VALSW 103 " --> pdb=" O LEUSW 126 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHESW 128 " --> pdb=" O PHESW 101 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N PHESW 101 " --> pdb=" O PHESW 128 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'SY' and resid 6 through 15 removed outlier: 6.081A pdb=" N ILESY 7 " --> pdb=" O LEUSY 28 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEUSY 28 " --> pdb=" O ILESY 7 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THRSY 9 " --> pdb=" O ASPSY 26 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASPSY 26 " --> pdb=" O THRSY 9 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYSSY 11 " --> pdb=" O VALSY 24 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VALSY 24 " --> pdb=" O LYSSY 11 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THRSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.376A 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 32 through 36 removed outlier: 4.891A pdb=" N PHESb 32 " --> pdb=" O LYSSb 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYSSb 82 " --> pdb=" O PHESb 32 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASPSb 34 " --> pdb=" O ARGSb 80 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Sb' and resid 64 through 65 Processing sheet with id=AG2, first strand: chain 'Sf' and resid 106 through 109 Processing sheet with id=AG3, first strand: chain 'Sf' and resid 138 through 141 Processing sheet with id=AG4, first strand: chain 'JC' and resid 23 through 26 removed outlier: 6.468A pdb=" N LEUJC 55 " --> pdb=" O VALJC 81 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEUJC 134 " --> pdb=" O ASNJC 159 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEUJC 158 " --> pdb=" O ALAJC 185 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'JC' and resid 373 through 379 removed outlier: 6.205A pdb=" N LEUJC 307 " --> pdb=" O THRJC 580 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VALJC 582 " --> pdb=" O LEUJC 307 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEUJC 309 " --> pdb=" O VALJC 582 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'JC' and resid 458 through 460 removed outlier: 3.570A pdb=" N SERJC 460 " --> pdb=" O LEUJC 451 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THRJC 322 " --> pdb=" O LEUJC 387 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYRJC 389 " --> pdb=" O THRJC 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARGJC 324 " --> pdb=" O TYRJC 389 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ALAJC 391 " --> pdb=" O ARGJC 324 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VALJC 323 " --> pdb=" O VALJC 556 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VALJC 553 " --> pdb=" O VALJC 565 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VALJC 565 " --> pdb=" O VALJC 553 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VALJC 555 " --> pdb=" O LYSJC 563 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'JC' and resid 398 through 399 1635 hydrogen bonds defined for protein. 4635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1317 hydrogen bonds 2030 hydrogen bond angles 0 basepair planarities 533 basepair parallelities 884 stacking parallelities Total time for adding SS restraints: 65.25 Time building geometry restraints manager: 16.33 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: 12415 1.33 - 1.45: 31396 1.45 - 1.58: 37921 1.58 - 1.70: 3471 1.70 - 1.82: 306 Bond restraints: 85509 Sorted by residual: bond pdb=" CA SERSF 52 " pdb=" CB SERSF 52 " ideal model delta sigma weight residual 1.530 1.475 0.056 1.69e-02 3.50e+03 1.08e+01 bond pdb=" N ARGSL 35 " pdb=" CA ARGSL 35 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.45e+00 bond pdb=" N LYSSF 18 " pdb=" CA LYSSF 18 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.24e-02 6.50e+03 9.13e+00 bond pdb=" O3' US21477 " pdb=" P US21478 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 8.80e+00 bond pdb=" O3' GS2 289 " pdb=" P US2 290 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.58e+00 ... (remaining 85504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 121412 2.65 - 5.30: 1980 5.30 - 7.95: 249 7.95 - 10.61: 47 10.61 - 13.26: 8 Bond angle restraints: 123696 Sorted by residual: angle pdb=" N ILESV 78 " pdb=" CA ILESV 78 " pdb=" C ILESV 78 " ideal model delta sigma weight residual 113.71 103.89 9.82 9.50e-01 1.11e+00 1.07e+02 angle pdb=" CA PROSF 67 " pdb=" N PROSF 67 " pdb=" CD PROSF 67 " ideal model delta sigma weight residual 112.00 101.48 10.52 1.40e+00 5.10e-01 5.65e+01 angle pdb=" O3' GS2 291 " pdb=" C3' GS2 291 " pdb=" C2' GS2 291 " ideal model delta sigma weight residual 113.70 124.19 -10.49 1.50e+00 4.44e-01 4.89e+01 angle pdb=" C2' CS2 501 " pdb=" C1' CS2 501 " pdb=" N1 CS2 501 " ideal model delta sigma weight residual 112.00 121.83 -9.83 1.50e+00 4.44e-01 4.29e+01 angle pdb=" C4' GS2 289 " pdb=" C3' GS2 289 " pdb=" O3' GS2 289 " ideal model delta sigma weight residual 113.00 103.96 9.04 1.50e+00 4.44e-01 3.63e+01 ... (remaining 123691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 49482 35.93 - 71.85: 4478 71.85 - 107.78: 542 107.78 - 143.70: 5 143.70 - 179.63: 17 Dihedral angle restraints: 54524 sinusoidal: 38806 harmonic: 15718 Sorted by residual: dihedral pdb=" O4' CS21139 " pdb=" C1' CS21139 " pdb=" N1 CS21139 " pdb=" C2 CS21139 " ideal model delta sinusoidal sigma weight residual -160.00 1.93 -161.93 1 1.50e+01 4.44e-03 8.32e+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 -160.00 0.99 -160.99 1 1.50e+01 4.44e-03 8.30e+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 43.37 156.63 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 54521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 13850 0.080 - 0.160: 1239 0.160 - 0.240: 126 0.240 - 0.320: 16 0.320 - 0.400: 3 Chirality restraints: 15234 Sorted by residual: chirality pdb=" CB VALSH 66 " pdb=" CA VALSH 66 " pdb=" CG1 VALSH 66 " pdb=" CG2 VALSH 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" P GS2 880 " pdb=" OP1 GS2 880 " pdb=" OP2 GS2 880 " pdb=" O5' GS2 880 " both_signs ideal model delta sigma weight residual True 2.41 -2.76 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1' US2 917 " pdb=" O4' US2 917 " pdb=" C2' US2 917 " pdb=" N1 US2 917 " both_signs ideal model delta sigma weight residual False 2.47 2.14 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 15231 not shown) Planarity restraints: 9311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GS2 841 " -0.027 2.00e-02 2.50e+03 3.60e-02 3.89e+01 pdb=" N9 GS2 841 " 0.038 2.00e-02 2.50e+03 pdb=" C8 GS2 841 " 0.009 2.00e-02 2.50e+03 pdb=" N7 GS2 841 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GS2 841 " -0.003 2.00e-02 2.50e+03 pdb=" C6 GS2 841 " -0.043 2.00e-02 2.50e+03 pdb=" O6 GS2 841 " 0.023 2.00e-02 2.50e+03 pdb=" N1 GS2 841 " 0.013 2.00e-02 2.50e+03 pdb=" C2 GS2 841 " -0.086 2.00e-02 2.50e+03 pdb=" N2 GS2 841 " 0.055 2.00e-02 2.50e+03 pdb=" N3 GS2 841 " 0.012 2.00e-02 2.50e+03 pdb=" C4 GS2 841 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLUSQ 43 " 0.089 5.00e-02 4.00e+02 1.35e-01 2.89e+01 pdb=" N PROSQ 44 " -0.233 5.00e-02 4.00e+02 pdb=" CA PROSQ 44 " 0.072 5.00e-02 4.00e+02 pdb=" CD PROSQ 44 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERSb 27 " -0.088 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PROSb 28 " 0.225 5.00e-02 4.00e+02 pdb=" CA PROSb 28 " -0.070 5.00e-02 4.00e+02 pdb=" CD PROSb 28 " -0.068 5.00e-02 4.00e+02 ... (remaining 9308 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 2158 2.65 - 3.21: 65184 3.21 - 3.77: 148277 3.77 - 4.34: 196378 4.34 - 4.90: 280014 Nonbonded interactions: 692011 Sorted by model distance: nonbonded pdb=" O2 CS2 834 " pdb=" O2 CS2 839 " model vdw 2.083 3.040 nonbonded pdb=" N4 CS2 834 " pdb=" N4 CS2 839 " model vdw 2.088 3.200 nonbonded pdb=" OH TYRSd 46 " pdb="ZN ZNSd 101 " model vdw 2.159 2.230 nonbonded pdb=" N3 CS2 834 " pdb=" N3 CS2 839 " model vdw 2.159 3.200 nonbonded pdb=" OG1 THRSE 247 " pdb=" OE1 GLUSE 250 " model vdw 2.186 3.040 ... (remaining 692006 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: 6.600 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: 0.080 Extract box with map and model: 2.300 Check model and map are aligned: 0.460 Set scattering table: 0.560 Process input model: 190.030 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.004 0.110 85509 Z= 0.268 Angle : 0.834 13.256 123696 Z= 0.434 Chirality : 0.047 0.400 15234 Planarity : 0.008 0.135 9311 Dihedral : 21.841 179.628 44376 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 0.25 % Allowed : 0.62 % Favored : 99.13 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: -2.36 (0.10), residues: 5385 helix: -2.71 (0.09), residues: 1671 sheet: -0.32 (0.17), residues: 989 loop : -1.17 (0.11), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRPSA 55 HIS 0.012 0.001 HISSO 94 PHE 0.041 0.002 PHESC 236 TYR 0.033 0.002 TYRSB 155 ARG 0.023 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1895 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1883 time to evaluate : 4.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 5 TRP cc_start: 0.8551 (m100) cc_final: 0.8260 (m100) REVERT: SA 174 MET cc_start: 0.8831 (mmm) cc_final: 0.8627 (mmm) REVERT: SB 179 ASN cc_start: 0.8037 (m-40) cc_final: 0.7437 (m110) REVERT: SD 77 PHE cc_start: 0.7567 (m-80) cc_final: 0.7347 (m-80) REVERT: SD 206 ASP cc_start: 0.8329 (m-30) cc_final: 0.8010 (m-30) REVERT: SF 49 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8779 (tp) REVERT: SH 34 SER cc_start: 0.8196 (m) cc_final: 0.7986 (p) REVERT: SI 97 VAL cc_start: 0.7328 (t) cc_final: 0.6669 (t) REVERT: SK 9 ILE cc_start: 0.8447 (pt) cc_final: 0.7793 (pt) REVERT: SK 25 LYS cc_start: 0.8084 (tttt) cc_final: 0.7608 (tttm) REVERT: SK 82 TYR cc_start: 0.7341 (t80) cc_final: 0.7038 (t80) REVERT: SK 89 ILE cc_start: 0.6349 (tp) cc_final: 0.6022 (mp) REVERT: SP 35 GLN cc_start: 0.9039 (mm110) cc_final: 0.8781 (mp10) REVERT: SP 46 ASN cc_start: 0.8283 (m-40) cc_final: 0.7931 (t0) REVERT: SP 90 VAL cc_start: 0.8279 (t) cc_final: 0.8060 (m) REVERT: SP 107 ILE cc_start: 0.7645 (mp) cc_final: 0.6777 (mt) REVERT: SP 109 PRO cc_start: 0.6232 (Cg_exo) cc_final: 0.5932 (Cg_endo) REVERT: SP 116 LEU cc_start: 0.8506 (mm) cc_final: 0.8212 (mm) REVERT: SQ 81 ILE cc_start: 0.9313 (pt) cc_final: 0.9095 (pt) REVERT: SQ 110 ASP cc_start: 0.6986 (m-30) cc_final: 0.6620 (m-30) REVERT: SR 118 GLN cc_start: 0.7946 (tt0) cc_final: 0.7628 (tm-30) REVERT: SR 130 THR cc_start: 0.8749 (t) cc_final: 0.8543 (p) REVERT: SS 92 ASP cc_start: 0.7402 (p0) cc_final: 0.7125 (p0) REVERT: SS 95 TYR cc_start: 0.7825 (m-80) cc_final: 0.7615 (m-10) REVERT: ST 28 LEU cc_start: 0.8010 (tp) cc_final: 0.7735 (tp) REVERT: ST 51 ASN cc_start: 0.8177 (m-40) cc_final: 0.7943 (m-40) REVERT: SU 40 ILE cc_start: 0.8949 (mm) cc_final: 0.8099 (mm) REVERT: SU 46 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7934 (mmmm) REVERT: SU 115 THR cc_start: 0.8154 (t) cc_final: 0.7948 (t) REVERT: SV 28 ASP cc_start: 0.7735 (t0) cc_final: 0.7361 (t0) REVERT: Sc 15 THR cc_start: 0.8578 (p) cc_final: 0.8020 (t) REVERT: Sg 132 TRP cc_start: 0.7093 (m100) cc_final: 0.6838 (m100) REVERT: Sg 137 VAL cc_start: 0.8389 (t) cc_final: 0.7870 (t) REVERT: Sg 249 CYS cc_start: 0.7891 (m) cc_final: 0.7531 (m) REVERT: SG 57 ASP cc_start: 0.7640 (t0) cc_final: 0.7106 (t0) REVERT: SJ 107 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7915 (mm-30) REVERT: SM 12 MET cc_start: 0.3564 (tmm) cc_final: 0.2652 (ttt) REVERT: SM 14 VAL cc_start: 0.6347 (p) cc_final: 0.6083 (t) REVERT: SM 42 LEU cc_start: 0.8808 (mm) cc_final: 0.8520 (mp) REVERT: SO 56 VAL cc_start: 0.8630 (t) cc_final: 0.8416 (t) REVERT: SO 63 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6353 (mmmt) REVERT: SZ 58 LEU cc_start: 0.8569 (tt) cc_final: 0.7935 (mt) REVERT: Sf 150 PHE cc_start: 0.6157 (t80) cc_final: 0.5770 (t80) REVERT: JC 231 ASN cc_start: 0.7574 (t0) cc_final: 0.7174 (t0) REVERT: JC 353 LYS cc_start: 0.8969 (pttp) cc_final: 0.8570 (mtmm) REVERT: JC 356 LEU cc_start: 0.9320 (mt) cc_final: 0.9052 (pp) REVERT: JC 366 LEU cc_start: 0.8429 (tp) cc_final: 0.7962 (tp) REVERT: JC 418 LEU cc_start: 0.8961 (mt) cc_final: 0.8409 (mm) REVERT: JC 442 LEU cc_start: 0.7095 (mt) cc_final: 0.6160 (mt) REVERT: JC 448 TYR cc_start: 0.6840 (m-10) cc_final: 0.6252 (m-80) REVERT: JC 469 LYS cc_start: 0.8534 (mttt) cc_final: 0.8265 (tttt) REVERT: JC 509 TYR cc_start: 0.6634 (t80) cc_final: 0.6430 (t80) outliers start: 12 outliers final: 1 residues processed: 1887 average time/residue: 0.8372 time to fit residues: 2585.6526 Evaluate side-chains 1056 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1054 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SF residue 49 LEU Chi-restraints excluded: chain SF residue 87 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 596 optimal weight: 10.0000 chunk 535 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 285 optimal weight: 0.0170 chunk 553 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 336 optimal weight: 0.9990 chunk 411 optimal weight: 10.0000 chunk 641 optimal weight: 4.