Starting phenix.real_space_refine on Sun Mar 10 14:43:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/03_2024/7wtp_32794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/03_2024/7wtp_32794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/03_2024/7wtp_32794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/03_2024/7wtp_32794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/03_2024/7wtp_32794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/03_2024/7wtp_32794.pdb" } resolution = 3.8 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 1255 5.49 5 S 53 5.16 5 C 28570 2.51 5 N 9632 2.21 5 O 13433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "SB PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB ASP 59": "OD1" <-> "OD2" Residue "SB GLU 122": "OE1" <-> "OE2" Residue "SB GLU 170": "OE1" <-> "OE2" Residue "SC PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 118": "OE1" <-> "OE2" Residue "SE TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG ASP 43": "OD1" <-> "OD2" Residue "SG PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 207": "OE1" <-> "OE2" Residue "SH PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH GLU 134": "OE1" <-> "OE2" Residue "SH ASP 155": "OD1" <-> "OD2" Residue "SH TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI GLU 70": "OE1" <-> "OE2" Residue "SI PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 41": "OE1" <-> "OE2" Residue "SJ GLU 72": "OE1" <-> "OE2" Residue "SJ ASP 157": "OD1" <-> "OD2" Residue "SL GLU 10": "OE1" <-> "OE2" Residue "SN TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 86": "OE1" <-> "OE2" Residue "SN TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO ASP 66": "OD1" <-> "OD2" Residue "SW ASP 9": "OD1" <-> "OD2" Residue "SW GLU 51": "OE1" <-> "OE2" Residue "SW ASP 85": "OD1" <-> "OD2" Residue "SW GLU 87": "OE1" <-> "OE2" Residue "SW GLU 115": "OE1" <-> "OE2" Residue "SX PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SX GLU 138": "OE1" <-> "OE2" Residue "SY PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 101": "OE1" <-> "OE2" Residue "Sb PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Se GLU 25": "OE1" <-> "OE2" Residue "CA ASP 179": "OD1" <-> "OD2" Residue "CA PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 217": "OE1" <-> "OE2" Residue "CA TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC GLU 213": "OE1" <-> "OE2" Residue "CC TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 234": "OD1" <-> "OD2" Residue "CC PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 573": "OD1" <-> "OD2" Residue "CC TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52944 Number of models: 1 Model: "" Number of chains: 20 Chain: "C2" Number of atoms: 26763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1255, 26763 Classifications: {'RNA': 1255} Modifications used: {'rna2p_pur': 103, 'rna2p_pyr': 92, 'rna3p_pur': 573, 'rna3p_pyr': 487} Link IDs: {'rna2p': 195, 'rna3p': 1059} Chain breaks: 8 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: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 313 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} 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: 5346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5346 Classifications: {'peptide': 661} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 628} 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} Time building chain proxies: 21.48, per 1000 atoms: 0.41 Number of scatterers: 52944 At special positions: 0 Unit cell: (169.44, 231.921, 214.977, 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 53 16.00 P 1255 15.00 O 13433 8.00 N 9632 7.00 C 28570 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: 21.54 Conformation dependent library (CDL) restraints added in 4.0 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6126 