Starting phenix.real_space_refine on Sun Mar 10 14:43:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtr_32796/03_2024/7wtr_32796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtr_32796/03_2024/7wtr_32796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtr_32796/03_2024/7wtr_32796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtr_32796/03_2024/7wtr_32796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtr_32796/03_2024/7wtr_32796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtr_32796/03_2024/7wtr_32796.pdb" } resolution = 3.5 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= 0.007 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 1 6.06 5 P 1298 5.49 5 S 52 5.16 5 C 28764 2.51 5 N 9733 2.21 5 O 13664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "SB PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB ASP 72": "OD1" <-> "OD2" Residue "SB GLU 90": "OE1" <-> "OE2" Residue "SB PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB ASP 108": "OD1" <-> "OD2" Residue "SB GLU 170": "OE1" <-> "OE2" Residue "SB GLU 198": "OE1" <-> "OE2" Residue "SB PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 60": "OE1" <-> "OE2" Residue "SE TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 199": "OE1" <-> "OE2" Residue "SE PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG ASP 152": "OD1" <-> "OD2" Residue "SG PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 155": "OD1" <-> "OD2" Residue "SH PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI GLU 28": "OE1" <-> "OE2" Residue "SI GLU 70": "OE1" <-> "OE2" Residue "SI GLU 89": "OE1" <-> "OE2" Residue "SI PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 64": "OE1" <-> "OE2" Residue "SJ ASP 66": "OD1" <-> "OD2" Residue "SJ GLU 88": "OE1" <-> "OE2" Residue "SJ ASP 89": "OD1" <-> "OD2" Residue "SJ TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 10": "OE1" <-> "OE2" Residue "SL GLU 50": "OE1" <-> "OE2" Residue "SL TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL GLU 101": "OE1" <-> "OE2" Residue "SN TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 86": "OE1" <-> "OE2" Residue "SN GLU 142": "OE1" <-> "OE2" Residue "SO TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 37": "OE1" <-> "OE2" Residue "SO TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 115": "OE1" <-> "OE2" Residue "SX TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SX GLU 60": "OE1" <-> "OE2" Residue "SX GLU 138": "OE1" <-> "OE2" Residue "SY PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY ASP 26": "OD1" <-> "OD2" Residue "SY PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 81": "OE1" <-> "OE2" Residue "SY GLU 101": "OE1" <-> "OE2" Residue "Sb ASP 34": "OD1" <-> "OD2" Residue "Se TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 138": "OE1" <-> "OE2" Residue "CA ASP 169": "OD1" <-> "OD2" Residue "CA ASP 178": "OD1" <-> "OD2" Residue "CA TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 186": "OE1" <-> "OE2" Residue "CA ASP 209": "OD1" <-> "OD2" Residue "CC TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 150": "OD1" <-> "OD2" Residue "CC GLU 181": "OE1" <-> "OE2" Residue "CC PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 649": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53512 Number of models: 1 Model: "" Number of chains: 20 Chain: "C2" Number of atoms: 27674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1298, 27674 Classifications: {'RNA': 1298} Modifications used: {'rna2p_pur': 106, 'rna2p_pyr': 92, 'rna3p_pur': 588, 'rna3p_pyr': 512} Link IDs: {'rna2p': 198, 'rna3p': 1099} Chain breaks: 6 Chain: "SB" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "SC" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "SE" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "SG" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "SH" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 171} Chain: "SI" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "SJ" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "SL" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "SN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "SO" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "SW" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "SX" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SY" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Sb" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Se" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain breaks: 1 Chain: "CA" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "CB" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 302 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "CC" Number of atoms: 4938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4938 Classifications: {'peptide': 615} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 584} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "Sb" 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 46267 SG CYSSb 56 49.614 162.535 162.209 1.00118.90 S Time building chain proxies: 21.58, per 1000 atoms: 0.40 Number of scatterers: 53512 At special positions: 0 Unit cell: (169.44, 235.098, 200.151, 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 1 29.99 S 52 16.00 P 1298 15.00 O 13664 8.00 N 9733 7.00 C 28764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.31 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNSb 101 " pdb="ZN ZNSb 101 " - pdb=" SG CYSSb 56 " 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6054 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 33 sheets defined 33.6% alpha, 18.5% beta 439 base pairs and 696 stacking pairs defined. Time for finding SS restraints: 17.69 Creating SS restraints... Processing helix chain 'SB' and resid 58 through 62 Processing helix chain 'SB' and resid 70 through 75 Processing helix chain 'SB' and resid 106 through 114 removed outlier: 4.142A pdb=" N VALSB 114 " --> pdb=" O LEUSB 110 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 178 Processing helix chain 'SB' and resid 180 through 189 removed outlier: 3.522A pdb=" N THRSB 185 " --> pdb=" O LEUSB 181 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SERSB 186 " --> pdb=" O ALASB 182 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILESB 189 " --> pdb=" O THRSB 185 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 202 removed outlier: 3.915A pdb=" N LYSSB 195 " --> pdb=" O GLUSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 232 removed outlier: 3.594A pdb=" N HISSB 232 " --> pdb=" O LEUSB 228 " (cutoff:3.500A) Processing helix chain 'SC' and resid 39 through 47 removed outlier: 3.806A pdb=" N ARGSC 43 " --> pdb=" O THRSC 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUSC 44 " --> pdb=" O LYSSC 40 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALASC 47 " --> pdb=" O ARGSC 43 " (cutoff:3.500A) Processing helix chain 'SC' and resid 52 through 59 removed outlier: 4.668A pdb=" N ILESC 56 " --> pdb=" O THRSC 52 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HISSC 59 " --> pdb=" O GLUSC 55 " (cutoff:3.500A) Processing helix chain 'SC' and resid 66 through 71 removed outlier: 3.913A pdb=" N ASPSC 70 " --> pdb=" O PHESC 66 " (cutoff:3.500A) Processing helix chain 'SC' and resid 120 through 135 removed outlier: 3.547A pdb=" N ILESC 125 " --> pdb=" O VALSC 121 " (cutoff:3.500A) Processing helix chain 'SC' and resid 181 through 192 Processing helix chain 'SC' and resid 206 through 224 removed outlier: 3.790A pdb=" N LYSSC 212 " --> pdb=" O GLUSC 208 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYRSC 222 " --> pdb=" O ILESC 218 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLYSC 223 " --> pdb=" O GLYSC 219 " (cutoff:3.500A) Processing helix chain 'SC' and resid 226 through 230 Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 44 through 50 Processing helix chain 'SE' and resid 57 through 66 removed outlier: 3.708A pdb=" N VALSE 61 " --> pdb=" O ASNSE 57 " (cutoff:3.500A) Processing helix chain 'SE' and resid 133 through 135 No H-bonds generated for 'chain 'SE' and resid 133 through 135' Processing helix chain 'SE' and resid 247 through 257 removed outlier: 3.652A pdb=" N ARGSE 252 " --> pdb=" O ILESE 248 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALASE 257 " --> pdb=" O ASPSE 253 " (cutoff:3.500A) Processing helix chain 'SG' and resid 24 through 28 removed outlier: 3.503A pdb=" N PHESG 28 " --> pdb=" O ARGSG 25 " (cutoff:3.500A) Processing helix chain 'SG' and resid 42 through 46 removed outlier: 4.097A pdb=" N LYSSG 46 " --> pdb=" O ASPSG 43 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 146 removed outlier: 3.598A pdb=" N ILESG 141 " --> pdb=" O ARGSG 137 " (cutoff:3.500A) Processing helix chain 'SG' and resid 152 through 156 removed outlier: 3.672A pdb=" N ASPSG 155 " --> pdb=" O ASPSG 152 " (cutoff:3.500A) Processing helix chain 'SG' and resid 180 through 217 removed outlier: 3.771A pdb=" N SERSG 217 " --> pdb=" O ALASG 213 " (cutoff:3.500A) Processing helix chain 'SH' and resid 14 through 28 removed outlier: 3.509A pdb=" N VALSH 20 " --> pdb=" O LEUSH 16 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VALSH 25 " --> pdb=" O ALASH 21 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLUSH 26 " --> pdb=" O GLNSH 22 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEUSH 27 " --> pdb=" O ALASH 23 " (cutoff:3.500A) Processing helix chain 'SH' and resid 31 through 39 removed outlier: 3.844A pdb=" N ALASH 36 " --> pdb=" O PROSH 32 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLUSH 37 " --> pdb=" O GLUSH 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEUSH 38 " --> pdb=" O LEUSH 34 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARGSH 39 " --> pdb=" O LYSSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 66 through 74 removed outlier: 3.853A pdb=" N PHESH 70 " --> pdb=" O SERSH 66 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VALSH 