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 9 GLN SB 95 ASN SB 160 GLN SB 202 GLN ** SD 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 67 GLN SH 44 ASN SH 163 GLN SI 168 GLN ** SL 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 19 ASN SL 106 HIS SL 108 ASN ** SL 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 11 GLN ** SQ 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 86 GLN SQ 114 GLN SR 26 ASN SR 31 ASN SR 48 ASN SR 93 GLN ** SS 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 33 GLN SG 186 GLN SJ 27 GLN ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 112 ASN Se 37 GLN Se 44 ASN JD 588 HIS JC 378 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.073692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054502 restraints weight = 316512.083| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.48 r_work: 0.2931 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 85509 Z= 0.211 Angle : 0.664 14.720 123696 Z= 0.340 Chirality : 0.039 0.345 15234 Planarity : 0.006 0.164 9311 Dihedral : 23.096 179.863 33116 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.51 % Allowed : 14.57 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -1.17 (0.11), residues: 5385 helix: -0.68 (0.11), residues: 1720 sheet: -0.13 (0.17), residues: 979 loop : -1.00 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRPSM 88 HIS 0.014 0.001 HISSg 14 PHE 0.031 0.002 PHESV 83 TYR 0.032 0.002 TYRSI 113 ARG 0.014 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1122 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 38 MET cc_start: 0.7876 (mpp) cc_final: 0.7668 (mpp) REVERT: SD 32 ASP cc_start: 0.8131 (m-30) cc_final: 0.7884 (m-30) REVERT: SD 116 ARG cc_start: 0.8541 (tpp-160) cc_final: 0.8327 (mmm-85) REVERT: SD 206 ASP cc_start: 0.8894 (m-30) cc_final: 0.8405 (m-30) REVERT: SE 251 GLU cc_start: 0.8768 (tp30) cc_final: 0.8413 (tp30) REVERT: SF 38 TYR cc_start: 0.8904 (m-80) cc_final: 0.8619 (m-80) REVERT: SF 45 TYR cc_start: 0.8482 (m-10) cc_final: 0.8282 (m-10) REVERT: SF 49 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9070 (mt) REVERT: SF 102 LEU cc_start: 0.9083 (mt) cc_final: 0.8362 (tp) REVERT: SF 175 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6876 (p0) REVERT: SF 176 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6949 (mm-30) REVERT: SH 32 MET cc_start: 0.7637 (mmm) cc_final: 0.7216 (mmm) REVERT: SI 111 GLN cc_start: 0.8648 (mt0) cc_final: 0.8366 (mt0) REVERT: SI 167 GLN cc_start: 0.9168 (mt0) cc_final: 0.8663 (tt0) REVERT: SI 168 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8210 (mm-40) REVERT: SK 1 MET cc_start: 0.5047 (tpt) cc_final: 0.4788 (tpt) REVERT: SK 3 MET cc_start: 0.7307 (ptt) cc_final: 0.7025 (ptt) REVERT: SK 25 LYS cc_start: 0.8090 (tttt) cc_final: 0.7473 (tttm) REVERT: SK 59 LYS cc_start: 0.8010 (ptpp) cc_final: 0.7764 (ptpp) REVERT: SK 68 TYR cc_start: 0.8319 (m-80) cc_final: 0.8114 (m-80) REVERT: SK 82 TYR cc_start: 0.7918 (t80) cc_final: 0.7454 (t80) REVERT: SK 89 ILE cc_start: 0.6489 (tp) cc_final: 0.6200 (mp) REVERT: SL 11 GLN cc_start: 0.8738 (mp10) cc_final: 0.8397 (mp10) REVERT: SL 48 LYS cc_start: 0.8549 (tptt) cc_final: 0.8305 (tptp) REVERT: SP 31 GLU cc_start: 0.8578 (pm20) cc_final: 0.8337 (pm20) REVERT: SP 35 GLN cc_start: 0.9016 (mm110) cc_final: 0.8314 (mm-40) REVERT: SP 90 VAL cc_start: 0.8715 (t) cc_final: 0.8435 (p) REVERT: SP 109 PRO cc_start: 0.6559 (Cg_exo) cc_final: 0.6351 (Cg_endo) REVERT: SP 118 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7496 (mm-30) REVERT: SQ 48 GLN cc_start: 0.8302 (tp40) cc_final: 0.8047 (tm-30) REVERT: SR 18 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8376 (mm-30) REVERT: SR 24 LEU cc_start: 0.9211 (mt) cc_final: 0.8966 (mt) REVERT: SR 82 ASP cc_start: 0.8283 (t0) cc_final: 0.8074 (t0) REVERT: SS 54 LYS cc_start: 0.7795 (tttt) cc_final: 0.7284 (tttt) REVERT: ST 13 GLU cc_start: 0.8898 (mp0) cc_final: 0.7931 (mp0) REVERT: ST 52 TRP cc_start: 0.9528 (p-90) cc_final: 0.9306 (p-90) REVERT: ST 137 GLN cc_start: 0.9300 (tt0) cc_final: 0.8999 (mt0) REVERT: SU 33 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8908 (mm-30) REVERT: SU 45 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7731 (tm-30) REVERT: SU 111 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8155 (tm-30) REVERT: SV 28 ASP cc_start: 0.8439 (t0) cc_final: 0.8017 (t0) REVERT: SX 71 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7988 (tpt90) REVERT: Sa 52 ASP cc_start: 0.8953 (t0) cc_final: 0.8679 (t0) REVERT: Sc 36 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6777 (p0) REVERT: Sc 52 GLU cc_start: 0.8882 (pp20) cc_final: 0.8526 (pm20) REVERT: Sg 5 MET cc_start: 0.8058 (tpp) cc_final: 0.7844 (tpp) REVERT: Sg 132 TRP cc_start: 0.7441 (m100) cc_final: 0.6974 (m100) REVERT: Sg 249 CYS cc_start: 0.7834 (m) cc_final: 0.7407 (p) REVERT: SG 5 ILE cc_start: 0.8444 (mp) cc_final: 0.8228 (mm) REVERT: SG 24 LEU cc_start: 0.8522 (mt) cc_final: 0.8221 (mt) REVERT: SG 152 ASP cc_start: 0.7760 (t0) cc_final: 0.7509 (t0) REVERT: SJ 27 GLN cc_start: 0.8812 (tp40) cc_final: 0.8448 (tp-100) REVERT: SJ 107 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8861 (mm-30) REVERT: SJ 132 GLN cc_start: 0.8569 (mt0) cc_final: 0.8084 (mm-40) REVERT: SM 12 MET cc_start: 0.3609 (tmm) cc_final: 0.2805 (ttt) REVERT: SM 46 GLN cc_start: 0.7082 (pm20) cc_final: 0.6533 (pm20) REVERT: SM 61 TYR cc_start: 0.7321 (t80) cc_final: 0.7117 (t80) REVERT: SM 112 LYS cc_start: 0.8503 (pttm) cc_final: 0.7477 (tptt) REVERT: SN 78 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8493 (ttmt) REVERT: SN 113 PHE cc_start: 0.8476 (t80) cc_final: 0.8165 (t80) REVERT: SO 63 LYS cc_start: 0.7334 (mmtt) cc_final: 0.6273 (mmmt) REVERT: SO 75 MET cc_start: 0.9099 (ppp) cc_final: 0.8884 (ppp) REVERT: SY 86 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8052 (tp30) REVERT: SZ 106 GLN cc_start: 0.8513 (tp40) cc_final: 0.8059 (mm110) REVERT: SZ 109 TYR cc_start: 0.7721 (m-80) cc_final: 0.7324 (m-80) REVERT: Sb 14 GLU cc_start: 0.8610 (mp0) cc_final: 0.8029 (mp0) REVERT: Sf 132 MET cc_start: 0.6790 (mmm) cc_final: 0.5205 (mmm) REVERT: Sf 150 PHE cc_start: 0.6163 (t80) cc_final: 0.5684 (t80) REVERT: JC 231 ASN cc_start: 0.8311 (t0) cc_final: 0.7567 (t0) REVERT: JC 355 PHE cc_start: 0.8258 (m-80) cc_final: 0.7750 (m-80) REVERT: JC 356 LEU cc_start: 0.9312 (mt) cc_final: 0.9011 (pp) REVERT: JC 359 GLN cc_start: 0.8800 (pt0) cc_final: 0.8487 (pp30) REVERT: JC 442 LEU cc_start: 0.7455 (mt) cc_final: 0.7078 (mm) REVERT: JC 448 TYR cc_start: 0.6986 (m-10) cc_final: 0.6572 (m-80) REVERT: JC 469 LYS cc_start: 0.8484 (mttt) cc_final: 0.8277 (tttt) REVERT: JC 577 PRO cc_start: 0.7547 (Cg_endo) cc_final: 0.7283 (Cg_exo) outliers start: 118 outliers final: 70 residues processed: 1191 average time/residue: 0.7337 time to fit residues: 1495.5097 Evaluate side-chains 1051 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 976 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SB residue 121 ILE Chi-restraints excluded: chain SB residue 185 VAL Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 154 ASP Chi-restraints excluded: chain SD residue 221 THR Chi-restraints excluded: chain SE residue 60 GLU Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SF residue 49 LEU Chi-restraints excluded: chain SF residue 149 GLN Chi-restraints excluded: chain SF residue 175 ASP Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 44 ASN Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 63 THR Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SR residue 55 THR Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 18 THR Chi-restraints excluded: chain SS residue 31 THR Chi-restraints excluded: chain SS residue 64 VAL Chi-restraints excluded: chain ST residue 74 SER Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain SU residue 26 SER Chi-restraints excluded: chain SU residue 105 SER Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SX residue 71 ARG Chi-restraints excluded: chain Sa residue 45 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 36 ASP Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sd residue 16 GLN Chi-restraints excluded: chain Sd residue 30 LEU Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 108 VAL Chi-restraints excluded: chain Sg residue 129 ILE Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 240 CYS Chi-restraints excluded: chain SC residue 95 ASP Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SJ residue 37 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SM residue 108 CYS Chi-restraints excluded: chain SN residue 48 SER Chi-restraints excluded: chain SN residue 78 LYS Chi-restraints excluded: chain SN residue 105 ASN Chi-restraints excluded: chain SO residue 40 THR Chi-restraints excluded: chain SO residue 86 LYS Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 122 SER Chi-restraints excluded: chain SW residue 55 ASP Chi-restraints excluded: chain SW residue 106 THR Chi-restraints excluded: chain SY residue 15 ASN Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sf residue 115 SER Chi-restraints excluded: chain JC residue 224 CYS Chi-restraints excluded: chain JC residue 375 LEU Chi-restraints excluded: chain JC residue 399 ILE Chi-restraints excluded: chain JC residue 548 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 575 optimal weight: 3.9990 chunk 600 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 695 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 chunk 609 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN SA 113 GLN SB 95 ASN SB 118 GLN ** SE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 179 ASN SF 83 ASN SI 22 HIS SK 44 HIS ** SL 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 77 HIS ** SQ 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 114 GLN ** SS 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SU 92 HIS SV 33 GLN SX 97 ASN Sg 188 HIS SC 120 GLN SC 277 HIS SG 227 GLN ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SZ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 49 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051899 restraints weight = 321838.328| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.50 r_work: 0.2862 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 85509 Z= 0.264 Angle : 0.650 11.359 123696 Z= 0.333 Chirality : 0.040 0.375 15234 Planarity : 0.006 0.146 9311 Dihedral : 22.982 179.903 33114 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 3.27 % Allowed : 17.06 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 5385 helix: 0.10 (0.12), residues: 1724 sheet: -0.08 (0.17), residues: 986 loop : -0.93 (0.12), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPSM 88 HIS 0.008 0.001 HISSg 14 PHE 0.036 0.002 PHESV 83 TYR 0.050 0.002 TYRSd 34 ARG 0.012 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1012 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 77 PHE cc_start: 0.7987 (m-80) cc_final: 0.7694 (m-10) REVERT: SD 116 ARG cc_start: 0.8574 (tpp-160) cc_final: 0.8358 (mmm-85) REVERT: SD 206 ASP cc_start: 0.8898 (m-30) cc_final: 0.8520 (m-30) REVERT: SE 182 MET cc_start: 0.8883 (tmm) cc_final: 0.8088 (tmm) REVERT: SF 33 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8369 (tp) REVERT: SF 65 GLN cc_start: 0.8721 (mp10) cc_final: 0.8330 (mp10) REVERT: SF 70 GLU cc_start: 0.8175 (tp30) cc_final: 0.7938 (mm-30) REVERT: SF 77 MET cc_start: 0.7985 (mtm) cc_final: 0.7403 (mtm) REVERT: SF 102 LEU cc_start: 0.9031 (mt) cc_final: 0.8081 (tt) REVERT: SF 163 PHE cc_start: 0.8369 (t80) cc_final: 0.8089 (t80) REVERT: SF 176 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7002 (mm-30) REVERT: SF 195 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8785 (tp30) REVERT: SF 197 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8441 (pp20) REVERT: SH 32 MET cc_start: 0.7824 (mmm) cc_final: 0.7334 (mmm) REVERT: SH 44 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7153 (p0) REVERT: SI 111 GLN cc_start: 0.8798 (mt0) cc_final: 0.8531 (mt0) REVERT: SI 165 GLN cc_start: 0.8414 (mt0) cc_final: 0.8167 (mt0) REVERT: SI 167 GLN cc_start: 0.9086 (mt0) cc_final: 0.8837 (tt0) REVERT: SK 3 MET cc_start: 0.7587 (ptt) cc_final: 0.7146 (ptt) REVERT: SK 38 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8603 (mmtm) REVERT: SK 82 TYR cc_start: 0.7876 (t80) cc_final: 0.7411 (t80) REVERT: SL 11 GLN cc_start: 0.8976 (mp10) cc_final: 0.8343 (mp10) REVERT: SL 18 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8989 (mt0) REVERT: SL 121 GLN cc_start: 0.8272 (pm20) cc_final: 0.7784 (pm20) REVERT: SL 124 ASP cc_start: 0.8227 (m-30) cc_final: 0.8018 (m-30) REVERT: SP 35 GLN cc_start: 0.9027 (mm110) cc_final: 0.8371 (mm-40) REVERT: SP 83 MET cc_start: 0.8798 (tpp) cc_final: 0.8106 (tpp) REVERT: SP 109 PRO cc_start: 0.6717 (Cg_exo) cc_final: 0.6511 (Cg_endo) REVERT: SP 124 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8344 (pttm) REVERT: SQ 86 GLN cc_start: 0.9197 (tt0) cc_final: 0.8954 (tt0) REVERT: SR 18 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8396 (mm-30) REVERT: SR 24 LEU cc_start: 0.9211 (mt) cc_final: 0.8969 (mt) REVERT: SR 82 ASP cc_start: 0.8363 (t0) cc_final: 0.8052 (t0) REVERT: SS 54 LYS cc_start: 0.7576 (tttt) cc_final: 0.7115 (tttt) REVERT: SS 72 GLN cc_start: 0.8702 (mp10) cc_final: 0.8476 (mp10) REVERT: ST 10 ASN cc_start: 0.8497 (t0) cc_final: 0.8129 (t0) REVERT: ST 13 GLU cc_start: 0.8955 (mp0) cc_final: 0.7912 (mp0) REVERT: ST 45 LEU cc_start: 0.9064 (tp) cc_final: 0.8760 (tt) REVERT: SU 76 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9047 (p) REVERT: SV 28 ASP cc_start: 0.8488 (t0) cc_final: 0.8085 (t0) REVERT: SV 72 LEU cc_start: 0.9534 (mm) cc_final: 0.9250 (mp) REVERT: SX 99 GLU cc_start: 0.7914 (tp30) cc_final: 0.7709 (tp30) REVERT: SX 140 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7375 (ttm-80) REVERT: Sa 52 ASP cc_start: 0.8920 (t0) cc_final: 0.8580 (t0) REVERT: Sc 52 GLU cc_start: 0.8792 (pp20) cc_final: 0.8549 (pm20) REVERT: Sd 33 LYS cc_start: 0.8573 (tppt) cc_final: 0.8083 (tptt) REVERT: Sg 132 TRP cc_start: 0.7370 (m100) cc_final: 0.6901 (m100) REVERT: Sg 249 CYS cc_start: 0.7620 (m) cc_final: 0.7141 (p) REVERT: SC 248 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8427 (t80) REVERT: SG 24 LEU cc_start: 0.8777 (mt) cc_final: 0.8438 (mt) REVERT: SG 152 ASP cc_start: 0.7677 (t0) cc_final: 0.7185 (t0) REVERT: SJ 27 GLN cc_start: 0.8895 (tp40) cc_final: 0.8486 (tp-100) REVERT: SJ 107 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8781 (mm-30) REVERT: SM 12 MET cc_start: 0.3526 (tmm) cc_final: 0.2850 (ttt) REVERT: SN 78 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8219 (ttmt) REVERT: SN 113 PHE cc_start: 0.8703 (t80) cc_final: 0.8478 (t80) REVERT: SO 75 MET cc_start: 0.9106 (ppp) cc_final: 0.8892 (ppp) REVERT: SZ 58 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7617 (mt) REVERT: SZ 106 GLN cc_start: 0.8560 (tp40) cc_final: 0.8067 (tp40) REVERT: SZ 109 TYR cc_start: 0.7499 (m-80) cc_final: 0.7254 (m-80) REVERT: Sb 14 GLU cc_start: 0.8549 (mp0) cc_final: 0.7773 (mp0) REVERT: Sb 17 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8488 (ttp80) REVERT: Sb 34 ASP cc_start: 0.8381 (m-30) cc_final: 0.8170 (m-30) REVERT: Sf 132 MET cc_start: 0.6449 (mmm) cc_final: 0.5027 (mmm) REVERT: Sf 150 PHE cc_start: 0.6171 (t80) cc_final: 0.5797 (t80) REVERT: JC 168 PHE cc_start: 0.8145 (m-80) cc_final: 0.7726 (m-10) REVERT: JC 245 MET cc_start: 0.9109 (ttt) cc_final: 0.8857 (ttt) REVERT: JC 335 TYR cc_start: 0.8714 (m-10) cc_final: 0.8439 (m-10) REVERT: JC 356 LEU cc_start: 0.9331 (mt) cc_final: 0.8986 (pp) REVERT: JC 359 GLN cc_start: 0.8797 (pt0) cc_final: 0.8467 (pp30) REVERT: JC 442 LEU cc_start: 0.7531 (mt) cc_final: 0.7213 (mm) REVERT: JC 448 TYR cc_start: 0.7024 (m-10) cc_final: 0.6696 (m-80) REVERT: JC 469 LYS cc_start: 0.8511 (mttt) cc_final: 0.8290 (tttt) outliers start: 154 outliers final: 94 residues processed: 1104 average time/residue: 0.6865 time to fit residues: 1306.3990 Evaluate side-chains 1015 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 914 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SB residue 121 ILE Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 122 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SE residue 177 THR Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 33 ILE Chi-restraints excluded: chain SF residue 169 ILE Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 44 ASN Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SH residue 119 SER Chi-restraints excluded: chain SI residue 3 ILE Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SK residue 22 VAL Chi-restraints excluded: chain SK residue 37 ASP Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 63 THR Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 62 LYS Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 94 VAL Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 68 ILE Chi-restraints excluded: chain SQ residue 119 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 55 THR Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 120 THR Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SR residue 130 THR Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain SU residue 29 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 76 THR Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 67 ASP Chi-restraints excluded: chain SX residue 58 GLU Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 32 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 108 VAL Chi-restraints excluded: chain Sg residue 197 THR Chi-restraints excluded: chain Sg residue 235 ILE Chi-restraints excluded: chain Sg residue 240 CYS Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SJ residue 12 THR Chi-restraints excluded: chain SJ residue 37 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SJ residue 141 VAL Chi-restraints excluded: chain SM residue 108 CYS Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 60 VAL Chi-restraints excluded: chain SN residue 78 LYS Chi-restraints excluded: chain SN residue 105 ASN Chi-restraints excluded: chain SO residue 40 THR Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 122 SER Chi-restraints excluded: chain SY residue 15 ASN Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 48 VAL Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain Sb residue 5 LYS Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain Sf residue 115 SER Chi-restraints excluded: chain JD residue 598 LEU Chi-restraints excluded: chain JD residue 612 ASP Chi-restraints excluded: chain JC residue 224 CYS Chi-restraints excluded: chain JC residue 464 ILE Chi-restraints excluded: chain JC residue 561 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 179 optimal weight: 5.9990 chunk 412 optimal weight: 5.9990 chunk 473 optimal weight: 5.9990 chunk 552 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 522 optimal weight: 0.7980 chunk 301 optimal weight: 0.7980 chunk 694 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 493 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN ** SL 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SQ 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 114 GLN ** SS 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 105 ASN ST 63 HIS ST 128 GLN SV 33 GLN SX 97 ASN SN 13 GLN ** SW 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.070653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051492 restraints weight = 322122.813| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.48 r_work: 0.2854 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 85509 Z= 0.239 Angle : 0.624 11.653 123696 Z= 0.319 Chirality : 0.039 0.391 15234 Planarity : 0.005 0.139 9311 Dihedral : 22.965 179.336 33112 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 3.55 % Allowed : 18.99 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.47 (0.11), residues: 5385 helix: 0.47 (0.12), residues: 1717 sheet: -0.05 (0.17), residues: 990 loop : -0.89 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPSM 88 HIS 0.007 0.001 HISSP 54 PHE 0.031 0.002 PHESV 83 TYR 0.026 0.002 TYRSd 34 ARG 0.014 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 975 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SD 31 GLU cc_start: 0.7426 (pm20) cc_final: 0.7097 (pm20) REVERT: SD 77 PHE cc_start: 0.7876 (m-80) cc_final: 0.7623 (m-80) REVERT: SD 116 ARG cc_start: 0.8607 (tpp-160) cc_final: 0.8391 (mmm-85) REVERT: SD 206 ASP cc_start: 0.8885 (m-30) cc_final: 0.8498 (m-30) REVERT: SE 182 MET cc_start: 0.8907 (tmm) cc_final: 0.8107 (tmm) REVERT: SF 70 GLU cc_start: 0.8179 (tp30) cc_final: 0.7755 (tp30) REVERT: SF 77 MET cc_start: 0.8103 (mtm) cc_final: 0.7634 (mtm) REVERT: SF 78 MET cc_start: 0.8415 (mmt) cc_final: 0.8123 (mmt) REVERT: SF 102 LEU cc_start: 0.8910 (mt) cc_final: 0.8222 (tt) REVERT: SF 175 ASP cc_start: 0.8065 (p0) cc_final: 0.7241 (p0) REVERT: SF 176 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7070 (mm-30) REVERT: SF 195 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8713 (tp30) REVERT: SH 32 MET cc_start: 0.7942 (mmm) cc_final: 0.7371 (mmm) REVERT: SI 111 GLN cc_start: 0.8775 (mt0) cc_final: 0.8546 (mt0) REVERT: SI 167 GLN cc_start: 0.9122 (mt0) cc_final: 0.8806 (tt0) REVERT: SK 3 MET cc_start: 0.7470 (ptt) cc_final: 0.7038 (ptt) REVERT: SK 18 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8600 (mm-30) REVERT: SK 31 LYS cc_start: 0.8482 (tppp) cc_final: 0.8162 (tppp) REVERT: SK 38 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8600 (mmtm) REVERT: SK 50 GLN cc_start: 0.8751 (tt0) cc_final: 0.8321 (tm-30) REVERT: SK 59 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7718 (ptpp) REVERT: SK 82 TYR cc_start: 0.7929 (t80) cc_final: 0.7482 (t80) REVERT: SL 11 GLN cc_start: 0.9046 (mp10) cc_final: 0.8383 (mp10) REVERT: SL 121 GLN cc_start: 0.8113 (pm20) cc_final: 0.7824 (pm20) REVERT: SL 124 ASP cc_start: 0.8397 (m-30) cc_final: 0.8123 (m-30) REVERT: SP 35 GLN cc_start: 0.9074 (mm110) cc_final: 0.8324 (mm-40) REVERT: SP 109 PRO cc_start: 0.6883 (Cg_exo) cc_final: 0.6667 (Cg_endo) REVERT: SP 118 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7827 (tp30) REVERT: SP 124 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8354 (pttm) REVERT: SQ 67 ASP cc_start: 0.8032 (m-30) cc_final: 0.7757 (t0) REVERT: SR 82 ASP cc_start: 0.8411 (t0) cc_final: 0.8068 (t0) REVERT: SS 54 LYS cc_start: 0.7465 (tttt) cc_final: 0.7182 (tttt) REVERT: SS 70 ILE cc_start: 0.8073 (mm) cc_final: 0.7838 (mm) REVERT: SS 109 GLU cc_start: 0.8608 (tp30) cc_final: 0.8377 (tp30) REVERT: ST 13 GLU cc_start: 0.8965 (mp0) cc_final: 0.8652 (mp0) REVERT: ST 41 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8452 (tttt) REVERT: ST 45 LEU cc_start: 0.9095 (tp) cc_final: 0.8822 (tt) REVERT: ST 128 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8798 (pp30) REVERT: SU 78 ASP cc_start: 0.8270 (t0) cc_final: 0.7815 (t0) REVERT: SV 28 ASP cc_start: 0.8448 (t0) cc_final: 0.8012 (t0) REVERT: SV 72 LEU cc_start: 0.9502 (mm) cc_final: 0.8960 (mp) REVERT: SX 95 GLU cc_start: 0.8962 (pm20) cc_final: 0.8157 (pm20) REVERT: SX 140 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6689 (ttm-80) REVERT: Sa 52 ASP cc_start: 0.8853 (t0) cc_final: 0.8615 (t0) REVERT: Sc 36 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6776 (p0) REVERT: Sc 52 GLU cc_start: 0.8810 (pp20) cc_final: 0.8546 (pm20) REVERT: Sc 66 ARG cc_start: 0.6465 (pmt-80) cc_final: 0.5950 (tmm160) REVERT: Sd 33 LYS cc_start: 0.8578 (tppt) cc_final: 0.7725 (tttt) REVERT: Sd 45 GLN cc_start: 0.8633 (tt0) cc_final: 0.8410 (tt0) REVERT: Sg 132 TRP cc_start: 0.7383 (m100) cc_final: 0.6997 (m100) REVERT: Sg 249 CYS cc_start: 0.7828 (m) cc_final: 0.7181 (p) REVERT: SC 61 MET cc_start: 0.8989 (mmm) cc_final: 0.8671 (mmm) REVERT: SC 248 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8457 (t80) REVERT: SC 267 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8879 (tm-30) REVERT: SG 24 LEU cc_start: 0.8846 (mt) cc_final: 0.8550 (mt) REVERT: SG 152 ASP cc_start: 0.7782 (t0) cc_final: 0.7354 (t0) REVERT: SJ 27 GLN cc_start: 0.8931 (tp40) cc_final: 0.8466 (tp-100) REVERT: SM 12 MET cc_start: 0.3472 (tmm) cc_final: 0.2753 (ttt) REVERT: SM 35 ILE cc_start: 0.8090 (mp) cc_final: 0.7838 (tp) REVERT: SM 112 LYS cc_start: 0.8327 (pttm) cc_final: 0.7493 (mmmm) REVERT: SN 78 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8293 (ttmt) REVERT: SN 105 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7820 (p0) REVERT: SN 113 PHE cc_start: 0.8645 (t80) cc_final: 0.8423 (t80) REVERT: SO 75 MET cc_start: 0.9110 (ppp) cc_final: 0.8877 (ppp) REVERT: SO 86 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8538 (ptpp) REVERT: SZ 78 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8031 (tptt) REVERT: SZ 90 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8060 (pp20) REVERT: SZ 106 GLN cc_start: 0.8404 (tp40) cc_final: 0.8000 (mm110) REVERT: Sb 14 GLU cc_start: 0.8512 (mp0) cc_final: 0.7877 (mp0) REVERT: Sb 34 ASP cc_start: 0.8454 (m-30) cc_final: 0.8235 (m-30) REVERT: Sb 45 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8452 (m) REVERT: Sf 105 TYR cc_start: 0.3214 (OUTLIER) cc_final: 0.2735 (t80) REVERT: Sf 132 MET cc_start: 0.6431 (mmm) cc_final: 0.5375 (mmm) REVERT: Sf 150 PHE cc_start: 0.6378 (t80) cc_final: 0.5900 (t80) REVERT: JC 56 GLU cc_start: 0.8355 (tp30) cc_final: 0.8063 (tp30) REVERT: JC 165 LEU cc_start: 0.8880 (tp) cc_final: 0.8588 (mm) REVERT: JC 245 MET cc_start: 0.9161 (ttt) cc_final: 0.8911 (ttt) REVERT: JC 313 HIS cc_start: 0.7732 (m90) cc_final: 0.7425 (t-90) REVERT: JC 344 MET cc_start: 0.6680 (tpt) cc_final: 0.6244 (tpt) REVERT: JC 356 LEU cc_start: 0.9314 (mt) cc_final: 0.8983 (pp) REVERT: JC 359 GLN cc_start: 0.8828 (pt0) cc_final: 0.8616 (pp30) REVERT: JC 448 TYR cc_start: 0.7046 (m-10) cc_final: 0.6727 (m-80) REVERT: JC 469 LYS cc_start: 0.8502 (mttt) cc_final: 0.8281 (tttt) outliers start: 167 outliers final: 100 residues processed: 1077 average time/residue: 0.6584 time to fit residues: 1225.8129 Evaluate side-chains 1000 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 891 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 131 HIS Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SD residue 154 ASP Chi-restraints excluded: chain SD residue 221 THR Chi-restraints excluded: chain SE residue 177 THR Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 126 THR Chi-restraints excluded: chain SF residue 169 ILE Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SH residue 119 SER Chi-restraints excluded: chain SH residue 149 ASP Chi-restraints excluded: chain SI residue 3 ILE Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 97 VAL Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SK residue 37 ASP Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 63 THR Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 124 LYS Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 119 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 55 THR Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 63 HIS Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain ST residue 128 GLN Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 29 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SU residue 48 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 64 THR Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 67 ASP Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 36 ASP Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 108 VAL Chi-restraints excluded: chain Sg residue 122 SER Chi-restraints excluded: chain