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 28 sheets defined 34.1% alpha, 19.9% beta 416 base pairs and 654 stacking pairs defined. Time for finding SS restraints: 17.11 Creating SS restraints... Processing helix chain 'SB' and resid 22 through 25 Processing helix chain 'SB' and resid 58 through 62 removed outlier: 3.663A pdb=" N LYSSB 62 " --> pdb=" O ASPSB 59 " (cutoff:3.500A) Processing helix chain 'SB' and resid 70 through 75 Processing helix chain 'SB' and resid 76 through 80 removed outlier: 3.672A pdb=" N HISSB 79 " --> pdb=" O SERSB 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SERSB 80 " --> pdb=" O GLUSB 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 76 through 80' Processing helix chain 'SB' and resid 106 through 114 Processing helix chain 'SB' and resid 157 through 178 removed outlier: 4.270A pdb=" N GLYSB 178 " --> pdb=" O LYSSB 174 " (cutoff:3.500A) Processing helix chain 'SB' and resid 180 through 189 Processing helix chain 'SB' and resid 191 through 201 removed outlier: 3.581A pdb=" N LYSSB 195 " --> pdb=" O GLUSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 232 removed outlier: 4.061A pdb=" N LEUSB 228 " --> pdb=" O ASPSB 224 " (cutoff:3.500A) Processing helix chain 'SC' and resid 39 through 47 removed outlier: 3.956A pdb=" N ALASC 47 " --> pdb=" O ARGSC 43 " (cutoff:3.500A) Processing helix chain 'SC' and resid 52 through 60 removed outlier: 4.282A pdb=" N ILESC 56 " --> pdb=" O THRSC 52 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HISSC 59 " --> pdb=" O GLUSC 55 " (cutoff:3.500A) Processing helix chain 'SC' and resid 66 through 73 removed outlier: 3.902A pdb=" N ASPSC 70 " --> pdb=" O PHESC 66 " (cutoff:3.500A) Processing helix chain 'SC' and resid 120 through 135 Processing helix chain 'SC' and resid 181 through 192 Processing helix chain 'SC' and resid 207 through 224 Processing helix chain 'SC' and resid 226 through 231 removed outlier: 4.200A pdb=" N ALASC 231 " --> pdb=" O ASNSC 228 " (cutoff:3.500A) Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 37 through 41 removed outlier: 3.863A pdb=" N SERSE 41 " --> pdb=" O LEUSE 38 " (cutoff:3.500A) Processing helix chain 'SE' and resid 43 through 51 removed outlier: 3.651A pdb=" N ARGSE 51 " --> pdb=" O PHESE 47 " (cutoff:3.500A) Processing helix chain 'SE' and resid 57 through 66 removed outlier: 3.767A 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 259 Processing helix chain 'SG' and resid 24 through 28 removed outlier: 3.513A pdb=" N PHESG 28 " --> pdb=" O ARGSG 25 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 152 through 157 removed outlier: 3.889A pdb=" N VALSG 157 " --> pdb=" O ARGSG 154 " (cutoff:3.500A) Processing helix chain 'SG' and resid 180 through 216 Processing helix chain 'SH' and resid 14 through 28 Processing helix chain 'SH' and resid 31 through 39 removed outlier: 3.978A pdb=" N ARGSH 39 " --> pdb=" O LYSSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 66 through 74 removed outlier: 3.965A pdb=" N PHESH 70 " --> pdb=" O SERSH 66 " (cutoff:3.500A) Processing helix chain 'SH' and resid 75 through 85 Processing helix chain 'SH' and resid 113 through 117 removed outlier: 3.793A pdb=" N THRSH 117 " --> pdb=" O ARGSH 114 " (cutoff:3.500A) Processing helix chain 'SH' and resid 118 through 130 removed outlier: 3.625A pdb=" N VALSH 130 " --> pdb=" O LEUSH 126 " (cutoff:3.500A) Processing helix chain 'SH' and resid 165 through 177 Processing helix chain 'SI' and resid 6 through 10 removed outlier: 4.317A pdb=" N HISSI 9 " --> pdb=" O ASPSI 6 " (cutoff:3.500A) Processing helix chain 'SI' and resid 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 88 through 94 removed outlier: 4.025A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 117 Processing helix chain 'SI' and resid 136 through 146 removed outlier: 3.722A pdb=" N GLUSI 140 " --> pdb=" O SERSI 136 