73 " --> pdb=" O GLYSH 69 " (cutoff:3.500A) Processing helix chain 'SH' and resid 75 through 85 removed outlier: 3.566A pdb=" N LEUSH 81 " --> pdb=" O LEUSH 77 " (cutoff:3.500A) Processing helix chain 'SH' and resid 117 through 130 removed outlier: 3.587A pdb=" N LEUSH 126 " --> pdb=" O HISSH 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASPSH 128 " --> pdb=" O LYSSH 124 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEUSH 129 " --> pdb=" O ILESH 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VALSH 130 " --> pdb=" O LEUSH 126 " (cutoff:3.500A) Processing helix chain 'SH' and resid 158 through 162 removed outlier: 4.196A pdb=" N GLNSH 161 " --> pdb=" O ASPSH 158 " (cutoff:3.500A) Processing helix chain 'SH' and resid 165 through 177 Processing helix chain 'SI' and resid 6 through 10 removed outlier: 4.149A pdb=" N HISSI 9 " --> pdb=" O ASPSI 6 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYSSI 10 " --> pdb=" O SERSI 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 6 through 10' Processing helix chain 'SI' and resid 88 through 93 removed outlier: 3.740A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 117 removed outlier: 3.823A pdb=" N GLUSI 114 " --> pdb=" O ARGSI 110 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALASI 115 " --> pdb=" O GLNSI 111 " (cutoff:3.500A) Processing helix chain 'SI' and resid 137 through 146 removed outlier: 3.691A pdb=" N ARGSI 141 " --> pdb=" O LYSSI 137 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 163 removed outlier: 3.854A pdb=" N SERSI 161 " --> pdb=" O GLUSI 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALASI 162 " --> pdb=" O SERSI 158 " (cutoff:3.500A) Processing helix chain 'SI' and resid 172 through 177 Processing helix chain 'SI' and resid 186 through 199 removed outlier: 3.602A pdb=" N ARGSI 194 " --> pdb=" O ALASI 190 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 20 through 35 Processing helix chain 'SJ' and resid 39 through 62 removed outlier: 3.911A pdb=" N ARGSJ 62 " --> pdb=" O ASPSJ 58 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 66 through 84 Processing helix chain 'SJ' and resid 92 through 97 removed outlier: 3.731A pdb=" N VALSJ 96 " --> pdb=" O LYSSJ 92 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEUSJ 97 " --> pdb=" O LEUSJ 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'SJ' and resid 92 through 97' Processing helix chain 'SJ' and resid 100 through 107 removed outlier: 3.850A pdb=" N PHESJ 104 " --> pdb=" O LYSSJ 100 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARGSJ 107 " --> pdb=" O ASPSJ 103 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 108 through 116 Processing helix chain 'SJ' and resid 121 through 131 removed outlier: 3.586A pdb=" N GLNSJ 131 " --> pdb=" O VALSJ 127 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 150 through 154 removed outlier: 3.555A pdb=" N GLUSJ 153 " --> pdb=" O LEUSJ 150 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYSSJ 154 " --> pdb=" O ASPSJ 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'SJ' and resid 150 through 154' Processing helix chain 'SJ' and resid 162 through 166 Processing helix chain 'SJ' and resid 170 through 184 Processing helix chain 'SL' and resid 45 through 50 removed outlier: 3.711A pdb=" N ILESL 49 " --> pdb=" O PROSL 45 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLUSL 50 " --> pdb=" O LYSSL 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 45 through 50' Processing helix chain 'SN' and resid 30 through 44 removed outlier: 3.932A pdb=" N ILESN 34 " --> pdb=" O SERSN 30 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLYSN 44 " --> pdb=" O TYRSN 40 " (cutoff:3.500A) Processing helix chain 'SN' and resid 46 through 58 removed outlier: 3.527A pdb=" N GLYSN 51 " --> pdb=" O PROSN 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARGSN 55 " --> pdb=" O GLYSN 51 " (cutoff:3.500A) Processing helix chain 'SN' and resid 62 through 68 Processing helix chain 'SN' and resid 70 through 78 Processing helix chain 'SN' and resid 85 through 105 removed outlier: 3.609A pdb=" N ARGSN 104 " --> pdb=" O LYSSN 100 " (cutoff:3.500A) Processing helix chain 'SN' and resid 108 through 130 Processing helix chain 'SN' and resid 145 through 151 removed outlier: 3.993A pdb=" N ASNSN 151 " --> pdb=" O SERSN 147 " (cutoff:3.500A) Processing helix chain 'SO' and resid 56 through 75 removed outlier: 3.581A pdb=" N GLNSO 65 " --> pdb=" O METSO 61 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASPSO 66 " --> pdb=" O LEUSO 62 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLUSO 73 " --> pdb=" O ALASO 69 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VALSO 74 " --> pdb=" O LYSSO 70 " (cutoff:3.500A) Processing helix chain 'SO' and resid 95 through 107 Processing helix chain 'SW' and resid 5 through 20 removed outlier: 3.862A pdb=" N ASPSW 9 " --> pdb=" O SERSW 5 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THRSW 20 " --> pdb=" O ASNSW 16 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 44 removed outlier: 3.683A pdb=" N VALSW 40 " --> pdb=" O LYSSW 36 " (cutoff:3.500A) Processing helix chain 'SW' and resid 82 through 84 No H-bonds generated for 'chain 'SW' and resid 82 through 84' Processing helix chain 'SW' and resid 85 through 94 removed outlier: 3.731A pdb=" N ASNSW 92 " --> pdb=" O LYSSW 88 " (cutoff:3.500A) Processing helix chain 'SW' and resid 112 through 120 Processing helix chain 'SX' and resid 11 through 23 removed outlier: 3.742A pdb=" N ARGSX 19 " --> pdb=" O LEUSX 15 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASNSX 21 " --> pdb=" O VALSX 17 " (cutoff:3.500A) Processing helix chain 'SX' and resid 24 through 26 No H-bonds generated for 'chain 'SX' and resid 24 through 26' Processing helix chain 'SX' and resid 27 through 34 Processing helix chain 'SX' and resid 132 through 137 Processing helix chain 'SY' and resid 36 through 44 Processing helix chain 'SY' and resid 51 through 53 No H-bonds generated for 'chain 'SY' and resid 51 through 53' Processing helix chain 'SY' and resid 78 through 86 removed outlier: 3.914A pdb=" N ALASY 82 " --> pdb=" O SERSY 78 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYSSY 84 " --> pdb=" O ALASY 80 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLUSY 86 " --> pdb=" O ALASY 82 " (cutoff:3.500A) Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 104 through 116 Processing helix chain 'SY' and resid 122 through 135 Processing helix chain 'Sb' and resid 11 through 18 Processing helix chain 'Se' and resid 32 through 44 removed outlier: 3.680A pdb=" N PHESe 44 " --> pdb=" O TYRSe 40 " (cutoff:3.500A) Processing helix chain 'CA' and resid 102 through 104 No H-bonds generated for 'chain 'CA' and resid 102 through 104' Processing helix chain 'CA' and resid 105 through 112 removed outlier: 3.502A pdb=" N ASNCA 111 " --> pdb=" O THRCA 107 " (cutoff:3.500A) Processing helix chain 'CA' and resid 113 through 115 No H-bonds generated for 'chain 'CA' and resid 113 through 115' Processing helix chain 'CA' and resid 116 through 122 removed outlier: 3.521A pdb=" N LEUCA 120 " --> pdb=" O ILECA 116 " (cutoff:3.500A) Processing helix chain 'CA' and resid 148 through 163 removed outlier: 4.265A pdb=" N LEUCA 152 " --> pdb=" O ASPCA 148 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLNCA 153 " --> pdb=" O PROCA 149 " (cutoff:3.500A) Processing helix chain 'CA' and resid 167 through 177 removed outlier: 3.558A pdb=" N SERCA 171 " --> pdb=" O ASPCA 167 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALACA 173 " --> pdb=" O ASPCA 169 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEUCA 174 " --> pdb=" O ASPCA 170 " (cutoff:3.500A) Processing helix chain 'CA' and resid 188 through 190 No H-bonds generated for 'chain 'CA' and resid 188 through 190' Processing helix chain 'CA' and resid 195 through 207 Processing helix chain 'CA' and resid 210 through 220 Processing helix chain 'CA' and resid 236 through 252 removed outlier: 3.716A pdb=" N SERCA 249 " --> pdb=" O GLUCA 245 " (cutoff:3.500A) Processing helix chain 'CA' and resid 255 through 272 removed outlier: 3.652A pdb=" N VALCA 259 " --> pdb=" O PROCA 255 " (cutoff:3.500A) Processing helix chain 'CB' and resid 242 through 251 removed outlier: 3.580A pdb=" N LYSCB 250 " --> pdb=" O ILECB 246 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLUCB 251 " --> pdb=" O LEUCB 247 " (cutoff:3.500A) Processing helix chain 'CB' and resid 251 through 257 Processing helix chain 'CC' and resid 23 through 32 removed outlier: 3.630A pdb=" N LYSCC 32 " --> pdb=" O LYSCC 28 " (cutoff:3.500A) Processing helix chain 'CC' and resid 50 through 73 Processing helix chain 'CC' and resid 74 through 77 removed outlier: 4.291A pdb=" N GLUCC 77 " --> pdb=" O LYSCC 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 74 through 77' Processing helix chain 'CC' and resid 96 through 106 removed outlier: 3.658A pdb=" N ILECC 100 " --> pdb=" O ASPCC 96 " (cutoff:3.500A) Processing helix chain 'CC' and resid 107 through 109 No H-bonds generated for 'chain 'CC' and resid 107 through 109' Processing helix chain 'CC' and resid 111 through 116 removed outlier: 3.575A pdb=" N VALCC 115 " --> pdb=" O GLUCC 111 " (cutoff:3.500A) Processing helix chain 'CC' and resid 144 through 155 removed outlier: 3.563A pdb=" N ALACC 152 " --> pdb=" O ILECC 148 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYSCC 153 " --> pdb=" O LEUCC 149 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VALCC 154 " --> pdb=" O ASPCC 150 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALACC 155 " --> pdb=" O CYSCC 151 " (cutoff:3.500A) Processing helix chain 'CC' and resid 172 through 183 removed outlier: 3.594A pdb=" N GLNCC 183 " --> pdb=" O ALACC 179 " (cutoff:3.500A) Processing helix chain 'CC' and resid 194 through 198 removed outlier: 3.658A pdb=" N VALCC 198 " --> pdb=" O LEUCC 195 " (cutoff:3.500A) Processing