Sg residue 129 ILE Chi-restraints excluded: chain Sg residue 137 VAL Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 235 ILE Chi-restraints excluded: chain Sg residue 240 CYS Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SJ residue 12 THR Chi-restraints excluded: chain SJ residue 37 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 60 VAL Chi-restraints excluded: chain SN residue 78 LYS Chi-restraints excluded: chain SN residue 105 ASN Chi-restraints excluded: chain SO residue 40 THR Chi-restraints excluded: chain SO residue 86 LYS Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 122 SER Chi-restraints excluded: chain SW residue 55 ASP Chi-restraints excluded: chain SW residue 69 LEU Chi-restraints excluded: chain SY residue 15 ASN Chi-restraints excluded: chain SY residue 77 ASP Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 65 TYR Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain Sf residue 115 SER Chi-restraints excluded: chain JC residue 224 CYS Chi-restraints excluded: chain JC residue 402 LEU Chi-restraints excluded: chain JC residue 464 ILE Chi-restraints excluded: chain JC residue 479 LEU Chi-restraints excluded: chain JC residue 561 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 242 optimal weight: 6.9990 chunk 471 optimal weight: 20.0000 chunk 518 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 659 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 375 optimal weight: 4.9990 chunk 590 optimal weight: 9.9990 chunk 416 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN SD 101 GLN SD 174 HIS ** SE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SF 107 ASN ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 154 GLN SP 46 ASN SQ 48 GLN SQ 114 GLN ST 42 HIS ST 51 ASN ST 63 HIS ST 128 GLN SV 33 GLN SX 97 ASN ** SC 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 92 ASN ** SW 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 15 ASN SY 63 HIS ** JC 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.067885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.048982 restraints weight = 325969.480| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.41 r_work: 0.2787 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 85509 Z= 0.403 Angle : 0.721 11.536 123696 Z= 0.367 Chirality : 0.043 0.396 15234 Planarity : 0.006 0.142 9311 Dihedral : 23.007 177.790 33112 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 4.33 % Allowed : 20.08 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 5385 helix: 0.38 (0.12), residues: 1727 sheet: -0.19 (0.16), residues: 1015 loop : -1.02 (0.12), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPSB 30 HIS 0.041 0.002 HISST 63 PHE 0.035 0.002 PHESH 135 TYR 0.031 0.002 TYRSK 78 ARG 0.017 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 894 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 7 LYS cc_start: 0.8589 (tttt) cc_final: 0.8275 (tttt) REVERT: SB 59 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.8921 (t) REVERT: SB 183 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8544 (tm-30) REVERT: SD 31 GLU cc_start: 0.7635 (pm20) cc_final: 0.7282 (pm20) REVERT: SD 116 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8427 (mmm-85) REVERT: SD 206 ASP cc_start: 0.8923 (m-30) cc_final: 0.8588 (m-30) REVERT: SE 182 MET cc_start: 0.8918 (tmm) cc_final: 0.8287 (tmm) REVERT: SF 70 GLU cc_start: 0.8155 (tp30) cc_final: 0.7725 (tp30) REVERT: SF 77 MET cc_start: 0.8192 (mtm) cc_final: 0.7771 (mtm) REVERT: SF 102 LEU cc_start: 0.8594 (mt) cc_final: 0.7959 (tp) REVERT: SF 107 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7296 (t0) REVERT: SF 195 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8783 (tp30) REVERT: SH 32 MET cc_start: 0.8067 (mmm) cc_final: 0.7470 (mmm) REVERT: SI 111 GLN cc_start: 0.8831 (mt0) cc_final: 0.8593 (mt0) REVERT: SI 167 GLN cc_start: 0.9215 (mt0) cc_final: 0.8815 (tt0) REVERT: SK 3 MET cc_start: 0.7855 (ptt) cc_final: 0.7358 (ptt) REVERT: SK 31 LYS cc_start: 0.8605 (tppp) cc_final: 0.8199 (tppp) REVERT: SK 50 GLN cc_start: 0.8697 (tt0) cc_final: 0.8236 (tm-30) REVERT: SK 82 TYR cc_start: 0.7952 (t80) cc_final: 0.7515 (t80) REVERT: SL 124 ASP cc_start: 0.8393 (m-30) cc_final: 0.8104 (m-30) REVERT: SP 35 GLN cc_start: 0.9088 (mm110) cc_final: 0.8633 (mm-40) REVERT: SP 37 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.5388 (m-80) REVERT: SP 109 PRO cc_start: 0.7301 (Cg_exo) cc_final: 0.7021 (Cg_endo) REVERT: SQ 48 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8520 (tp-100) REVERT: SQ 86 GLN cc_start: 0.9217 (tt0) cc_final: 0.9003 (tt0) REVERT: SQ 102 GLU cc_start: 0.8600 (mp0) cc_final: 0.8388 (mp0) REVERT: SQ 129 SER cc_start: 0.9216 (m) cc_final: 0.9005 (m) REVERT: SR 1 MET cc_start: 0.5608 (mtt) cc_final: 0.5387 (mmm) REVERT: SR 82 ASP cc_start: 0.8430 (t0) cc_final: 0.8161 (t0) REVERT: SS 54 LYS cc_start: 0.7438 (tttt) cc_final: 0.7093 (tttt) REVERT: ST 13 GLU cc_start: 0.8928 (mp0) cc_final: 0.8624 (mp0) REVERT: ST 45 LEU cc_start: 0.9156 (tp) cc_final: 0.8858 (tt) REVERT: ST 128 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8671 (pp30) REVERT: SU 78 ASP cc_start: 0.8290 (t0) cc_final: 0.7859 (t0) REVERT: SU 107 GLU cc_start: 0.7796 (tp30) cc_final: 0.7396 (tp30) REVERT: SV 28 ASP cc_start: 0.8478 (t0) cc_final: 0.7989 (t0) REVERT: SX 61 GLN cc_start: 0.8499 (tp-100) cc_final: 0.8275 (tp-100) REVERT: Sa 52 ASP cc_start: 0.8757 (t0) cc_final: 0.8538 (t0) REVERT: Sa 68 TYR cc_start: 0.8709 (m-80) cc_final: 0.8318 (m-80) REVERT: Sc 58 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7465 (mm) REVERT: Sc 66 ARG cc_start: 0.6206 (pmt-80) cc_final: 0.5876 (pmt-80) REVERT: Sd 33 LYS cc_start: 0.8851 (tppt) cc_final: 0.8588 (tttm) REVERT: Sd 45 GLN cc_start: 0.8342 (tt0) cc_final: 0.8124 (tt0) REVERT: Sd 49 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8441 (p0) REVERT: Sg 49 GLU cc_start: 0.8420 (pm20) cc_final: 0.8061 (pm20) REVERT: Sg 132 TRP cc_start: 0.7433 (m100) cc_final: 0.6785 (m100) REVERT: Sg 154 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7909 (t) REVERT: SC 248 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8405 (t80) REVERT: SG 24 LEU cc_start: 0.8860 (mt) cc_final: 0.8573 (mt) REVERT: SG 124 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8818 (tp) REVERT: SJ 27 GLN cc_start: 0.8958 (tp40) cc_final: 0.8473 (tp-100) REVERT: SM 12 MET cc_start: 0.3645 (tmm) cc_final: 0.2945 (ttt) REVERT: SM 35 ILE cc_start: 0.8141 (mp) cc_final: 0.7896 (tp) REVERT: SM 60 MET cc_start: 0.5274 (tmm) cc_final: 0.4578 (tmm) REVERT: SN 78 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: SN 113 PHE cc_start: 0.9045 (t80) cc_final: 0.8842 (t80) REVERT: SO 75 MET cc_start: 0.9176 (ppp) cc_final: 0.8928 (ppp) REVERT: SW 97 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8150 (mtm-85) REVERT: SY 85 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (p0) REVERT: SZ 104 ARG cc_start: 0.7083 (mmm160) cc_final: 0.6672 (ttm110) REVERT: SZ 106 GLN cc_start: 0.8474 (tp40) cc_final: 0.8109 (tp40) REVERT: Sb 14 GLU cc_start: 0.8482 (mp0) cc_final: 0.7991 (mp0) REVERT: Sb 17 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8489 (ttp80) REVERT: Sb 34 ASP cc_start: 0.8446 (m-30) cc_final: 0.8209 (m-30) REVERT: Sf 132 MET cc_start: 0.6749 (mmm) cc_final: 0.5640 (mmm) REVERT: Sf 150 PHE cc_start: 0.6359 (t80) cc_final: 0.5902 (t80) REVERT: JC 47 PHE cc_start: 0.5088 (m-10) cc_final: 0.4877 (m-10) REVERT: JC 56 GLU cc_start: 0.8271 (tp30) cc_final: 0.7924 (tp30) REVERT: JC 313 HIS cc_start: 0.7395 (m90) cc_final: 0.7033 (t-90) REVERT: JC 359 GLN cc_start: 0.8955 (pt0) cc_final: 0.8544 (pp30) REVERT: JC 442 LEU cc_start: 0.7492 (mt) cc_final: 0.6780 (mt) REVERT: JC 445 ASN cc_start: 0.6226 (m110) cc_final: 0.5797 (t0) REVERT: JC 448 TYR cc_start: 0.6888 (m-10) cc_final: 0.5925 (m-80) REVERT: JC 469 LYS cc_start: 0.8529 (mttt) cc_final: 0.8282 (tttt) outliers start: 204 outliers final: 137 residues processed: 1029 average time/residue: 0.6379 time to fit residues: 1138.8433 Evaluate side-chains 985 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 835 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 79 SER Chi-restraints excluded: chain SA residue 131 HIS Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SB residue 59 SER Chi-restraints excluded: chain SB residue 114 VAL Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 97 CYS Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SD residue 221 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 177 THR Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 72 LEU Chi-restraints excluded: chain SF residue 107 ASN Chi-restraints excluded: chain SF residue 126 THR Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SH residue 119 SER Chi-restraints excluded: chain SH residue 149 ASP Chi-restraints excluded: chain SI residue 3 ILE Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SK residue 37 ASP Chi-restraints excluded: chain SK residue 49 MET Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 57 ASP Chi-restraints excluded: chain SL residue 63 THR Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 16 THR Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 107 ILE Chi-restraints excluded: chain SQ residue 20 THR Chi-restraints excluded: chain SQ residue 48 GLN Chi-restraints excluded: chain SQ residue 119 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 55 THR Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 123 THR Chi-restraints excluded: chain SR residue 130 THR Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 5 ILE Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 87 VAL Chi-restraints excluded: chain ST residue 99 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain ST residue 128 GLN Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SU residue 48 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 60 THR Chi-restraints excluded: chain SU residue 64 THR Chi-restraints excluded: chain SU residue 65 THR Chi-restraints excluded: chain SU residue 105 SER Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 41 LYS Chi-restraints excluded: chain SV residue 78 ILE Chi-restraints excluded: chain SV residue 83 PHE Chi-restraints excluded: chain SX residue 128 VAL Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 58 VAL Chi-restraints excluded: chain Sa residue 60 ASP Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 17 VAL Chi-restraints excluded: chain Sc residue 30 VAL Chi-restraints excluded: chain Sc residue 32 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sd residue 6 LEU Chi-restraints excluded: chain Sd residue 8 TRP Chi-restraints excluded: chain Sd residue 49 ASP Chi-restraints excluded: chain Sg residue 66 VAL Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 108 VAL Chi-restraints excluded: chain Sg residue 122 SER Chi-restraints excluded: chain Sg residue 129 ILE Chi-restraints excluded: chain Sg residue 137 VAL Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 154 VAL Chi-restraints excluded: chain Sg residue 176 VAL Chi-restraints excluded: chain Sg residue 266 ILE Chi-restraints excluded: chain Sg residue 273 GLU Chi-restraints excluded: chain SC residue 95 ASP Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 16 ILE Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 124 LEU Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SJ residue 12 THR Chi-restraints excluded: chain SJ residue 37 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SJ residue 141 VAL Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SM residue 111 VAL Chi-restraints excluded: chain SN residue 4 MET Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 60 VAL Chi-restraints excluded: chain SN residue 78 LYS Chi-restraints excluded: chain SN residue 144 SER Chi-restraints excluded: chain SO residue 47 LEU Chi-restraints excluded: chain SO residue 56 VAL Chi-restraints excluded: chain SO residue 57 THR Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 122 SER Chi-restraints excluded: chain SW residue 55 ASP Chi-restraints excluded: chain SW residue 69 LEU Chi-restraints excluded: chain SW residue 97 ARG Chi-restraints excluded: chain SY residue 77 ASP Chi-restraints excluded: chain SY residue 85 ASN Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain Sb residue 5 LYS Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 52 THR Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Sf residue 115 SER Chi-restraints excluded: chain JD residue 588 HIS Chi-restraints excluded: chain JC residue 224 CYS Chi-restraints excluded: chain JC residue 246 VAL Chi-restraints excluded: chain JC residue 402 LEU Chi-restraints excluded: chain JC residue 464 ILE Chi-restraints excluded: chain JC residue 561 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 392 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 627 optimal weight: 0.9980 chunk 165 optimal weight: 30.0000 chunk 205 optimal weight: 2.9990 chunk 588 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 686 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 39 ASN ** SK 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 48 GLN SQ 114 GLN ST 128 GLN SX 97 ASN ** SG 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 92 ASN ** SW 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 15 ASN Se 15 GLN Sf 91 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050567 restraints weight = 320953.942| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.43 r_work: 0.2829 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 85509 Z= 0.206 Angle : 0.624 12.516 123696 Z= 