helix chain 'CC' and resid 201 through 220 removed outlier: 3.558A pdb=" N SERCC 211 " --> pdb=" O ASPCC 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHECC 219 " --> pdb=" O TYRCC 215 " (cutoff:3.500A) Processing helix chain 'CC' and resid 231 through 245 removed outlier: 3.510A pdb=" N CYSCC 243 " --> pdb=" O LEUCC 239 " (cutoff:3.500A) Processing helix chain 'CC' and resid 250 through 255 Processing helix chain 'CC' and resid 350 through 354 removed outlier: 3.545A pdb=" N THRCC 354 " --> pdb=" O PROCC 351 " (cutoff:3.500A) Processing helix chain 'CC' and resid 495 through 499 removed outlier: 4.286A pdb=" N LYSCC 499 " --> pdb=" O GLUCC 496 " (cutoff:3.500A) Processing helix chain 'CC' and resid 522 through 526 removed outlier: 3.981A pdb=" N LYSCC 526 " --> pdb=" O ALACC 523 " (cutoff:3.500A) Processing helix chain 'CC' and resid 533 through 548 removed outlier: 3.889A pdb=" N THRCC 537 " --> pdb=" O ASNCC 533 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYSCC 543 " --> pdb=" O ASNCC 539 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASNCC 547 " --> pdb=" O LYSCC 543 " (cutoff:3.500A) Processing helix chain 'CC' and resid 566 through 568 No H-bonds generated for 'chain 'CC' and resid 566 through 568' Processing helix chain 'CC' and resid 723 through 730 removed outlier: 3.695A pdb=" N VALCC 727 " --> pdb=" O ARGCC 723 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SB' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'SB' and resid 65 through 69 removed outlier: 5.232A pdb=" N ARGSB 87 " --> pdb=" O PHESB 100 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHESB 100 " --> pdb=" O ARGSB 87 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASPSB 89 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THRSB 98 " --> pdb=" O ASPSB 89 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VALSB 91 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEUSB 96 " --> pdb=" O VALSB 91 " (cutoff:3.500A) removed outlier: 13.487A pdb=" N ASNSB 99 " --> pdb=" O LYSSB 219 " (cutoff:3.500A) removed outlier: 13.486A pdb=" N LYSSB 219 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEUSB 217 " --> pdb=" O HISSB 101 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ARGSB 213 " --> pdb=" O PHESB 105 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILESB 210 " --> pdb=" O PHESB 142 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHESB 142 " --> pdb=" O ILESB 210 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VALSB 212 " --> pdb=" O ILESB 140 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILESB 140 " --> pdb=" O VALSB 212 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYSSB 214 " --> pdb=" O PHESB 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYSSB 216 " --> pdb=" O ARGSB 136 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VALSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SC' and resid 77 through 89 removed outlier: 4.867A pdb=" N ASPSC 78 " --> pdb=" O GLYSC 105 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLYSC 105 " --> pdb=" O ASPSC 78 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VALSC 80 " --> pdb=" O VALSC 103 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VALSC 103 " --> pdb=" O VALSC 80 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYSSC 116 " --> pdb=" O ALASC 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VALSC 102 " --> pdb=" O GLYSC 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VALSC 111 " --> pdb=" O ILESC 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SC' and resid 141 through 142 Processing sheet with id=AA5, first strand: chain 'SC' and resid 158 through 161 WARNING: can't find start of bonding for strands! previous: chain 'SC' and resid 165 through 171 current: chain 'SC' and resid 196 through 197 Processing sheet with id=AA6, first strand: chain 'SE' and resid 42 through 43 Processing sheet with id=AA7, first strand: chain 'SE' and resid 75 through 76 removed outlier: 4.283A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'SE' and resid 102 through 103 removed outlier: 4.031A pdb=" N VALSE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SE' and resid 122 through 126 removed outlier: 3.776A pdb=" N ASPSE 158 " --> pdb=" O VALSE 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SE' and resid 128 through 131 removed outlier: 3.513A pdb=" N LYSSE 128 " --> pdb=" O VALSE 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'SE' and resid 217 through 221 removed outlier: 3.823A pdb=" N LEUSE 207 " --> pdb=" O GLUSE 199 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HISSE 197 " --> pdb=" O HISSE 209 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LYSSE 211 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILESE 195 " --> pdb=" O LYSSE 211 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYRSE 182 " --> pdb=" O VALSE 227 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VALSE 227 " --> pdb=" O TYRSE 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SG' and resid 12 through 17 removed outlier: 6.512A pdb=" N VALSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILESG 52 " --> pdb=" O VALSG 112 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VALSG 114 " --> pdb=" O PHESG 50 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHESG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SG' and resid 72 through 76 Processing sheet with id=AB5, first strand: chain 'SG' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'SH' and resid 45 through 50 Processing sheet with id=AB7, first strand: chain 'SH' and resid 180 through 184 removed outlier: 4.901A pdb=" N GLNSH 180 " --> pdb=" O LYSSH 148 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYSSH 138 " --> pdb=" O ASPSW 54 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHESW 50 " --> pdb=" O TYRSH 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SI' and resid 3 through 4 removed outlier: 3.734A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SI' and resid 37 through 38 removed outlier: 6.467A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SI' and resid 72 through 75 removed outlier: 6.514A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 181 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILESI 183 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SERSI 66 " --> pdb=" O ILESI 183 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILESI 101 " --> pdb=" O VALSI 81 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VALSI 81 " --> pdb=" O ILESI 101 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLNSI 103 " --> pdb=" O ALASI 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SJ' and resid 139 through 140 removed outlier: 3.561A pdb=" N ASPSJ 157 " --> pdb=" O ALASJ 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SL' and resid 70 through 77 removed outlier: 17.971A pdb=" N ILESL 70 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 15.332A pdb=" N LEUSL 91 " --> pdb=" O ILESL 70 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N THRSL 72 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ALASL 89 " --> pdb=" O THRSL 72 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VALSL 85 " --> pdb=" O VALSL 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARGSL 99 " --> pdb=" O ILESL 94 " (cutoff:3.500A) removed outlier: 16.314A pdb=" N VALSL 135 " --> pdb=" O HISSL 104 " (cutoff:3.500A) removed outlier: 13.802A pdb=" N ASNSL 106 " --> pdb=" O VALSL 135 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N PHESL 137 " --> pdb=" O ASNSL 106 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VALSL 139 " --> pdb=" O PROSL 108 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N HISSL 110 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LYSSL 141 " --> pdb=" O HISSL 110 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARGSL 136 " --> pdb=" O CYSSL 128 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THRSL 124 " --> pdb=" O VALSL 140 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VALSL 142 " --> pdb=" O ILESL 122 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILESL 122 " --> pdb=" O VALSL 142 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASPSL 121 " --> pdb=" O VALSL 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALSL 75 " --> pdb=" O ASPSL 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SO' and resid 38 through 43 removed outlier: 7.026A pdb=" N VALSO 30 " --> pdb=" O ILESO 39 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARGSO 41 " --> pdb=" O VALSO 28 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VALSO 28 " --> pdb=" O ARGSO 41 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THRSO 43 " --> pdb=" O THRSO 26 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THRSO 26 " --> pdb=" O THRSO 43 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VALSO 81 " --> pdb=" O GLYSO 113 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILESO 115 " --> pdb=" O VALSO 81 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILESO 83 " --> pdb=" O ILESO 115 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASPSO 117 " --> pdb=" O ILESO 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'SW' and resid 71 through 74 WARNING: can't find start of bonding for strands! previous: chain 'SW' and resid 71 through 74 current: chain 'SW' and resid 109 through 111 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'SX' and resid 82 through 84 removed outlier: 3.668A pdb=" N GLUSX 55 " --> pdb=" O ARGSX 73 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLNSX 75 " --> pdb=" O VALSX 53 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VALSX 53 " --> pdb=" O GLNSX 75 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALASX 105 " --> pdb=" O VALSX 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VALSX 124 " --> pdb=" O ALASX 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'SY' and resid 6 through 15 removed outlier: 4.330A pdb=" N VALSY 12 " --> pdb=" O GLNSY 22 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLNSY 22 " --> pdb=" O VALSY 12 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SERSY 14 " --> pdb=" O ARGSY 20 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARGSY 20 " --> pdb=" O SERSY 14 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VALSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHESY 60 " --> pdb=" O VALSY 70 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHESY 72 " --> pdb=" O PHESY 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Sb' and resid 43 through 47 removed outlier: 3.700A pdb=" N SERSb 78 " --> pdb=" O LYSSb 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Sb' and resid 64 through 65 Processing sheet with id=AD1, first strand: chain 'CA' and resid 99 through 100 removed outlier: 3.570A pdb=" N GLUCA 138 " --> pdb=" O ARGCA 129 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'CA' and resid 181 through 186 Processing sheet with id=AD3, first strand: chain 'CC' and resid 123 through 128 removed outlier: 9.125A pdb=" N TYRCC 227 " --> pdb=" O TYRCC 188 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLYCC 190 " --> pdb=" O TYRCC 227 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'CC' and resid 336 through 338 removed outlier: 10.926A pdb=" N PHECC 301 " --> pdb=" O PROCC 564 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEUCC 303 " --> pdb=" O ARGCC 562 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARGCC 562 " --> pdb=" O LEUCC 303 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THRCC 281 " --> pdb=" O ALACC 261 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALACC 261 " --> pdb=" O THRCC 281 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARGCC 283 " --> pdb=" O VALCC 259 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VALCC 259 " --> pdb=" O ARGCC 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'CC' and resid 485 through 486 WARNING: can't find start of bonding for strands! previous: chain 'CC' and resid 485 through 486 current: chain 'CC' and resid 696 through 710 removed outlier: 6.380A pdb=" N THRCC 716 " --> pdb=" O PHECC 708 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'CC' and resid 715 through 718 current: chain 'CC' and resid 742 through 748 removed outlier: 6.460A pdb=" N LYSCC 756 " --> pdb=" O LYSCC 746 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'CC' and resid 628 through 630 removed outlier: 3.530A pdb=" N ALACC 658 " --> pdb=" O ALACC 592 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASNCC 595 " --> pdb=" O LEUCC 689 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THRCC 687 " --> pdb=" O SERCC 597 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEUCC 682 " --> pdb=" O LYSCC 671 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYSCC 671 " --> pdb=" O LEUCC 682 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1055 hydrogen bonds 1632 hydrogen bond angles 0 basepair planarities 439 basepair parallelities 696 stacking parallelities Total time for adding SS restraints: 30.72 Time building geometry restraints manager: 22.15 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: 7738 1.33 - 1.45: 21820 1.45 - 1.57: 25025 1.57 - 1.69: 2590 1.69 - 1.82: 82 Bond restraints: 57255 Sorted by residual: bond pdb=" C GLNSC 150 " pdb=" N PROSC 151 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.27e-02 6.20e+03 5.32e+00 bond pdb=" C GLNSX 63 " pdb=" N PROSX 64 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.28e+00 bond pdb=" C PHESH 131 " pdb=" N PROSH 132 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.44e-02 4.82e+03 4.50e+00 bond pdb=" C2 GC2 430 " pdb=" N2 GC2 430 " ideal model delta sigma weight residual 1.341 1.299 0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" CB PROSC 138 " pdb=" CG PROSC 138 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.69e+00 ... (remaining 57250 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.91: 7325 105.91 - 114.06: 35659 114.06 - 122.20: 28957 122.20 - 130.35: 10983 130.35 - 138.49: 655 Bond angle restraints: 83579 Sorted by residual: angle pdb=" CA LYSSY 49 " pdb=" CB LYSSY 49 " pdb=" CG LYSSY 49 " ideal model delta sigma weight residual 114.10 127.82 -13.72 2.00e+00 2.50e-01 4.71e+01 angle pdb=" C TYRSY 48 " pdb=" N LYSSY 49 " pdb=" CA LYSSY 49 " ideal model delta sigma weight residual 121.58 131.30 -9.72 1.62e+00 3.81e-01 3.60e+01 angle pdb=" CA PROSC 138 " pdb=" N PROSC 138 " pdb=" CD PROSC 138 " ideal model delta sigma weight residual 112.00 104.00 8.00 1.40e+00 5.10e-01 3.27e+01 angle pdb=" C SERSH 30 " pdb=" N SERSH 31 " pdb=" CA SERSH 31 " ideal model delta sigma weight residual 121.70 131.84 -10.14 1.80e+00 3.09e-01 3.17e+01 angle pdb=" N THRSO 91 " pdb=" CA THRSO 91 " pdb=" C THRSO 91 " ideal model delta sigma weight residual 111.33 117.77 -6.44 1.21e+00 6.83e-01 2.83e+01 ... (remaining 83574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 32602 35.95 - 71.90: 3170 71.90 - 107.86: 317 107.86 - 143.81: 15 143.81 - 179.76: 18 Dihedral angle restraints: 36122 sinusoidal: 26748 harmonic: 9374 Sorted by residual: dihedral pdb=" CA GLNSX 63 " pdb=" C GLNSX 63 " pdb=" N PROSX 64 " pdb=" CA PROSX 64 " ideal model delta harmonic sigma weight residual 180.00 -129.00 -51.00 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" O4' CC2 934 " pdb=" C1' CC2 934 " pdb=" N1 CC2 934 " pdb=" C2 CC2 934 " ideal model delta sinusoidal sigma weight residual 200.00 35.25 164.75 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' UC2 767 " pdb=" C1' UC2 767 " pdb=" N1 UC2 767 " pdb=" C2 UC2 767 " ideal model delta sinusoidal sigma weight residual 200.00 35.93 164.07 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 36119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 9786 0.093 - 0.186: 581 0.186 - 0.279: 56 0.279 - 0.372: 7 0.372 - 0.465: 1 Chirality restraints: 10431 Sorted by residual: chirality pdb=" CB ILESX 59 " pdb=" CA ILESX 59 " pdb=" CG1 ILESX 59 " pdb=" CG2 ILESX 59 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1' UC2 861 " pdb=" O4' UC2 861 " pdb=" C2' UC2 861 " pdb=" N1 UC2 861 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C3' CC21652 " pdb=" C4' CC21652 " pdb=" O3' CC21652 " pdb=" C2' CC21652 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 10428 not shown) Planarity restraints: 5821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CC21121 " 0.012 2.00e-02 2.50e+03 3.76e-02 3.17e+01 pdb=" N1 CC21121 " 0.009 2.00e-02 2.50e+03 pdb=" C2 CC21121 " -0.093 2.00e-02 2.50e+03 pdb=" O2 CC21121 " 0.047 2.00e-02 2.50e+03 pdb=" N3 CC21121 " 0.012 2.00e-02 2.50e+03 pdb=" C4 CC21121 " -0.027 2.00e-02 2.50e+03 pdb=" N4 CC21121 " 0.027 2.00e-02 2.50e+03 pdb=" C5 CC21121 " 0.006 2.00e-02 2.50e+03 pdb=" C6 CC21121 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC2 430 " -0.007 2.00e-02 2.50e+03 3.13e-02 2.93e+01 pdb=" N9 GC2 430 " -0.002 2.00e-02 2.50e+03 pdb=" C8 GC2 430 " -0.001 2.00e-02 2.50e+03 pdb=" N7 GC2 430 " -0.004 2.00e-02 2.50e+03 pdb=" C5 GC2 430 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GC2 430 " 0.017 2.00e-02 2.50e+03 pdb=" O6 GC2 430 " -0.020 2.00e-02 2.50e+03 pdb=" N1 GC2 430 " -0.004 2.00e-02 2.50e+03 pdb=" C2 GC2 430 " 0.087 2.00e-02 2.50e+03 pdb=" N2 GC2 430 " -0.058 2.00e-02 2.50e+03 pdb=" N3 GC2 430 " -0.001 2.00e-02 2.50e+03 pdb=" C4 GC2 430 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC21141 " -0.040 2.00e-02 2.50e+03 3.06e-02 2.81e+01 pdb=" N9 GC21141 " 0.025 2.00e-02 2.50e+03 pdb=" C8 GC21141 " 0.003 2.00e-02 2.50e+03 pdb=" N7 GC21141 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GC21141 " 0.003 2.00e-02 2.50e+03 pdb=" C6 GC21141 " 0.016 2.00e-02 2.50e+03 pdb=" O6 GC21141 " -0.033 2.00e-02 2.50e+03 pdb=" N1 GC21141 " -0.009 2.00e-02 2.50e+03 pdb=" C2 GC21141 " 0.074 2.00e-02 2.50e+03 pdb=" N2 GC21141 " -0.044 2.00e-02 2.50e+03 pdb=" N3 GC21141 " 0.004 2.00e-02 2.50e+03 pdb=" C4 GC21141 " 0.004 2.00e-02 2.50e+03 ... (remaining 5818 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 1621 2.64 - 3.21: 43560 3.21 - 3.77: 97857 3.77 - 4.34: 129197 4.34 - 4.90: 184116 Nonbonded interactions: 456351 Sorted by model distance: nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.080 3.040 nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.116 3.040 nonbonded pdb=" O2 UC2 231 " pdb=" O6 GC2 234 " model vdw 2.195 3.040 nonbonded pdb=" O4 UC2 715 " pdb=" O6 GC2 723 " model vdw 2.199 2.432 nonbonded pdb=" O2 UC2 152 " pdb=" N2 GC2 163 " model vdw 2.204 2.496 ... (remaining 456346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.050 Extract box with map and model: 10.680 Check model and map are aligned: 0.570 Set scattering table: 0.370 Process input model: 138.890 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.006 0.096 57255 Z= 0.385 Angle : 0.884 13.721 83579 Z= 0.446 Chirality : 0.048 0.465 10431 Planarity : 0.007 0.122 5821 Dihedral : 22.222 179.760 30068 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 1.42 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.13), residues: 3213 helix: -2.80 (0.12), residues: 902 sheet: -0.78 (0.20), residues: 652 loop : -2.10 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCC 525 HIS 0.011 0.001 HISSW 56 PHE 0.045 0.002 PHESe 44 TYR 0.030 0.003 TYRSE 121 ARG 0.021 0.001 ARGSL 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 97 LEU cc_start: 0.8180 (mt) cc_final: 0.7933 (mt) REVERT: SC 144 TRP cc_start: 0.8609 (t60) cc_final: 0.8358 (t-100) REVERT: SJ 140 ILE cc_start: 0.9061 (mt) cc_final: 0.8802 (mt) REVERT: SW 2 THR cc_start: 0.8211 (p) cc_final: 0.7875 (m) REVERT: SW 43 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8430 (tptp) REVERT: CB 265 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7870 (mptt) REVERT: CC 28 LYS cc_start: 0.7216 (tttt) cc_final: 0.6940 (tttp) REVERT: CC 601 TRP cc_start: 0.8538 (t-100) cc_final: 0.7974 (t-100) REVERT: CC 771 MET cc_start: 0.5839 (mmm) cc_final: 0.5370 (mmm) outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.5722 time to fit residues: 479.1913 Evaluate side-chains 406 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 376 optimal weight: 3.9990 chunk 338 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 228 optimal weight: 0.0570 chunk 180 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 405 optimal weight: 6.