0.318 Chirality : 0.038 0.393 15234 Planarity : 0.005 0.136 9311 Dihedral : 23.005 179.221 33112 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 3.46 % Allowed : 21.73 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.45 (0.11), residues: 5385 helix: 0.56 (0.12), residues: 1735 sheet: -0.05 (0.17), residues: 987 loop : -0.93 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPSS 82 HIS 0.011 0.001 HISSg 14 PHE 0.030 0.002 PHESH 135 TYR 0.023 0.002 TYRSA 156 ARG 0.014 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 937 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 7 LYS cc_start: 0.8518 (tttt) cc_final: 0.8232 (tttt) REVERT: SB 59 SER cc_start: 0.9258 (p) cc_final: 0.8849 (t) REVERT: SB 92 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7761 (mm110) REVERT: SB 183 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8456 (tm-30) REVERT: SD 31 GLU cc_start: 0.7572 (pm20) cc_final: 0.7235 (pm20) REVERT: SD 116 ARG cc_start: 0.8611 (tpp-160) cc_final: 0.8362 (mmm-85) REVERT: SD 206 ASP cc_start: 0.8860 (m-30) cc_final: 0.8462 (m-30) REVERT: SF 70 GLU cc_start: 0.8077 (tp30) cc_final: 0.7600 (tp30) REVERT: SF 77 MET cc_start: 0.8075 (mtm) cc_final: 0.7483 (mtm) REVERT: SF 102 LEU cc_start: 0.8603 (mt) cc_final: 0.7965 (tp) REVERT: SF 175 ASP cc_start: 0.8166 (p0) cc_final: 0.7049 (p0) REVERT: SF 176 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7221 (mm-30) REVERT: SF 195 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8802 (tp30) REVERT: SH 32 MET cc_start: 0.8108 (mmm) cc_final: 0.7555 (mmm) REVERT: SI 111 GLN cc_start: 0.8808 (mt0) cc_final: 0.8551 (mt0) REVERT: SI 167 GLN cc_start: 0.9285 (mt0) cc_final: 0.9070 (mm110) REVERT: SK 3 MET cc_start: 0.7695 (ptt) cc_final: 0.7186 (ptt) REVERT: SK 16 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: SK 21 MET cc_start: 0.6647 (pmm) cc_final: 0.5980 (ptp) REVERT: SK 50 GLN cc_start: 0.8686 (tt0) cc_final: 0.8277 (tm-30) REVERT: SK 59 LYS cc_start: 0.8098 (ptpp) cc_final: 0.7867 (ptpp) REVERT: SK 70 TYR cc_start: 0.8044 (m-80) cc_final: 0.7623 (m-80) REVERT: SK 82 TYR cc_start: 0.7949 (t80) cc_final: 0.7527 (t80) REVERT: SL 124 ASP cc_start: 0.8378 (m-30) cc_final: 0.8093 (m-30) REVERT: SP 35 GLN cc_start: 0.9105 (mm110) cc_final: 0.8664 (mm-40) REVERT: SP 37 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.5429 (m-80) REVERT: SP 109 PRO cc_start: 0.7292 (Cg_exo) cc_final: 0.7083 (Cg_endo) REVERT: SP 118 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7985 (tp30) REVERT: SQ 67 ASP cc_start: 0.8060 (m-30) cc_final: 0.7814 (t70) REVERT: SQ 129 SER cc_start: 0.9179 (m) cc_final: 0.8842 (p) REVERT: SR 82 ASP cc_start: 0.8398 (t0) cc_final: 0.8125 (t0) REVERT: SS 9 PHE cc_start: 0.7074 (t80) cc_final: 0.6824 (t80) REVERT: SS 54 LYS cc_start: 0.7449 (tttt) cc_final: 0.7091 (tttt) REVERT: ST 13 GLU cc_start: 0.8962 (mp0) cc_final: 0.8623 (mp0) REVERT: ST 41 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8559 (tttt) REVERT: ST 45 LEU cc_start: 0.9134 (tp) cc_final: 0.8895 (tt) REVERT: ST 67 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: SU 78 ASP cc_start: 0.8271 (t0) cc_final: 0.7840 (t0) REVERT: SV 28 ASP cc_start: 0.8437 (t0) cc_final: 0.7987 (t0) REVERT: SX 61 GLN cc_start: 0.8437 (tp-100) cc_final: 0.8235 (tp-100) REVERT: SX 95 GLU cc_start: 0.8912 (pm20) cc_final: 0.8659 (pm20) REVERT: Sa 52 ASP cc_start: 0.8664 (t0) cc_final: 0.8400 (t0) REVERT: Sc 13 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7920 (ttm-80) REVERT: Sc 56 LEU cc_start: 0.9074 (mp) cc_final: 0.8588 (tp) REVERT: Sc 58 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7486 (mm) REVERT: Sc 66 ARG cc_start: 0.6106 (pmt-80) cc_final: 0.5767 (pmt-80) REVERT: Sd 33 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8471 (tttm) REVERT: Sd 45 GLN cc_start: 0.8279 (tt0) cc_final: 0.8072 (tt0) REVERT: Sg 49 GLU cc_start: 0.8466 (pm20) cc_final: 0.8125 (pm20) REVERT: Sg 132 TRP cc_start: 0.7364 (m100) cc_final: 0.6890 (m100) REVERT: Sg 154 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (t) REVERT: SC 248 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8453 (t80) REVERT: SC 267 GLN cc_start: 0.9232 (tm-30) cc_final: 0.9023 (tm-30) REVERT: SG 126 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.8774 (p0) REVERT: SG 152 ASP cc_start: 0.7833 (t0) cc_final: 0.7605 (t0) REVERT: SJ 27 GLN cc_start: 0.8924 (tp40) cc_final: 0.8396 (tp-100) REVERT: SJ 73 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8452 (mt-10) REVERT: SM 12 MET cc_start: 0.3672 (tmm) cc_final: 0.2946 (ttt) REVERT: SM 35 ILE cc_start: 0.8051 (mp) cc_final: 0.7845 (tp) REVERT: SM 45 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6878 (ptt-90) REVERT: SM 112 LYS cc_start: 0.8450 (pttm) cc_final: 0.7584 (mmmt) REVERT: SN 78 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8305 (ttmt) REVERT: SN 86 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6853 (tm-30) REVERT: SN 90 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8506 (m-70) REVERT: SN 113 PHE cc_start: 0.8734 (t80) cc_final: 0.8528 (t80) REVERT: SO 75 MET cc_start: 0.9144 (ppp) cc_final: 0.8916 (ppp) REVERT: SO 83 GLN cc_start: 0.9056 (pp30) cc_final: 0.8797 (pp30) REVERT: SO 96 LYS cc_start: 0.8592 (mttt) cc_final: 0.8369 (mmtp) REVERT: SO 146 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9158 (ttm-80) REVERT: SW 55 ASP cc_start: 0.9040 (p0) cc_final: 0.8800 (p0) REVERT: SW 97 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8087 (mtm-85) REVERT: SY 74 MET cc_start: 0.8633 (mmm) cc_final: 0.8027 (mtt) REVERT: SZ 52 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8449 (tppt) REVERT: SZ 77 LEU cc_start: 0.8354 (mm) cc_final: 0.8145 (mp) REVERT: SZ 104 ARG cc_start: 0.6822 (mmm160) cc_final: 0.6618 (ttm110) REVERT: SZ 106 GLN cc_start: 0.8487 (tp40) cc_final: 0.8154 (mm110) REVERT: Sb 14 GLU cc_start: 0.8593 (mp0) cc_final: 0.8115 (mp0) REVERT: Sb 17 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8441 (ttp80) REVERT: Sb 34 ASP cc_start: 0.8437 (m-30) cc_final: 0.8178 (m-30) REVERT: Sf 105 TYR cc_start: 0.3448 (OUTLIER) cc_final: 0.2398 (t80) REVERT: Sf 114 ILE cc_start: 0.6931 (mm) cc_final: 0.6596 (mp) REVERT: Sf 150 PHE cc_start: 0.6532 (t80) cc_final: 0.6069 (t80) REVERT: JC 56 GLU cc_start: 0.8326 (tp30) cc_final: 0.8031 (tp30) REVERT: JC 165 LEU cc_start: 0.8892 (tp) cc_final: 0.8600 (mm) REVERT: JC 245 MET cc_start: 0.9215 (ttt) cc_final: 0.8904 (ttt) REVERT: JC 313 HIS cc_start: 0.7384 (m90) cc_final: 0.7014 (t-90) REVERT: JC 359 GLN cc_start: 0.8913 (pt0) cc_final: 0.8454 (pp30) REVERT: JC 445 ASN cc_start: 0.6115 (m110) cc_final: 0.5777 (t0) REVERT: JC 448 TYR cc_start: 0.6838 (m-10) cc_final: 0.5871 (m-80) REVERT: JC 469 LYS cc_start: 0.8451 (mttt) cc_final: 0.8210 (tttt) outliers start: 163 outliers final: 99 residues processed: 1040 average time/residue: 0.6275 time to fit residues: 1127.3665 Evaluate side-chains 995 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 882 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 75 SER Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SB residue 161 VAL Chi-restraints excluded: chain SB residue 224 GLU Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SD residue 221 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 126 THR Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 37 ASP Chi-restraints excluded: chain SK residue 39 ASN Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SK residue 89 ILE Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 63 THR Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 107 ILE Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 119 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 22 THR Chi-restraints excluded: chain SR residue 55 THR Chi-restraints excluded: chain SR residue 71 ILE Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 111 PHE Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 67 ARG Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain SU residue 20 ILE Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SU residue 48 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 60 THR Chi-restraints excluded: chain SU residue 105 SER Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 83 PHE Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sd residue 6 LEU Chi-restraints excluded: chain Sd residue 8 TRP Chi-restraints excluded: chain Sd residue 33 LYS Chi-restraints excluded: chain Sg residue 96 THR Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 154 VAL Chi-restraints excluded: chain Sg residue 176 VAL Chi-restraints excluded: chain Sg residue 273 GLU Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SJ residue 37 LEU Chi-restraints excluded: chain SJ residue 62 THR Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SM residue 45 ARG Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SM residue 108 CYS Chi-restraints excluded: chain SM residue 111 VAL Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 78 LYS Chi-restraints excluded: chain SN residue 90 HIS Chi-restraints excluded: chain SN residue 144 SER Chi-restraints excluded: chain SO residue 47 LEU Chi-restraints excluded: chain SO residue 56 VAL Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 146 ARG Chi-restraints excluded: chain SW residue 97 ARG Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 77 ASP Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 5 LYS Chi-restraints excluded: chain Sb residue 8 LEU Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 62 VAL Chi-restraints excluded: chain Sf residue 91 ASN Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JC residue 224 CYS Chi-restraints excluded: chain JC residue 356 LEU Chi-restraints excluded: chain JC residue 402 LEU Chi-restraints excluded: chain JC residue 464 ILE Chi-restraints excluded: chain JC residue 479 LEU Chi-restraints excluded: chain JC residue 561 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 661 optimal weight: 0.9980 chunk 431 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 423 optimal weight: 0.0020 chunk 473 optimal weight: 7.9990 chunk 539 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 446 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 513 optimal weight: 3.9990 chunk 444 optimal weight: 0.3980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN ** SA 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 GLN SH 44 ASN ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 168 GLN SK 42 ASN ** SP 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 48 GLN SQ 86 GLN ** SS 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SX 97 ASN ** SG 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SM 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 101 HIS SW 92 ASN SW 98 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052439 restraints weight = 322196.351| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.47 r_work: 0.2885 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 85509 Z= 0.156 Angle : 0.607 11.881 123696 Z= 0.308 Chirality : 0.037 0.418 15234 Planarity : 0.005 0.135 9311 Dihedral : 22.935 179.083 33112 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 2.72 % Allowed : 22.54 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 5385 helix: 0.71 (0.13), residues: 1732 sheet: 0.01 (0.17), residues: 975 loop : -0.81 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPSS 82 HIS 0.009 0.001 HISSP 54 PHE 0.018 0.002 PHESV 83 TYR 0.022 0.002 TYRSK 78 ARG 0.013 0.000 ARGSe 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 961 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 1 MET cc_start: 0.8114 (ttt) cc_final: 0.7803 (ttt) REVERT: Ln 7 LYS cc_start: 0.8420 (tttt) cc_final: 0.8087 (ttpt) REVERT: SA 18 PHE cc_start: 0.9094 (m-80) cc_final: 0.8864 (m-10) REVERT: SB 90 ASP cc_start: 0.8369 (t0) cc_final: 0.7658 (t0) REVERT: SB 92 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7422 (mm110) REVERT: SB 183 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8419 (tm-30) REVERT: SD 31 GLU cc_start: 0.7427 (pm20) cc_final: 0.7142 (pm20) REVERT: SD 116 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8322 (mmm-85) REVERT: SD 169 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: SD 206 ASP cc_start: 0.8938 (m-30) cc_final: 0.8493 (m-30) REVERT: SF 70 GLU cc_start: 0.8033 (tp30) cc_final: 0.7663 (tp30) REVERT: SF 77 MET cc_start: 0.7830 (mtm) cc_final: 0.7226 (mtm) REVERT: SF 78 MET cc_start: 0.8173 (tpp) cc_final: 0.7585 (mmt) REVERT: SF 102 LEU cc_start: 0.8583 (mt) cc_final: 0.7959 (tp) REVERT: SF 175 ASP cc_start: 0.8113 (p0) cc_final: 0.6944 (p0) REVERT: SF 176 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7239 (mm-30) REVERT: SF 194 ASP cc_start: 0.9404 (m-30) cc_final: 0.9173 (m-30) REVERT: SH 25 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7329 (mm-40) REVERT: SH 32 MET cc_start: 0.8126 (mmm) cc_final: 0.7539 (mmm) REVERT: SI 111 GLN cc_start: 0.8776 (mt0) cc_final: 0.8491 (mt0) REVERT: SI 167 GLN cc_start: 0.9269 (mt0) cc_final: 0.8930 (mm110) REVERT: SK 3 MET cc_start: 0.7743 (ptt) cc_final: 0.7251 (ptt) REVERT: SK 16 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: SK 50 GLN cc_start: 0.8633 (tt0) cc_final: 0.8300 (tm-30) REVERT: SK 68 TYR cc_start: 0.8280 (m-80) cc_final: 0.8041 (m-80) REVERT: SK 70 TYR cc_start: 0.7956 (m-80) cc_final: 0.7548 (m-80) REVERT: SK 82 TYR cc_start: 0.7765 (t80) cc_final: 0.7387 (t80) REVERT: SL 124 ASP cc_start: 0.8310 (m-30) cc_final: 0.8049 (m-30) REVERT: SP 35 GLN cc_start: 0.9104 (mm110) cc_final: 0.8596 (mm-40) REVERT: SP 37 