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 40 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 36 HIS SG 139 ASN ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 123 HIS SN 21 ASN ** SO 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 42 GLN SW 66 ASN SY 22 GLN ** CA 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 218 HIS CC 244 GLN ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 626 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 57255 Z= 0.259 Angle : 0.647 12.673 83579 Z= 0.332 Chirality : 0.039 0.291 10431 Planarity : 0.006 0.090 5821 Dihedral : 23.182 179.697 23519 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 1.48 % Allowed : 9.99 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 1.42 % Twisted General : 0.10 % 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: -2.04 (0.14), residues: 3213 helix: -0.70 (0.16), residues: 947 sheet: -0.87 (0.19), residues: 674 loop : -1.98 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPSX 24 HIS 0.004 0.001 HISSW 44 PHE 0.029 0.002 PHESH 24 TYR 0.019 0.001 TYRSJ 19 ARG 0.004 0.000 ARGSE 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 418 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 49 ASN cc_start: 0.7661 (p0) cc_final: 0.7436 (p0) REVERT: SB 89 ASP cc_start: 0.7785 (p0) cc_final: 0.7382 (p0) REVERT: SB 175 GLU cc_start: 0.7358 (tp30) cc_final: 0.7009 (tp30) REVERT: SH 87 ASP cc_start: 0.7614 (t70) cc_final: 0.7369 (t0) REVERT: SW 2 THR cc_start: 0.8218 (p) cc_final: 0.7824 (m) REVERT: SW 118 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8239 (ttp-110) REVERT: SY 22 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: CA 158 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8412 (t80) REVERT: CA 181 TYR cc_start: 0.8910 (m-80) cc_final: 0.8627 (m-80) REVERT: CC 28 LYS cc_start: 0.7102 (tttt) cc_final: 0.6838 (tttp) REVERT: CC 780 MET cc_start: 0.7496 (ppp) cc_final: 0.7227 (ppp) outliers start: 41 outliers final: 33 residues processed: 439 average time/residue: 0.5073 time to fit residues: 373.6773 Evaluate side-chains 425 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 390 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SC residue 103 VAL Chi-restraints excluded: chain SC residue 113 LEU Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 139 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SG residue 10 ASN Chi-restraints excluded: chain SG residue 78 THR Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 76 ILE Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SX residue 28 ASN Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SY residue 22 GLN Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 107 THR Chi-restraints excluded: chain CA residue 136 SER Chi-restraints excluded: chain CA residue 158 PHE Chi-restraints excluded: chain CA residue 249 SER Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CB residue 260 VAL Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 194 ASN Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 633 SER Chi-restraints excluded: chain CC residue 687 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 225 optimal weight: 7.9990 chunk 125 optimal weight: 50.0000 chunk 337 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 405 optimal weight: 6.9990 chunk 438 optimal weight: 9.9990 chunk 361 optimal weight: 0.9980 chunk 402 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 325 optimal weight: 0.6980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 153 HIS ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 57 ASN SG 119 GLN ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN SN 36 GLN SO 12 GLN SW 66 ASN SX 22 ASN SX 89 ASN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 131 ASN CC 64 GLN ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 57255 Z= 0.264 Angle : 0.626 12.848 83579 Z= 0.318 Chirality : 0.039 0.288 10431 Planarity : 0.005 0.082 5821 Dihedral : 23.086 179.604 23519 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.44 % Rotamer: Outliers : 2.45 % Allowed : 12.69 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.66 (0.14), residues: 3213 helix: -0.03 (0.17), residues: 951 sheet: -0.83 (0.20), residues: 673 loop : -1.90 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPCC 729 HIS 0.005 0.001 HISSB 211 PHE 0.029 0.002 PHESH 24 TYR 0.023 0.001 TYRSJ 19 ARG 0.006 0.000 ARGSX 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 441 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 49 ASN cc_start: 0.8196 (p0) cc_final: 0.7934 (p0) REVERT: SE 251 GLU cc_start: 0.8004 (tp30) cc_final: 0.7730 (tp30) REVERT: SJ 139 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7437 (tm-30) REVERT: SO 65 GLN cc_start: 0.8731 (mp10) cc_final: 0.8481 (mp10) REVERT: SW 2 THR cc_start: 0.8279 (p) cc_final: 0.7845 (m) REVERT: SW 114 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7834 (mm-30) REVERT: SY 15 ASN cc_start: 0.8910 (t0) cc_final: 0.8652 (t0) REVERT: Se 56 MET cc_start: 0.5086 (pmm) cc_final: 0.4789 (ppp) REVERT: CA 123 HIS cc_start: 0.7136 (t-90) cc_final: 0.6933 (t70) REVERT: CA 264 ARG cc_start: 0.6731 (mtt180) cc_final: 0.6439 (mtt180) REVERT: CC 28 LYS cc_start: 0.7181 (tttt) cc_final: 0.6946 (tttp) REVERT: CC 771 MET cc_start: 0.5587 (mmm) cc_final: 0.5335 (mmm) REVERT: CC 780 MET cc_start: 0.7381 (ppp) cc_final: 0.6891 (ppp) outliers start: 68 outliers final: 52 residues processed: 478 average time/residue: 0.5065 time to fit residues: 407.9836 Evaluate side-chains 461 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 409 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SC residue 129 ILE Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 139 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 10 ASN Chi-restraints excluded: chain SG residue 78 THR Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 109 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SJ residue 9 SER Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 77 SER Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 76 ILE Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SX residue 28 ASN Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SX residue 89 ASN Chi-restraints excluded: chain SY residue 25 VAL Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Sb residue 63 LEU Chi-restraints excluded: chain Sb residue 65 THR Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 131 ASN Chi-restraints excluded: chain CA residue 136 SER Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 249 SER Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CB residue 260 VAL Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 194 ASN Chi-restraints excluded: chain CC residue 212 LEU Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 633 SER Chi-restraints excluded: chain CC residue 655 THR Chi-restraints excluded: chain CC residue 687 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 400 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 431 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 385 optimal weight: 0.0020 chunk 116 optimal weight: 10.0000 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 119 GLN ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 98 GLN SY 22 GLN CA 131 ASN CC 116 GLN ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 57255 Z= 0.355 Angle : 0.677 13.627 83579 Z= 0.343 Chirality : 0.041 0.288 10431 Planarity : 0.005 0.082 5821 Dihedral : 23.081 179.545 23519 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 3.28 % Allowed : 14.89 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.13 % 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: -1.54 (0.14), residues: 3213 helix: 0.29 (0.17), residues: 941 sheet: -0.97 (0.20), residues: 665 loop : -1.87 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPCC 729 HIS 0.008 0.001 HISSE 8 PHE 0.025 0.002 PHESH 43 TYR 0.030 0.002 TYRSJ 19 ARG 0.007 0.001 ARGSI 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 414 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 48 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8753 (t) REVERT: SB 49 ASN cc_start: 0.8619 (p0) cc_final: 0.8262 (p0) REVERT: SE 251 GLU cc_start: 0.8086 (tp30) cc_final: 0.7885 (tp30) REVERT: SG 169 TYR cc_start: 0.7929 (p90) cc_final: 0.7607 (p90) REVERT: SH 24 PHE cc_start: 0.8735 (m-80) cc_final: 0.8074 (m-80) REVERT: SI 141 ARG cc_start: 0.8444 (ptp-170) cc_final: 0.8231 (ptp90) REVERT: SO 65 GLN cc_start: 0.8676 (mt0) cc_final: 0.8386 (mp10) REVERT: SX 94 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8626 (p0) REVERT: SY 22 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: Se 56 MET cc_start: 0.5197 (pmm) cc_final: 0.3615 (ppp) REVERT: CA 123 HIS cc_start: 0.7329 (t-90) cc_final: 0.7011 (t70) REVERT: CA 169 ASP cc_start: 0.7756 (p0) cc_final: 0.7470 (p0) REVERT: CA 260 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7351 (t80) REVERT: CA 264 ARG cc_start: 0.6864 (mtt180) cc_final: 0.6498 (mtt180) REVERT: CC 28 LYS cc_start: 0.7267 (tttt) cc_final: 0.7036 (tttp) REVERT: CC 137 ILE cc_start: 0.8936 (mm) cc_final: 0.8494 (mt) REVERT: CC 771 MET cc_start: 0.5915 (mmm) cc_final: 0.5711 (mmm) outliers start: 91 outliers final: 70 residues processed: 465 average time/residue: 0.5531 time to fit residues: 434.4325 Evaluate side-chains 463 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 389 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 48 VAL Chi-restraints excluded: chain SB residue 52 THR Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SC residue 103 VAL Chi-restraints excluded: chain SC residue 113 LEU Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 200 SER Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 139 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 10 ASN Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 78 THR Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 179 VAL Chi-restraints excluded: chain SH residue 9 LEU Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 109 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SI residue 82 VAL Chi-restraints excluded: chain SJ residue 9 SER Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 77 SER Chi-restraints excluded: chain SL residue 111 VAL Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 46 MET Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 76 ILE Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 118 VAL Chi-restraints excluded: chain SW residue 6 VAL Chi-restraints excluded: chain SX residue 28 ASN Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 72 VAL Chi-restraints excluded: chain SX residue 74 VAL Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SX residue 89 ASN Chi-restraints excluded: chain SX residue 94 ASN Chi-restraints excluded: chain SX residue 102 VAL Chi-restraints excluded: chain SY residue 22 GLN Chi-restraints excluded: chain SY residue 25 VAL Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Sb residue 63 LEU Chi-restraints excluded: chain Sb residue 65 THR Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 249 SER Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 194 ASN Chi-restraints excluded: chain CC residue 212 LEU Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 282 VAL Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 633 SER Chi-restraints excluded: chain CC residue 655 THR Chi-restraints excluded: chain CC residue 687 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 359 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 320 optimal weight: 0.7980 chunk 177 optimal weight: 0.4980 chunk 367 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 386 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 57 ASN SG 119 GLN ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 89 ASN SY 22 GLN ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 57255 Z= 0.201 Angle : 0.596 13.070 83579 Z= 0.303 Chirality : 0.037 0.285 10431 Planarity : 0.005 0.075 5821 Dihedral : 23.046 179.671 23519 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 2.85 % Allowed : 15.93 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.35 (0.15), residues: 3213 helix: 0.55 (0.17), residues: 948 sheet: -0.93 (0.20), residues: 661 loop : -1.80 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPCC 729 HIS 0.003 0.001 HISSI 9 PHE 0.028 0.001 PHESb 79 TYR 0.025 0.001 TYRSJ 19 ARG 0.006 0.000 ARGSL 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 436 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 45 LYS cc_start: 0.8390 (tptt) cc_final: 0.7931 (tptt) REVERT: SB 48 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8767 (t) REVERT: SB 49 ASN cc_start: 0.8716 (p0) cc_final: 0.8401 (p0) REVERT: SE 251 GLU cc_start: 0.8046 (tp30) cc_final: 0.7832 (tp30) REVERT: SG 169 TYR cc_start: 0.7804 (p90) cc_final: 0.7482 (p90) REVERT: SH 24 PHE cc_start: 0.8730 (m-80) cc_final: 0.8154 (m-80) REVERT: SJ 41 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: SO 32 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7602 (p0) REVERT: SO 65 GLN cc_start: 0.8618 (mt0) cc_final: 0.8320 (mp10) REVERT: SW 114 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7766 (mm-30) REVERT: SX 104 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9061 (pp) REVERT: Sb 36 LYS cc_start: 0.8747 (tttp) cc_final: 0.8536 (tptp) REVERT: CA 123 HIS cc_start: 0.7315 (t-90) cc_final: 0.7065 (t70) REVERT: CA 260 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7391 (t80) REVERT: CA 264 ARG cc_start: 0.6745 (mtt180) cc_final: 0.6400 (mtt180) REVERT: CC 28 LYS cc_start: 0.7252 (tttt) cc_final: 0.7050 (tttp) REVERT: CC 137 ILE cc_start: 0.8918 (mm) cc_final: 0.8625 (mm) outliers start: 79 outliers final: 56 residues processed: 482 average time/residue: 0.5094 time to fit residues: 412.0124 Evaluate side-chains 459 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 398 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 48 VAL Chi-restraints excluded: chain SB residue 52 THR Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 146 GLN Chi-restraints excluded: chain SC residue 113 LEU Chi-restraints excluded: chain SC residue 200 SER Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 10 ASN Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 78 THR Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 179 VAL Chi-restraints excluded: chain SH residue 9 LEU Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SJ residue 9 SER Chi-restraints excluded: chain SJ residue 41 GLU Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 77 SER Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 28 VAL Chi-restraints excluded: chain SO residue 32 ASP Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 76 ILE Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 74 VAL Chi-restraints excluded: chain SX residue 89 ASN Chi-restraints excluded: chain SX residue 104 LEU Chi-restraints excluded: chain SY residue 25 VAL Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Sb residue 65 THR Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CC residue 107 CYS Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 165 VAL Chi-restraints excluded: chain CC residue 194 ASN Chi-restraints excluded: chain CC residue 212 LEU Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 300 ASP Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 633 SER Chi-restraints excluded: chain CC residue 687 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 145 optimal weight: 5.9990 chunk 388 optimal weight: 0.0370 chunk 85 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 431 optimal weight: 6.9990 chunk 358 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 57 ASN ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 89 ASN SY 110 GLN ** CA 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 57255 Z= 0.372 Angle : 0.687 13.777 83579 Z= 0.346 Chirality : 0.041 0.287 10431 Planarity : 0.005 0.077 5821 Dihedral : 23.045 179.751 23519 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.43 % Favored : 91.47 % Rotamer: Outliers : 3.82 % Allowed : 16.55 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.45 (0.15), residues: 3213 helix: 0.49 (0.17), residues: 950 sheet: -1.00 (0.20), residues: 656 loop : -1.86 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPSN 139 HIS 0.004 0.001 HISSW 56 PHE 0.032 0.002 PHESb 79 TYR 0.039 0.002 TYRSJ 19 ARG 0.015 0.001 ARGSI 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 401 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 45 LYS cc_start: 0.8527 (tptt) cc_final: 0.8276 (tptt) REVERT: SB 48 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (t) REVERT: SB 49 ASN cc_start: 0.8837 (p0) cc_final: 0.8584 (p0) REVERT: SB 194 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8044 (m-40) REVERT: SG 169 TYR cc_start: 0.7921 (p90) cc_final: 0.7626 (p90) REVERT: SH 24 PHE cc_start: 0.8794 (m-80) cc_final: 0.8487 (m-80) REVERT: SI 141 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (ptp90) REVERT: SJ 41 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: SJ 139 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7529 (tm-30) REVERT: SN 80 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8865 (mm) REVERT: SN 102 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8260 (tt) REVERT: SO 32 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7588 (p0) REVERT: SO 65 GLN cc_start: 0.8667 (mt0) cc_final: 0.8294 (mp10) REVERT: SW 114 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7777 (mm-30) REVERT: SX 94 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8587 (p0) REVERT: SX 104 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9081 (pp) REVERT: Se 56 MET cc_start: 0.5259 (pmm) cc_final: 0.3707 (ppp) REVERT: CA 123 HIS cc_start: 0.7491 (t-90) cc_final: 0.7281 (t70) REVERT: CA 260 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7408 (t80) REVERT: CA 264 ARG cc_start: 0.6858 (mtt180) cc_final: 0.6496 (mtt180) REVERT: CC 28 LYS cc_start: 0.7330 (tttt) cc_final: 0.7100 (tttp) REVERT: CC 137 ILE cc_start: 0.8959 (mm) cc_final: 0.8518 (mt) REVERT: CC 771 MET cc_start: 0.5785 (mmm) cc_final: 0.5343 (mmm) outliers start: 106 outliers final: 77 residues processed: 467 average time/residue: 0.5107 time to fit residues: 401.2568 Evaluate side-chains 470 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 383 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 48 VAL Chi-restraints excluded: chain SB residue 52 THR Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 146 GLN Chi-restraints excluded: chain SB residue 194 ASN Chi-restraints excluded: chain SB residue 215 VAL Chi-restraints excluded: chain SC residue 86 VAL Chi-restraints excluded: chain SC residue 103 VAL Chi-restraints excluded: chain SC residue 113 LEU Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 200 SER Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 139 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 10 ASN Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 78 THR Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 179 VAL Chi-restraints excluded: chain SH residue 9 LEU Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 39 ARG Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 109 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SI residue 82 VAL Chi-restraints excluded: chain SI residue 