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: SP 109 PRO cc_start: 0.7317 (Cg_exo) cc_final: 0.7028 (Cg_endo) REVERT: SP 118 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8122 (tp30) REVERT: SQ 67 ASP cc_start: 0.8063 (m-30) cc_final: 0.7837 (t0) REVERT: SR 82 ASP cc_start: 0.8338 (t0) cc_final: 0.8036 (t0) REVERT: SS 54 LYS cc_start: 0.7372 (tttt) cc_final: 0.7020 (tttt) REVERT: ST 13 GLU cc_start: 0.8955 (mp0) cc_final: 0.8026 (mp0) REVERT: ST 41 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8554 (tttt) REVERT: ST 134 ILE cc_start: 0.9136 (tt) cc_final: 0.8510 (tt) REVERT: ST 137 GLN cc_start: 0.9257 (tt0) cc_final: 0.9056 (pt0) REVERT: SU 107 GLU cc_start: 0.7498 (tp30) cc_final: 0.7094 (tp30) REVERT: SV 28 ASP cc_start: 0.8329 (t0) cc_final: 0.7928 (t0) REVERT: Sa 52 ASP cc_start: 0.8652 (t0) cc_final: 0.8343 (t0) REVERT: Sc 56 LEU cc_start: 0.9073 (mp) cc_final: 0.8571 (tp) REVERT: Sc 58 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7382 (mm) REVERT: Sc 66 ARG cc_start: 0.6020 (pmt-80) cc_final: 0.5792 (pmt-80) REVERT: Sd 27 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7915 (ttm170) REVERT: Sd 45 GLN cc_start: 0.8363 (tt0) cc_final: 0.8116 (tt0) REVERT: Sg 49 GLU cc_start: 0.8521 (pm20) cc_final: 0.8209 (pm20) REVERT: Sg 132 TRP cc_start: 0.7263 (m100) cc_final: 0.6899 (m100) REVERT: Sg 154 VAL cc_start: 0.8209 (OUTLIER) cc_final: 0.7920 (t) REVERT: Sg 217 MET cc_start: 0.8445 (mmm) cc_final: 0.8006 (mmm) REVERT: SC 248 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8254 (t80) REVERT: SG 124 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8795 (tp) REVERT: SG 126 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8754 (p0) REVERT: SG 152 ASP cc_start: 0.7841 (t0) cc_final: 0.7382 (t0) REVERT: SJ 27 GLN cc_start: 0.8949 (tp40) cc_final: 0.8400 (tp-100) REVERT: SJ 73 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8379 (mt-10) REVERT: SM 12 MET cc_start: 0.3720 (tmm) cc_final: 0.2950 (ttt) REVERT: SM 45 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6915 (ptt-90) REVERT: SM 112 LYS cc_start: 0.8452 (pttm) cc_final: 0.7463 (tttm) REVERT: SN 86 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6893 (tm-30) REVERT: SN 90 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8607 (m90) REVERT: SO 41 PHE cc_start: 0.8816 (m-80) cc_final: 0.8614 (m-10) REVERT: SO 75 MET cc_start: 0.9128 (ppp) cc_final: 0.8911 (ppp) REVERT: SO 80 ASP cc_start: 0.8932 (t0) cc_final: 0.8680 (t0) REVERT: SO 83 GLN cc_start: 0.9040 (pp30) cc_final: 0.8783 (pp30) REVERT: SW 46 TYR cc_start: 0.9158 (m-80) cc_final: 0.8845 (m-80) REVERT: SW 97 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8198 (mtm-85) REVERT: SY 74 MET cc_start: 0.8639 (mmm) cc_final: 0.8008 (mtt) REVERT: SZ 52 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8541 (tppt) REVERT: SZ 58 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8130 (pp) REVERT: SZ 60 LYS cc_start: 0.9084 (tptm) cc_final: 0.8406 (tttm) REVERT: SZ 61 GLU cc_start: 0.8867 (mp0) cc_final: 0.8483 (pm20) REVERT: SZ 106 GLN cc_start: 0.8556 (tp40) cc_final: 0.8198 (mm110) REVERT: Sb 13 GLU cc_start: 0.8297 (pm20) cc_final: 0.7771 (pm20) REVERT: Sb 14 GLU cc_start: 0.8571 (mp0) cc_final: 0.8041 (mp0) REVERT: Sb 17 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8552 (ttp80) REVERT: Sb 34 ASP cc_start: 0.8432 (m-30) cc_final: 0.8166 (m-30) REVERT: Sf 131 PHE cc_start: 0.7647 (m-10) cc_final: 0.7304 (m-10) REVERT: Sf 132 MET cc_start: 0.6833 (tpp) cc_final: 0.5128 (tpp) REVERT: Sf 150 PHE cc_start: 0.6572 (t80) cc_final: 0.6063 (t80) REVERT: JC 56 GLU cc_start: 0.8229 (tp30) cc_final: 0.7912 (tp30) REVERT: JC 165 LEU cc_start: 0.8777 (tp) cc_final: 0.8503 (mt) REVERT: JC 245 MET cc_start: 0.9044 (ttt) cc_final: 0.8826 (ttt) REVERT: JC 313 HIS cc_start: 0.7225 (m90) cc_final: 0.6859 (t-90) REVERT: JC 359 GLN cc_start: 0.8847 (pt0) cc_final: 0.8398 (pp30) REVERT: JC 448 TYR cc_start: 0.6757 (m-10) cc_final: 0.5969 (m-80) REVERT: JC 469 LYS cc_start: 0.8331 (mttt) cc_final: 0.8128 (tttt) REVERT: JC 566 TYR cc_start: 0.5539 (t80) cc_final: 0.5320 (t80) outliers start: 128 outliers final: 92 residues processed: 1038 average time/residue: 0.6264 time to fit residues: 1122.2023 Evaluate side-chains 995 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 891 time to evaluate : 3.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 111 GLN Chi-restraints excluded: chain SA residue 112 ILE Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SB residue 114 VAL Chi-restraints excluded: chain SB residue 179 ASN Chi-restraints excluded: chain SB residue 224 GLU Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 51 LEU Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SD residue 169 ASP Chi-restraints excluded: chain SD residue 221 THR Chi-restraints excluded: chain SE residue 111 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 126 THR Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 12 ASN Chi-restraints excluded: chain SH residue 44 ASN Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SI residue 3 ILE Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 89 ILE Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 107 ILE Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 119 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 111 PHE Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 114 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain SU residue 20 ILE Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 29 VAL Chi-restraints excluded: chain SU residue 48 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 60 THR Chi-restraints excluded: chain SU residue 105 SER Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 83 PHE Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 32 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sd residue 6 LEU Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 154 VAL Chi-restraints excluded: chain Sg residue 176 VAL Chi-restraints excluded: chain Sg residue 273 GLU Chi-restraints excluded: chain SC residue 107 LEU Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 124 LEU Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SJ residue 12 THR Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SJ residue 141 VAL Chi-restraints excluded: chain SM residue 45 ARG Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SM residue 108 CYS Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SM residue 111 VAL Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 90 HIS Chi-restraints excluded: chain SO residue 47 LEU Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SW residue 97 ARG Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 77 ASP Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 58 LEU Chi-restraints excluded: chain SZ residue 65 TYR Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 5 LYS Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 62 VAL Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 635 VAL Chi-restraints excluded: chain JC residue 356 LEU Chi-restraints excluded: chain JC residue 464 ILE Chi-restraints excluded: chain JC residue 479 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 206 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 361 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 668 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 303 optimal weight: 0.6980 chunk 258 optimal weight: 4.9990 chunk 469 optimal weight: 5.9990 chunk 441 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN ** SA 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 95 ASN SF 29 GLN ** SH 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 48 GLN SQ 86 GLN SR 83 ASN ST 51 ASN SU 100 GLN ** SV 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 97 ASN Sg 119 GLN ** SG 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 154 GLN ** SM 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 91 ASN SW 92 ASN ** SZ 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JC 445 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049624 restraints weight = 324876.785| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.40 r_work: 0.2807 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 85509 Z= 0.320 Angle : 0.678 12.580 123696 Z= 0.344 Chirality : 0.041 0.418 15234 Planarity : 0.006 0.138 9311 Dihedral : 22.917 178.294 33112 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 3.10 % Allowed : 22.73 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 5385 helix: 0.56 (0.12), residues: 1737 sheet: -0.02 (0.17), residues: 972 loop : -0.90 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPSd 8 HIS 0.009 0.001 HISSg 14 PHE 0.021 0.002 PHESV 83 TYR 0.053 0.002 TYRSd 34 ARG 0.018 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 879 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 7 LYS cc_start: 0.8531 (tttt) cc_final: 0.8294 (tttt) REVERT: SD 31 GLU cc_start: 0.7557 (pm20) cc_final: 0.7277 (pm20) REVERT: SD 116 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8406 (mmm-85) REVERT: SD 157 MET cc_start: 0.8929 (tpp) cc_final: 0.8727 (tpp) REVERT: SD 206 ASP cc_start: 0.8917 (m-30) cc_final: 0.8575 (m-30) REVERT: SD 214 LYS cc_start: 0.8443 (ptpt) cc_final: 0.8210 (mmmt) REVERT: SF 70 GLU cc_start: 0.8010 (tp30) cc_final: 0.7626 (tp30) REVERT: SF 77 MET cc_start: 0.8121 (mtm) cc_final: 0.7678 (mtm) REVERT: SF 78 MET cc_start: 0.8325 (tpp) cc_final: 0.7769 (mmt) REVERT: SF 102 LEU cc_start: 0.8575 (mt) cc_final: 0.7936 (tp) REVERT: SH 25 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7535 (mm-40) REVERT: SH 32 MET cc_start: 0.8179 (mmm) cc_final: 0.7751 (mmm) REVERT: SI 111 GLN cc_start: 0.8851 (mt0) cc_final: 0.8584 (mt0) REVERT: SI 167 GLN cc_start: 0.9302 (mt0) cc_final: 0.9033 (mm110) REVERT: SK 3 MET cc_start: 0.7917 (ptt) cc_final: 0.7526 (ptt) REVERT: SK 16 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: SK 31 LYS cc_start: 0.8580 (tppp) cc_final: 0.8376 (tppt) REVERT: SK 38 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8325 (mmtm) REVERT: SK 82 TYR cc_start: 0.7799 (t80) cc_final: 0.7400 (t80) REVERT: SL 124 ASP cc_start: 0.8377 (m-30) cc_final: 0.8111 (m-30) REVERT: SP 35 GLN cc_start: 0.9049 (mm110) cc_final: 0.8606 (mm-40) REVERT: SP 37 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: SP 109 PRO cc_start: 0.7384 (Cg_exo) cc_final: 0.7174 (Cg_endo) REVERT: SP 118 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8128 (tp30) REVERT: SQ 86 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8664 (tm-30) REVERT: SQ 110 ASP cc_start: 0.8577 (p0) cc_final: 0.8360 (p0) REVERT: SQ 129 SER cc_start: 0.9158 (m) cc_final: 0.8951 (m) REVERT: SR 1 MET cc_start: 0.5424 (mmm) cc_final: 0.5149 (mmm) REVERT: SR 82 ASP cc_start: 0.8362 (t0) cc_final: 0.8088 (t0) REVERT: SR 126 MET cc_start: 0.8735 (mtp) cc_final: 0.8425 (mtm) REVERT: SS 54 LYS cc_start: 0.7459 (tttt) cc_final: 0.7005 (tptm) REVERT: ST 13 GLU cc_start: 0.9013 (mp0) cc_final: 0.8626 (mp0) REVERT: ST 41 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8605 (tttt) REVERT: SU 78 ASP cc_start: 0.8313 (t0) cc_final: 0.7856 (t0) REVERT: SV 28 ASP cc_start: 0.8469 (t0) cc_final: 0.8007 (t0) REVERT: Sa 52 ASP cc_start: 0.8687 (t0) cc_final: 0.8415 (t0) REVERT: Sa 68 TYR cc_start: 0.8573 (m-80) cc_final: 0.8101 (m-80) REVERT: Sc 56 LEU cc_start: 0.9131 (mp) cc_final: 0.8602 (tp) REVERT: Sc 58 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7385 (mm) REVERT: Sc 66 ARG cc_start: 0.6043 (pmt-80) cc_final: 0.5746 (pmt-80) REVERT: Sd 45 GLN cc_start: 0.8326 (tt0) cc_final: 0.8060 (tt0) REVERT: Sg 5 MET cc_start: 0.7003 (tpt) cc_final: 0.4611 (pmm) REVERT: Sg 49 GLU cc_start: 0.8559 (pm20) cc_final: 0.8259 (pm20) REVERT: SG 124 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8781 (tp) REVERT: SG 126 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8730 (p0) REVERT: SJ 27 GLN cc_start: 0.8988 (tp40) cc_final: 0.8472 (tp-100) REVERT: SM 12 MET cc_start: 0.3834 (tmm) cc_final: 0.3008 (ttt) REVERT: SM 45 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6808 (ptt-90) REVERT: SO 124 MET cc_start: 0.8984 (mmm) cc_final: 0.8587 (mtt) REVERT: SO 146 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.9079 (ttm-80) REVERT: SW 97 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8256 (mtm-85) REVERT: SZ 52 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8553 (tppt) REVERT: SZ 60 LYS cc_start: 0.9050 (tptm) cc_final: 0.8341 (tttm) REVERT: SZ 61 GLU cc_start: 0.8773 (mp0) cc_final: 0.8528 (pm20) REVERT: SZ 106 GLN cc_start: 0.8575 (tp40) cc_final: 0.8211 (mm110) REVERT: Sb 13 GLU cc_start: 0.8239 (pm20) cc_final: 0.7867 (pm20) REVERT: Sb 14 GLU cc_start: 0.8570 (mp0) cc_final: 0.8047 (mp0) REVERT: Sb 34 ASP cc_start: 0.8469 (m-30) cc_final: 0.8232 (m-30) REVERT: Sb 45 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8664 (m) REVERT: Sf 132 MET cc_start: 0.6781 (tpp) cc_final: 0.5434 (tpp) REVERT: Sf 150 PHE cc_start: 0.6358 (t80) cc_final: 0.5777 (t80) REVERT: JC 56 GLU cc_start: 0.8408 (tp30) cc_final: 0.8100 (tp30) REVERT: JC 245 MET cc_start: 0.9216 (ttt) cc_final: 0.8991 (ttt) REVERT: JC 313 HIS cc_start: 0.7309 (m90) cc_final: 0.6798 (t-90) REVERT: JC 355 PHE cc_start: 0.8674 (m-80) cc_final: 0.8466 (m-80) REVERT: JC 359 GLN cc_start: 0.8905 (pt0) cc_final: 0.8459 (pp30) REVERT: JC 469 LYS cc_start: 0.8457 (mttt) cc_final: 0.8233 (tttt) outliers start: 146 outliers final: 114 residues processed: 967 average time/residue: 0.6247 time to fit residues: 1046.3031 Evaluate side-chains 967 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 