141 ARG Chi-restraints excluded: chain SJ residue 9 SER Chi-restraints excluded: chain SJ residue 41 GLU Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 77 SER Chi-restraints excluded: chain SL residue 111 VAL Chi-restraints excluded: chain SN residue 16 ILE Chi-restraints excluded: chain SN residue 56 ASP Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SN residue 80 LEU Chi-restraints excluded: chain SN residue 102 LEU Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 28 VAL Chi-restraints excluded: chain SO residue 32 ASP Chi-restraints excluded: chain SO residue 42 VAL Chi-restraints excluded: chain SO residue 46 MET Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 76 ILE Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 118 VAL Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 72 VAL Chi-restraints excluded: chain SX residue 74 VAL Chi-restraints excluded: chain SX residue 94 ASN Chi-restraints excluded: chain SX residue 104 LEU Chi-restraints excluded: chain SY residue 25 VAL Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Sb residue 65 THR Chi-restraints excluded: chain Sb residue 82 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CC residue 107 CYS Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 165 VAL Chi-restraints excluded: chain CC residue 194 ASN Chi-restraints excluded: chain CC residue 212 LEU Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 282 VAL Chi-restraints excluded: chain CC residue 300 ASP Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 633 SER Chi-restraints excluded: chain CC residue 655 THR Chi-restraints excluded: chain CC residue 687 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 416 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 363 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 429 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 22 GLN ** CA 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 57255 Z= 0.175 Angle : 0.587 12.880 83579 Z= 0.297 Chirality : 0.036 0.281 10431 Planarity : 0.004 0.071 5821 Dihedral : 23.000 179.381 23519 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 3.03 % Allowed : 17.74 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3213 helix: 0.73 (0.17), residues: 949 sheet: -0.93 (0.20), residues: 664 loop : -1.68 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPSX 24 HIS 0.003 0.001 HISSI 9 PHE 0.029 0.001 PHESb 79 TYR 0.026 0.001 TYRSJ 19 ARG 0.011 0.000 ARGSI 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 423 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 45 LYS cc_start: 0.8418 (tptt) cc_final: 0.7421 (mmmt) REVERT: SB 194 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7991 (m-40) REVERT: SE 251 GLU cc_start: 0.7838 (tp30) cc_final: 0.7610 (tp30) REVERT: SG 169 TYR cc_start: 0.7795 (p90) cc_final: 0.7441 (p90) REVERT: SH 43 PHE cc_start: 0.7334 (p90) cc_final: 0.7096 (p90) REVERT: SI 94 ASN cc_start: 0.8583 (m110) cc_final: 0.8124 (m-40) REVERT: SJ 41 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: SJ 48 GLN cc_start: 0.8350 (pt0) cc_final: 0.8087 (pt0) REVERT: SJ 139 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7481 (tm-30) REVERT: SL 55 ASP cc_start: 0.8047 (t70) cc_final: 0.7815 (t70) REVERT: SN 80 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8828 (mm) REVERT: SN 102 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8317 (tt) REVERT: SO 32 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7610 (p0) REVERT: SO 65 GLN cc_start: 0.8628 (mt0) cc_final: 0.8411 (mp10) REVERT: SW 114 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7673 (mm-30) REVERT: SX 94 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8589 (p0) REVERT: SX 104 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9032 (pp) REVERT: Se 56 MET cc_start: 0.5287 (pmm) cc_final: 0.3625 (ppp) REVERT: CA 260 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7277 (t80) REVERT: CC 137 ILE cc_start: 0.8934 (mm) cc_final: 0.8520 (mt) REVERT: CC 688 PHE cc_start: 0.7569 (t80) cc_final: 0.7318 (t80) REVERT: CC 771 MET cc_start: 0.5934 (mmm) cc_final: 0.5632 (mmm) outliers start: 84 outliers final: 62 residues processed: 470 average time/residue: 0.5119 time to fit residues: 405.1272 Evaluate side-chains 477 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 407 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 52 THR Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 146 GLN Chi-restraints excluded: chain SB residue 194 ASN Chi-restraints excluded: chain SC residue 86 VAL Chi-restraints excluded: chain SC residue 113 LEU Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 200 SER Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 179 VAL Chi-restraints excluded: chain SH residue 9 LEU Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 39 ARG Chi-restraints excluded: chain SH residue 50 ASP Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 141 ARG Chi-restraints excluded: chain SJ residue 9 SER Chi-restraints excluded: chain SJ residue 41 GLU Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 111 VAL Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SN residue 80 LEU Chi-restraints excluded: chain SN residue 102 LEU Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 32 ASP Chi-restraints excluded: chain SO residue 46 MET Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 76 ILE Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 94 ASN Chi-restraints excluded: chain SX residue 102 VAL Chi-restraints excluded: chain SX residue 104 LEU Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 7 LEU Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Sb residue 65 THR Chi-restraints excluded: chain Sb residue 82 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 100 MET Chi-restraints excluded: chain CA residue 136 SER Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CB residue 247 LEU Chi-restraints excluded: chain CC residue 107 CYS Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 165 VAL Chi-restraints excluded: chain CC residue 194 ASN Chi-restraints excluded: chain CC residue 212 LEU Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 300 ASP Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 777 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 265 optimal weight: 0.3980 chunk 171 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 273 optimal weight: 0.2980 chunk 292 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 337 optimal weight: 0.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 57 ASN ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN SW 15 ASN SW 70 ASN SX 89 ASN CA 123 HIS ** CA 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 57255 Z= 0.135 Angle : 0.560 14.044 83579 Z= 0.282 Chirality : 0.034 0.301 10431 Planarity : 0.004 0.067 5821 Dihedral : 22.885 179.337 23519 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.78 % Favored : 93.09 % Rotamer: Outliers : 2.49 % Allowed : 18.93 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.01 (0.15), residues: 3213 helix: 0.92 (0.17), residues: 946 sheet: -0.87 (0.20), residues: 668 loop : -1.58 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPCC 729 HIS 0.014 0.001 HISCA 123 PHE 0.033 0.001 PHESb 79 TYR 0.026 0.001 TYRSE 121 ARG 0.010 0.000 ARGSI 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 457 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 45 LYS cc_start: 0.8297 (tptt) cc_final: 0.7350 (mmmt) REVERT: SB 194 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8063 (m-40) REVERT: SE 251 GLU cc_start: 0.7822 (tp30) cc_final: 0.7589 (tp30) REVERT: SG 23 ARG cc_start: 0.7398 (mmp-170) cc_final: 0.7185 (mmm160) REVERT: SH 87 ASP cc_start: 0.7561 (t70) cc_final: 0.7314 (t0) REVERT: SI 94 ASN cc_start: 0.8542 (m110) cc_final: 0.8124 (m-40) REVERT: SJ 41 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: SN 80 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8772 (mm) REVERT: SO 65 GLN cc_start: 0.8597 (mt0) cc_final: 0.8368 (mp10) REVERT: SW 43 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8351 (tptp) REVERT: SW 114 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7651 (mm-30) REVERT: Se 56 MET cc_start: 0.5452 (pmm) cc_final: 0.4143 (ppp) REVERT: CA 123 HIS cc_start: 0.7254 (t-90) cc_final: 0.6970 (t-90) REVERT: CC 688 PHE cc_start: 0.7444 (t80) cc_final: 0.7180 (t80) outliers start: 69 outliers final: 48 residues processed: 496 average time/residue: 0.5821 time to fit residues: 489.8173 Evaluate side-chains 473 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 422 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 52 THR Chi-restraints excluded: chain SB residue 105 PHE Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 146 GLN Chi-restraints excluded: chain SB residue 194 ASN Chi-restraints excluded: chain SC residue 86 VAL Chi-restraints excluded: chain SC residue 103 VAL Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 166 THR Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 179 VAL Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 39 ARG Chi-restraints excluded: chain SH residue 50 ASP Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SJ residue 41 GLU Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 111 VAL Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SN residue 80 LEU Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 46 MET Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 89 ASN Chi-restraints excluded: chain SY residue 25 VAL Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 7 LEU Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 136 SER Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 165 VAL Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 282 VAL Chi-restraints excluded: chain CC residue 300 ASP Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 655 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 391 optimal weight: 9.9990 chunk 411 optimal weight: 7.9990 chunk 375 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 314 optimal weight: 0.1980 chunk 122 optimal weight: 7.9990 chunk 361 optimal weight: 0.0020 chunk 378 optimal weight: 0.8980 chunk 399 optimal weight: 10.0000 overall best weight: 2.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SW 70 ASN SX 89 ASN ** CA 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 57255 Z= 0.228 Angle : 0.605 13.578 83579 Z= 0.304 Chirality : 0.037 0.277 10431 Planarity : 0.005 0.068 5821 Dihedral : 22.850 179.992 23519 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.31 % Rotamer: Outliers : 2.63 % Allowed : 19.47 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3213 helix: 0.90 (0.17), residues: 950 sheet: -0.90 (0.20), residues: 652 loop : -1.61 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPCC 729 HIS 0.003 0.001 HISCA 123 PHE 0.033 0.001 PHESb 79 TYR 0.038 0.001 TYRSJ 19 ARG 0.011 0.000 ARGSI 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 408 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 194 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8052 (m-40) REVERT: SE 251 GLU cc_start: 0.7897 (tp30) cc_final: 0.7639 (tp30) REVERT: SH 87 ASP cc_start: 0.7587 (t70) cc_final: 0.7333 (t0) REVERT: SI 94 ASN cc_start: 0.8568 (m110) cc_final: 0.8139 (m-40) REVERT: SI 119 GLN cc_start: 0.7941 (mp10) cc_final: 0.7725 (mp10) REVERT: SJ 19 TYR cc_start: 0.7985 (m-10) cc_final: 0.7614 (m-80) REVERT: SJ 41 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: SN 80 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8816 (mm) REVERT: SO 65 GLN cc_start: 0.8672 (mt0) cc_final: 0.8401 (mp10) REVERT: SW 114 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7668 (mm-30) REVERT: SX 94 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8560 (p0) REVERT: Se 49 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7187 (pp) REVERT: Se 56 MET cc_start: 0.5313 (pmm) cc_final: 0.4124 (ppp) REVERT: CA 260 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7305 (t80) REVERT: CC 137 ILE cc_start: 0.8894 (mm) cc_final: 0.8453 (mt) REVERT: CC 688 PHE cc_start: 0.7544 (t80) cc_final: 0.7302 (t80) outliers start: 73 outliers final: 60 residues processed: 451 average time/residue: 0.5072 time to fit residues: 384.7290 Evaluate side-chains 467 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 401 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 52 THR Chi-restraints excluded: chain SB residue 105 PHE Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 146 GLN Chi-restraints excluded: chain SB residue 194 ASN Chi-restraints excluded: chain SC residue 86 VAL Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 166 THR Chi-restraints excluded: chain SC residue 200 SER Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 76 LEU Chi-restraints excluded: chain SG residue 78 THR Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 179 VAL Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 39 ARG Chi-restraints excluded: chain SH residue 50 ASP Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 129 LEU Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SJ residue 41 GLU Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 111 VAL Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SN residue 80 LEU Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 28 VAL Chi-restraints excluded: chain SO residue 46 MET Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 94 ASN Chi-restraints excluded: chain SX residue 102 VAL Chi-restraints excluded: chain SY residue 25 VAL Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain Se residue 49 LEU Chi-restraints excluded: chain CA residue 100 MET Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 167 ASP Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CB residue 265 LYS Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 165 VAL Chi-restraints excluded: chain CC residue 242 LEU Chi-restraints excluded: chain CC residue 282 VAL Chi-restraints excluded: chain CC residue 300 ASP Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 655 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 263 optimal weight: 0.6980 chunk 423 optimal weight: 9.9990 chunk 258 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 444 optimal weight: 7.9990 chunk 408 optimal weight: 8.9990 chunk 353 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 273 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SX 22 ASN ** CA 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 57255 Z= 0.175 Angle : 0.587 14.113 83579 Z= 0.294 Chirality : 0.035 0.275 10431 Planarity : 0.004 0.069 5821 Dihedral : 22.858 179.922 23519 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 2.31 % Allowed : 19.90 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.00 (0.15), residues: 3213 helix: 0.94 (0.17), residues: 951 sheet: -0.89 (0.20), residues: 654 loop : -1.56 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPCC 525 HIS 0.003 0.001 HISSW 56 PHE 0.032 0.001 PHESb 79 TYR 0.030 0.001 TYRSJ 19 ARG 0.010 0.000 ARGSI 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 409 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 194 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: SE 251 GLU cc_start: 0.7886 (tp30) cc_final: 0.7627 (tp30) REVERT: SG 23 ARG cc_start: 0.7395 (mmp-170) cc_final: 0.7161 (mmm160) REVERT: SH 87 ASP cc_start: 0.7564 (t70) cc_final: 0.7311 (t0) REVERT: SI 94 ASN cc_start: 0.8552 (m110) cc_final: 0.8137 (m-40) REVERT: SJ 19 TYR cc_start: 0.7928 (m-10) cc_final: 0.7571 (m-80) REVERT: SJ 41 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: SN 80 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8789 (mm) REVERT: SO 65 GLN cc_start: 0.8641 (mt0) cc_final: 0.8379 (mp10) REVERT: SW 114 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7648 (mm-30) REVERT: SX 94 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8550 (p0) REVERT: Se 49 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7251 (pp) REVERT: Se 56 MET cc_start: 0.5277 (pmm) cc_final: 0.4104 (ppp) REVERT: CA 260 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7303 (t80) REVERT: CA 264 ARG cc_start: 0.6563 (mtt180) cc_final: 0.6333 (mtt180) REVERT: CC 137 ILE cc_start: 0.8925 (mm) cc_final: 0.8486 (mt) REVERT: CC 688 PHE cc_start: 0.7527 (t80) cc_final: 0.7285 (t80) outliers start: 64 outliers final: 55 residues processed: 450 average time/residue: 0.5163 time to fit residues: 389.2659 Evaluate side-chains 462 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 401 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 52 THR Chi-restraints excluded: chain SB residue 105 PHE Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 146 GLN Chi-restraints excluded: chain SB residue 194 ASN Chi-restraints excluded: chain SC residue 86 VAL Chi-restraints excluded: chain SC residue 103 VAL Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 166 THR Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 106 LEU Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 179 VAL Chi-restraints excluded: chain SH residue 14 THR Chi-restraints excluded: chain SH residue 39 ARG Chi-restraints excluded: chain SH residue 50 ASP Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 129 LEU Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 76 THR Chi-restraints excluded: chain SJ residue 41 GLU Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 111 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 61 THR Chi-restraints excluded: chain SN residue 80 LEU Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SN residue 129 TYR Chi-restraints excluded: chain SO residue 13 VAL Chi-restraints excluded: chain SO residue 28 VAL Chi-restraints excluded: chain SO residue 46 MET Chi-restraints excluded: chain SO residue 74 VAL Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SX residue 36 THR Chi-restraints excluded: chain SX residue 94 ASN Chi-restraints excluded: chain SX residue 102 VAL Chi-restraints excluded: chain SY residue 25 VAL Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 42 ASN Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain Se residue 49 LEU Chi-restraints excluded: chain CA residue 100 MET Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CB residue 265 LYS Chi-restraints excluded: chain CC residue 114 MET Chi-restraints excluded: chain CC residue 165 VAL Chi-restraints excluded: chain CC residue 282 VAL Chi-restraints excluded: chain CC residue 300 ASP Chi-restraints excluded: chain CC residue 508 TYR Chi-restraints excluded: chain CC residue 655 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 281 optimal weight: 2.9990 chunk 376 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 326 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.123574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.083648 restraints weight = 120956.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082076 restraints weight = 114638.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082698 restraints weight = 77969.320| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 57255 Z= 0.409 Angle : 0.732 14.219 83579 Z= 0.366 Chirality : 0.042 0.289 10431 Planarity : 0.006 0.072 5821 Dihedral : 22.968 179.348 23519 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.93 % Favored : 90.97 % Rotamer: Outliers : 2.56 % Allowed : 20.04 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % Cis-general : 0.06 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.26 (0.15), residues: 3213 helix: 0.70 (0.17), residues: 948 sheet: -1.02 (0.20), residues: 658 loop : -1.71 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPCC 729 HIS 0.005 0.001 HISSE 8 PHE 0.033 0.002 PHESb 79 TYR 0.054 0.002 TYRSJ 19 ARG 0.015 0.001 ARGSH 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7812.22 seconds wall clock time: 141 minutes 0.92 seconds (8460.92 seconds total)