843 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 112 ILE Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SB residue 114 VAL Chi-restraints excluded: chain SB residue 224 GLU Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SD residue 221 THR Chi-restraints excluded: chain SE residue 111 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 87 LEU Chi-restraints excluded: chain SF residue 116 ILE Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SH residue 119 SER Chi-restraints excluded: chain SH residue 149 ASP Chi-restraints excluded: chain SI residue 3 ILE Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SK residue 83 LEU Chi-restraints excluded: chain SK residue 89 ILE Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 57 ASP Chi-restraints excluded: chain SL residue 87 VAL Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 16 THR Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 107 ILE Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 86 GLN Chi-restraints excluded: chain SQ residue 119 LEU Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 55 THR Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 114 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 29 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SU residue 48 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 60 THR Chi-restraints excluded: chain SU residue 64 THR Chi-restraints excluded: chain SU residue 105 SER Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 83 PHE Chi-restraints excluded: chain SX residue 66 ILE Chi-restraints excluded: chain Sa residue 40 VAL Chi-restraints excluded: chain Sa residue 58 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 30 VAL Chi-restraints excluded: chain Sc residue 32 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sd residue 6 LEU Chi-restraints excluded: chain Sd residue 8 TRP Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 176 VAL Chi-restraints excluded: chain Sg residue 273 GLU Chi-restraints excluded: chain SC residue 95 ASP Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 83 CYS Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 124 LEU Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SJ residue 141 VAL Chi-restraints excluded: chain SM residue 45 ARG Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SM residue 109 VAL Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SM residue 111 VAL Chi-restraints excluded: chain SN residue 4 MET Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 144 SER Chi-restraints excluded: chain SO residue 47 LEU Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 122 SER Chi-restraints excluded: chain SO residue 146 ARG Chi-restraints excluded: chain SW residue 80 ASP Chi-restraints excluded: chain SW residue 97 ARG Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 65 TYR Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 5 LYS Chi-restraints excluded: chain Sb residue 8 LEU Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 VAL Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain JD residue 635 VAL Chi-restraints excluded: chain JC residue 224 CYS Chi-restraints excluded: chain JC residue 356 LEU Chi-restraints excluded: chain JC residue 402 LEU Chi-restraints excluded: chain JC residue 464 ILE Chi-restraints excluded: chain JC residue 479 LEU Chi-restraints excluded: chain JC residue 548 LEU Chi-restraints excluded: chain JC residue 561 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 686 optimal weight: 6.9990 chunk 647 optimal weight: 50.0000 chunk 539 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 615 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 663 optimal weight: 0.5980 chunk 268 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 chunk 340 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN SF 29 GLN SH 44 ASN ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 168 GLN SQ 86 GLN SQ 97 GLN SQ 114 GLN SS 42 HIS SV 33 GLN ** SG 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 91 ASN SW 92 ASN ** SZ 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.070709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051974 restraints weight = 321035.886| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.44 r_work: 0.2873 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 85509 Z= 0.162 Angle : 0.624 12.653 123696 Z= 0.315 Chirality : 0.037 0.414 15234 Planarity : 0.005 0.135 9311 Dihedral : 22.912 179.511 33112 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 2.72 % Allowed : 23.33 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.30 (0.11), residues: 5385 helix: 0.65 (0.13), residues: 1728 sheet: 0.09 (0.17), residues: 948 loop : -0.82 (0.12), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPSg 132 HIS 0.008 0.001 HISSK 84 PHE 0.026 0.001 PHEST 14 TYR 0.039 0.002 TYRSd 34 ARG 0.017 0.001 ARGSD 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 915 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 7 LYS cc_start: 0.8419 (tttt) cc_final: 0.7998 (ttpt) REVERT: SD 31 GLU cc_start: 0.7408 (pm20) cc_final: 0.7129 (pm20) REVERT: SD 87 TYR cc_start: 0.7349 (m-10) cc_final: 0.6494 (m-10) REVERT: SD 116 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8355 (mmm-85) REVERT: SD 169 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: SD 206 ASP cc_start: 0.8953 (m-30) cc_final: 0.8490 (m-30) REVERT: SD 214 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8222 (mmmt) REVERT: SF 70 GLU cc_start: 0.7941 (tp30) cc_final: 0.7672 (tp30) REVERT: SF 77 MET cc_start: 0.7922 (mtm) cc_final: 0.7280 (mtm) REVERT: SF 78 MET cc_start: 0.8250 (tpp) cc_final: 0.7702 (mmt) REVERT: SF 102 LEU cc_start: 0.8559 (mt) cc_final: 0.7875 (tp) REVERT: SH 25 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7308 (mm-40) REVERT: SH 32 MET cc_start: 0.8195 (mmm) cc_final: 0.7742 (mmm) REVERT: SI 111 GLN cc_start: 0.8828 (mt0) cc_final: 0.8516 (mt0) REVERT: SI 167 GLN cc_start: 0.9253 (mt0) cc_final: 0.9003 (mm110) REVERT: SK 3 MET cc_start: 0.7769 (ptt) cc_final: 0.7353 (ptt) REVERT: SK 16 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: SK 38 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8300 (mmtm) REVERT: SK 68 TYR cc_start: 0.8438 (m-80) cc_final: 0.8085 (m-80) REVERT: SK 70 TYR cc_start: 0.7931 (m-80) cc_final: 0.7562 (m-80) REVERT: SL 124 ASP cc_start: 0.8355 (m-30) cc_final: 0.8078 (m-30) REVERT: SP 13 ARG cc_start: 0.6814 (mpp-170) cc_final: 0.6356 (mpp80) REVERT: SP 35 GLN cc_start: 0.9090 (mm110) cc_final: 0.8641 (mm-40) REVERT: SP 37 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.5313 (m-80) REVERT: SP 109 PRO cc_start: 0.7389 (Cg_exo) cc_final: 0.7167 (Cg_endo) REVERT: SP 118 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8064 (tp30) REVERT: SQ 67 ASP cc_start: 0.7982 (m-30) cc_final: 0.7733 (t0) REVERT: SQ 110 ASP cc_start: 0.8683 (p0) cc_final: 0.8462 (p0) REVERT: SR 82 ASP cc_start: 0.8207 (t0) cc_final: 0.7935 (t0) REVERT: SS 105 ASN cc_start: 0.8745 (m110) cc_final: 0.8434 (p0) REVERT: ST 13 GLU cc_start: 0.8951 (mp0) cc_final: 0.8091 (mp0) REVERT: ST 41 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8590 (tttt) REVERT: ST 137 GLN cc_start: 0.9271 (tt0) cc_final: 0.9044 (pt0) REVERT: SU 107 GLU cc_start: 0.7302 (tp30) cc_final: 0.6991 (tp30) REVERT: SV 28 ASP cc_start: 0.8399 (t0) cc_final: 0.7997 (t0) REVERT: SX 139 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8272 (tm-30) REVERT: Sa 52 ASP cc_start: 0.8605 (t0) cc_final: 0.8289 (t0) REVERT: Sc 13 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7929 (ttm-80) REVERT: Sc 56 LEU cc_start: 0.9076 (mp) cc_final: 0.8552 (tp) REVERT: Sc 58 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7324 (mm) REVERT: Sc 66 ARG cc_start: 0.5969 (pmt-80) cc_final: 0.5629 (pmt-80) REVERT: Sd 45 GLN cc_start: 0.8338 (tt0) cc_final: 0.8071 (tt0) REVERT: Sg 5 MET cc_start: 0.6760 (tpt) cc_final: 0.4395 (pmm) REVERT: Sg 49 GLU cc_start: 0.8544 (pm20) cc_final: 0.8231 (pm20) REVERT: Sg 138 CYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7099 (p) REVERT: SC 248 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8220 (t80) REVERT: SG 124 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8808 (tp) REVERT: SG 126 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8702 (p0) REVERT: SJ 27 GLN cc_start: 0.8989 (tp40) cc_final: 0.8394 (tp-100) REVERT: SJ 73 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8381 (mt-10) REVERT: SM 12 MET cc_start: 0.3785 (tmm) cc_final: 0.2973 (ttt) REVERT: SM 45 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6861 (ptt-90) REVERT: SM 112 LYS cc_start: 0.8465 (pttm) cc_final: 0.7486 (tttt) REVERT: SN 113 PHE cc_start: 0.8289 (t80) cc_final: 0.8033 (t80) REVERT: SO 81 VAL cc_start: 0.9421 (t) cc_final: 0.9114 (p) REVERT: SO 124 MET cc_start: 0.8938 (mmm) cc_final: 0.8570 (mtt) REVERT: SO 146 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.9102 (ttm-80) REVERT: SW 97 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8195 (mtm-85) REVERT: SZ 52 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8547 (tppt) REVERT: SZ 60 LYS cc_start: 0.9017 (tptm) cc_final: 0.8333 (tttm) REVERT: SZ 106 GLN cc_start: 0.8513 (tp40) cc_final: 0.8164 (tp40) REVERT: Sb 13 GLU cc_start: 0.8293 (pm20) cc_final: 0.7939 (pm20) REVERT: Sb 14 GLU cc_start: 0.8525 (mp0) cc_final: 0.7990 (mp0) REVERT: Sb 17 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8474 (ttt90) REVERT: Sb 34 ASP cc_start: 0.8435 (m-30) cc_final: 0.8169 (m-30) REVERT: Sf 105 TYR cc_start: 0.2982 (OUTLIER) cc_final: 0.2114 (t80) REVERT: Sf 132 MET cc_start: 0.6564 (tpp) cc_final: 0.5387 (tpp) REVERT: Sf 150 PHE cc_start: 0.6344 (t80) cc_final: 0.5782 (t80) REVERT: JC 56 GLU cc_start: 0.8322 (tp30) cc_final: 0.8024 (tp30) REVERT: JC 165 LEU cc_start: 0.8845 (tp) cc_final: 0.8603 (mp) REVERT: JC 313 HIS cc_start: 0.7275 (m90) cc_final: 0.6764 (t-90) REVERT: JC 359 GLN cc_start: 0.8877 (pt0) cc_final: 0.8465 (pp30) REVERT: JC 566 TYR cc_start: 0.5614 (t80) cc_final: 0.5339 (t80) outliers start: 128 outliers final: 101 residues processed: 988 average time/residue: 0.6354 time to fit residues: 1083.9141 Evaluate side-chains 993 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 880 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 112 ILE Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SB residue 114 VAL Chi-restraints excluded: chain SB residue 179 ASN Chi-restraints excluded: chain SB residue 224 GLU Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SD residue 169 ASP Chi-restraints excluded: chain SE residue 111 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 44 ASN Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SI residue 31 ARG Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 89 ILE Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 107 ILE Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 86 GLN Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 111 PHE Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 33 ILE Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 114 LEU Chi-restraints excluded: chain SS residue 131 VAL Chi-restraints excluded: chain ST residue 4 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain SU residue 20 ILE Chi-restraints excluded: chain SU residue 25 THR Chi-restraints excluded: chain SU residue 29 VAL Chi-restraints excluded: chain SU residue 48 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 60 THR Chi-restraints excluded: chain SU residue 105 SER Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 69 ILE Chi-restraints excluded: chain SV residue 83 PHE Chi-restraints excluded: chain Sa residue 53 ILE Chi-restraints excluded: chain Sa residue 58 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 32 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sd residue 6 LEU Chi-restraints excluded: chain Sd residue 8 TRP Chi-restraints excluded: chain Sg residue 137 VAL Chi-restraints excluded: chain Sg residue 138 CYS Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 176 VAL Chi-restraints excluded: chain SC residue 79 GLU Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 124 LEU Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SJ residue 12 THR Chi-restraints excluded: chain SJ residue 14 VAL Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SJ residue 141 VAL Chi-restraints excluded: chain SM residue 45 ARG Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SM residue 111 VAL Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 87 ASP Chi-restraints excluded: chain SN residue 144 SER Chi-restraints excluded: chain SO residue 47 LEU Chi-restraints excluded: chain SO residue 56 VAL Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 146 ARG Chi-restraints excluded: chain SW residue 97 ARG Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 65 TYR Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 5 LYS Chi-restraints excluded: chain Sb residue 8 LEU Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 62 VAL Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Se residue 43 VAL Chi-restraints excluded: chain Sf residue 102 VAL Chi-restraints excluded: chain Sf residue 105 TYR Chi-restraints excluded: chain JD residue 588 HIS Chi-restraints excluded: chain JC residue 440 HIS Chi-restraints excluded: chain JC residue 464 ILE Chi-restraints excluded: chain JC residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 553 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 499 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 183 optimal weight: 0.0030 chunk 138 optimal weight: 10.0000 chunk 331 optimal weight: 0.0010 chunk 667 optimal weight: 8.9990 chunk 557 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN SF 29 GLN SH 44 ASN ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SP 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 48 GLN SQ 86 GLN SV 33 GLN SX 97 ASN ** SG 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 91 ASN ** SZ 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.069395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050736 restraints weight = 322368.659| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.39 r_work: 0.2838 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 85509 Z= 0.240 Angle : 0.649 13.594 123696 Z= 0.328 Chirality : 0.039 0.410 15234 Planarity : 0.005 0.138 9311 Dihedral : 22.861 178.894 33112 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 2.57 % Allowed : 23.94 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 5385 helix: 0.62 (0.12), residues: 1742 sheet: 0.14 (0.17), residues: 948 loop : -0.85 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPSg 132 HIS 0.008 0.001 HISSK 84 PHE 0.026 0.002 PHEST 14 TYR 0.045 0.002 TYRSd 34 ARG 0.017 0.001 ARGSD 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10770 Ramachandran restraints generated. 5385 Oldfield, 0 Emsley, 5385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 879 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ln 7 LYS cc_start: 0.8479 (tttt) cc_final: 0.8263 (tttt) REVERT: SD 31 GLU cc_start: 0.7489 (pm20) cc_final: 0.7209 (pm20) REVERT: SD 87 TYR cc_start: 0.7503 (m-10) cc_final: 0.6650 (m-10) REVERT: SD 116 ARG cc_start: 0.8624 (tpp-160) cc_final: 0.8384 (mmm-85) REVERT: SD 169 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: SD 206 ASP cc_start: 0.8933 (m-30) cc_final: 0.8515 (m-30) REVERT: SD 214 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8211 (mmmt) REVERT: SF 70 GLU cc_start: 0.8009 (tp30) cc_final: 0.7756 (tp30) REVERT: SF 77 MET cc_start: 0.7984 (mtm) cc_final: 0.7527 (mtm) REVERT: SF 78 MET cc_start: 0.8161 (tpp) cc_final: 0.7626 (mmt) REVERT: SF 102 LEU cc_start: 0.8611 (mt) cc_final: 0.7985 (tp) REVERT: SH 25 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7404 (mm-40) REVERT: SH 32 MET cc_start: 0.8203 (mmm) cc_final: 0.7782 (mmm) REVERT: SI 111 GLN cc_start: 0.8851 (mt0) cc_final: 0.8521 (mt0) REVERT: SI 167 GLN cc_start: 0.9302 (mt0) cc_final: 0.9057 (mm110) REVERT: SI 168 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8375 (mm110) REVERT: SK 3 MET cc_start: 0.7867 (ptt) cc_final: 0.7500 (ptt) REVERT: SK 16 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: SK 21 MET cc_start: 0.6728 (pmm) cc_final: 0.6165 (pmm) REVERT: SK 38 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8290 (mmtm) REVERT: SK 70 TYR cc_start: 0.8110 (m-80) cc_final: 0.7716 (m-80) REVERT: SL 124 ASP cc_start: 0.8343 (m-30) cc_final: 0.8107 (m-30) REVERT: SP 13 ARG cc_start: 0.6725 (mpp-170) cc_final: 0.6296 (mpp80) REVERT: SP 35 GLN cc_start: 0.9063 (mm110) cc_final: 0.8621 (mm-40) REVERT: SP 37 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.5423 (m-80) REVERT: SP 109 PRO cc_start: 0.7519 (Cg_exo) cc_final: 0.7295 (Cg_endo) REVERT: SP 118 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8084 (tp30) REVERT: SQ 48 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8452 (tp-100) REVERT: SQ 67 ASP cc_start: 0.8011 (m-30) cc_final: 0.7804 (t0) REVERT: SQ 86 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8547 (tm-30) REVERT: SQ 110 ASP cc_start: 0.8815 (p0) cc_final: 0.8561 (p0) REVERT: SQ 129 SER cc_start: 0.9140 (m) cc_final: 0.8749 (p) REVERT: SR 82 ASP cc_start: 0.8256 (t0) cc_final: 0.7986 (t0) REVERT: SR 126 MET cc_start: 0.8830 (mtp) cc_final: 0.8567 (mtm) REVERT: SS 54 LYS cc_start: 0.7450 (tttt) cc_final: 0.7019 (tptm) REVERT: ST 13 GLU cc_start: 0.8948 (mp0) cc_final: 0.8045 (mp0) REVERT: ST 41 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8627 (tttt) REVERT: SU 111 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8035 (tm-30) REVERT: SV 28 ASP cc_start: 0.8455 (t0) cc_final: 0.8012 (t0) REVERT: SX 139 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8249 (tm-30) REVERT: Sa 52 ASP cc_start: 0.8669 (t0) cc_final: 0.8352 (t0) REVERT: Sc 13 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8037 (ttm-80) REVERT: Sc 56 LEU cc_start: 0.9081 (mp) cc_final: 0.8561 (tp) REVERT: Sc 58 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7537 (mm) REVERT: Sc 66 ARG cc_start: 0.6145 (pmt-80) cc_final: 0.5803 (pmt-80) REVERT: Sd 45 GLN cc_start: 0.8369 (tt0) cc_final: 0.8111 (tt0) REVERT: Sg 5 MET cc_start: 0.6834 (tpt) cc_final: 0.4522 (pmm) REVERT: Sg 49 GLU cc_start: 0.8477 (pm20) cc_final: 0.8184 (pm20) REVERT: SC 248 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8292 (t80) REVERT: SG 27 PHE cc_start: 0.9258 (m-80) cc_final: 0.9033 (m-80) REVERT: SG 63 MET cc_start: 0.8396 (mtp) cc_final: 0.8178 (mtm) REVERT: SG 124 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8802 (tp) REVERT: SG 126 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8699 (p0) REVERT: SJ 27 GLN cc_start: 0.9038 (tp40) cc_final: 0.8487 (tp-100) REVERT: SM 12 MET cc_start: 0.3797 (tmm) cc_final: 0.2993 (ttt) REVERT: SM 45 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6842 (ptt-90) REVERT: SO 81 VAL cc_start: 0.9467 (t) cc_final: 0.9164 (p) REVERT: SO 124 MET cc_start: 0.8970 (mmm) cc_final: 0.8643 (mtt) REVERT: SW 24 GLN cc_start: 0.8875 (mt0) cc_final: 0.8621 (mt0) REVERT: SW 97 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8275 (mtm-85) REVERT: SZ 52 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8515 (tppt) REVERT: SZ 78 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7974 (tptt) REVERT: SZ 106 GLN cc_start: 0.8552 (tp40) cc_final: 0.8217 (tp40) REVERT: Sb 13 GLU cc_start: 0.8326 (pm20) cc_final: 0.7845 (pm20) REVERT: Sb 14 GLU cc_start: 0.8537 (mp0) cc_final: 0.7963 (mp0) REVERT: Sb 34 ASP cc_start: 0.8442 (m-30) cc_final: 0.8186 (m-30) REVERT: Sb 45 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8634 (m) REVERT: Sf 131 PHE cc_start: 0.7984 (m-10) cc_final: 0.7704 (m-10) REVERT: Sf 132 MET cc_start: 0.6388 (tpp) cc_final: 0.5432 (tpp) REVERT: Sf 150 PHE cc_start: 0.6486 (t80) cc_final: 0.5857 (t80) REVERT: JC 56 GLU cc_start: 0.8350 (tp30) cc_final: 0.8036 (tp30) REVERT: JC 313 HIS cc_start: 0.7165 (m90) cc_final: 0.6486 (t-90) REVERT: JC 359 GLN cc_start: 0.8897 (pt0) cc_final: 0.8454 (pp30) REVERT: JC 566 TYR cc_start: 0.5984 (t80) cc_final: 0.5713 (t80) outliers start: 121 outliers final: 100 residues processed: 951 average time/residue: 0.6044 time to fit residues: 997.2442 Evaluate side-chains 973 residues out of total 4709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 861 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SA residue 112 ILE Chi-restraints excluded: chain SA residue 170 SER Chi-restraints excluded: chain SA residue 178 LEU Chi-restraints excluded: chain SB residue 114 VAL Chi-restraints excluded: chain SB residue 179 ASN Chi-restraints excluded: chain SB residue 224 GLU Chi-restraints excluded: chain SD residue 50 ILE Chi-restraints excluded: chain SD residue 55 THR Chi-restraints excluded: chain SD residue 115 VAL Chi-restraints excluded: chain SD residue 123 LEU Chi-restraints excluded: chain SD residue 169 ASP Chi-restraints excluded: chain SE residue 111 VAL Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 223 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 247 THR Chi-restraints excluded: chain SF residue 116 ILE Chi-restraints excluded: chain SF residue 185 SER Chi-restraints excluded: chain SH residue 9 VAL Chi-restraints excluded: chain SH residue 66 VAL Chi-restraints excluded: chain SH residue 119 SER Chi-restraints excluded: chain SI residue 3 ILE Chi-restraints excluded: chain SI residue 31 ARG Chi-restraints excluded: chain SI residue 60 LEU Chi-restraints excluded: chain SI residue 62 VAL Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SK residue 16 PHE Chi-restraints excluded: chain SK residue 79 LEU Chi-restraints excluded: chain SK residue 89 ILE Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 39 ASN Chi-restraints excluded: chain SL residue 114 SER Chi-restraints excluded: chain SL residue 127 THR Chi-restraints excluded: chain SP residue 37 TYR Chi-restraints excluded: chain SP residue 80 LEU Chi-restraints excluded: chain SP residue 107 ILE Chi-restraints excluded: chain SQ residue 31 LEU Chi-restraints excluded: chain SQ residue 48 GLN Chi-restraints excluded: chain SQ residue 86 GLN Chi-restraints excluded: chain SQ residue 145 TYR Chi-restraints excluded: chain SR residue 24 LEU Chi-restraints excluded: chain SR residue 102 THR Chi-restraints excluded: chain SR residue 111 PHE Chi-restraints excluded: chain SS residue 4 VAL Chi-restraints excluded: chain SS residue 33 ILE Chi-restraints excluded: chain SS residue 89 ASP Chi-restraints excluded: chain SS residue 114 LEU Chi-restraints excluded: chain ST residue 4 VAL Chi-restraints excluded: chain ST residue 110 LEU Chi-restraints excluded: chain ST residue 123 LEU Chi-restraints excluded: chain SU residue 20 ILE Chi-restraints excluded: chain SU residue 29 VAL Chi-restraints excluded: chain SU residue 39 LEU Chi-restraints excluded: chain SU residue 48 LEU Chi-restraints excluded: chain SU residue 56 MET Chi-restraints excluded: chain SU residue 60 THR Chi-restraints excluded: chain SU residue 110 VAL Chi-restraints excluded: chain SU residue 114 VAL Chi-restraints excluded: chain SV residue 83 PHE Chi-restraints excluded: chain Sa residue 58 VAL Chi-restraints excluded: chain Sa residue 63 VAL Chi-restraints excluded: chain Sc residue 32 VAL Chi-restraints excluded: chain Sc residue 50 VAL Chi-restraints excluded: chain Sc residue 58 LEU Chi-restraints excluded: chain Sd residue 6 LEU Chi-restraints excluded: chain Sd residue 8 TRP Chi-restraints excluded: chain Sg residue 134 THR Chi-restraints excluded: chain Sg residue 153 CYS Chi-restraints excluded: chain Sg residue 176 VAL Chi-restraints excluded: chain SC residue 79 GLU Chi-restraints excluded: chain SC residue 121 ARG Chi-restraints excluded: chain SC residue 248 TYR Chi-restraints excluded: chain SC residue 280 VAL Chi-restraints excluded: chain SG residue 113 ILE Chi-restraints excluded: chain SG residue 124 LEU Chi-restraints excluded: chain SG residue 126 ASP Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SJ residue 12 THR Chi-restraints excluded: chain SJ residue 14 VAL Chi-restraints excluded: chain SJ residue 121 LYS Chi-restraints excluded: chain SJ residue 141 VAL Chi-restraints excluded: chain SM residue 45 ARG Chi-restraints excluded: chain SM residue 72 HIS Chi-restraints excluded: chain SM residue 110 VAL Chi-restraints excluded: chain SM residue 111 VAL Chi-restraints excluded: chain SN residue 37 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 144 SER Chi-restraints excluded: chain SO residue 47 LEU Chi-restraints excluded: chain SO residue 56 VAL Chi-restraints excluded: chain SO residue 97 LEU Chi-restraints excluded: chain SO residue 105 THR Chi-restraints excluded: chain SO residue 126 ILE Chi-restraints excluded: chain SW residue 97 ARG Chi-restraints excluded: chain SY residue 25 ILE Chi-restraints excluded: chain SY residue 125 VAL Chi-restraints excluded: chain SZ residue 65 TYR Chi-restraints excluded: chain SZ residue 67 LEU Chi-restraints excluded: chain SZ residue 96 LEU Chi-restraints excluded: chain SZ residue 107 VAL Chi-restraints excluded: chain Sb residue 5 LYS Chi-restraints excluded: chain Sb residue 8 LEU Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 VAL Chi-restraints excluded: chain Se residue 6 LEU Chi-restraints excluded: chain Se residue 43 VAL Chi-restraints excluded: chain JD residue 635 VAL Chi-restraints excluded: chain JC residue 356 LEU Chi-restraints excluded: chain JC residue 402 LEU Chi-restraints excluded: chain JC residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 211 optimal weight: 7.9990 chunk 692 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 638 optimal weight: 10.0000 chunk 187 optimal weight: 0.0870 chunk 649 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 700 optimal weight: 9.9990 chunk 642 optimal weight: 0.9980 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SA 33 GLN ** SI 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 48 GLN SQ 86 GLN SQ 114 GLN SV 33 GLN ** SN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 92 ASN ** SZ 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** JC 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050538 restraints weight = 322887.056| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.37 r_work: 0.2835 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 85509 Z= 0.238 Angle : 0.651 13.479 123696 Z= 0.329 Chirality : 0.039 0.407 15234 Planarity : 0.005 0.139 9311 Dihedral : 22.873 178.750 33112 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.34 % Rotamer: Outliers : 2.78 % Allowed : 23.82 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % 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: -0.33 (0.11), residues: 5385 helix: 0.63 (0.12), residues: 1737 sheet: 0.13 (0.17), residues: 950 loop : -0.87 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPSg 132 HIS 0.008 0.001 HISSg 14 PHE 0.030 0.002 PHEJC 480 TYR 0.042 0.002 TYRSd 34 ARG 0.017 0.001 ARGSD 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33080.47 seconds wall clock time: 568 minutes 31.59 seconds (34111.59 seconds total)