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 163 removed outlier: 3.624A pdb=" N GLUSI 157 " --> pdb=" O GLUSI 153 " (cutoff:3.500A) Processing helix chain 'SI' and resid 172 through 177 Processing helix chain 'SI' and resid 186 through 200 removed outlier: 3.635A pdb=" N ALASI 190 " --> pdb=" O GLYSI 186 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 20 through 35 Processing helix chain 'SJ' and resid 39 through 61 Processing helix chain 'SJ' and resid 66 through 83 Processing helix chain 'SJ' and resid 92 through 97 removed outlier: 3.532A pdb=" N VALSJ 96 " --> pdb=" O LYSSJ 92 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 100 through 106 removed outlier: 3.600A pdb=" N PHESJ 104 " --> pdb=" O LYSSJ 100 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 108 through 116 removed outlier: 3.735A pdb=" N GLNSJ 112 " --> pdb=" O ARGSJ 108 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 121 through 131 Processing helix chain 'SJ' and resid 150 through 154 removed outlier: 3.982A pdb=" N GLUSJ 153 " --> pdb=" O LEUSJ 150 " (cutoff:3.500A) removed outlier: 4.016A 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 183 Processing helix chain 'SL' and resid 45 through 51 removed outlier: 3.684A pdb=" N ILESL 49 " --> pdb=" O PROSL 45 " (cutoff:3.500A) Processing helix chain 'SN' and resid 31 through 44 Processing helix chain 'SN' and resid 46 through 58 Processing helix chain 'SN' and resid 62 through 67 removed outlier: 3.550A pdb=" N ILESN 66 " --> pdb=" O GLNSN 62 " (cutoff:3.500A) Processing helix chain 'SN' and resid 70 through 78 Processing helix chain 'SN' and resid 85 through 105 Processing helix chain 'SN' and resid 108 through 131 Processing helix chain 'SN' and resid 145 through 151 Processing helix chain 'SO' and resid 56 through 75 Processing helix chain 'SO' and resid 95 through 107 Processing helix chain 'SW' and resid 5 through 21 removed outlier: 3.743A pdb=" N ASPSW 9 " --> pdb=" O SERSW 5 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 44 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 Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SX' and resid 11 through 25 Processing helix chain 'SX' and resid 27 through 34 removed outlier: 3.521A pdb=" N LEUSX 34 " --> pdb=" O LYSSX 30 " (cutoff:3.500A) Processing helix chain 'SX' and resid 132 through 137 Processing helix chain 'SY' and resid 36 through 48 Processing helix chain 'SY' and resid 51 through 53 No H-bonds generated for 'chain 'SY' and resid 51 through 53' Processing helix chain 'SY' and resid 78 through 85 removed outlier: 3.572A pdb=" N ALASY 82 " --> pdb=" O SERSY 78 " (cutoff:3.500A) Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 104 through 115 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 Processing helix chain 'CA' and resid 102 through 112 removed outlier: 3.574A pdb=" N THRCA 107 " --> pdb=" O PROCA 103 " (cutoff:3.500A) Proline residue: CA 108 - end of helix removed outlier: 3.927A pdb=" N ASNCA 111 " --> pdb=" O THRCA 107 " (cutoff:3.500A) Processing helix chain 'CA' and resid 112 through 123 removed outlier: 3.561A pdb=" N TYRCA 117 " --> pdb=" O TRPCA 113 " (cutoff:3.500A) Proline residue: CA 118 - end of helix Processing helix chain 'CA' and resid 148 through 163 removed outlier: 4.052A pdb=" N LEUCA 152 " --> pdb=" O ASPCA 148 " (cutoff:3.500A) Processing helix chain 'CA' and resid 167 through 177 Processing helix chain 'CA' and resid 187 through 191 Processing helix chain 'CA' and resid 194 through 207 removed outlier: 3.792A pdb=" N SERCA 199 " --> pdb=" O GLYCA 195 " (cutoff:3.500A) Processing helix chain 'CA' and resid 210 through 219 Processing helix chain 'CA' and resid 236 through 252 Processing helix chain 'CA' and resid 255 through 272 removed outlier: 3.565A pdb=" N VALCA 259 " --> pdb=" O PROCA 255 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLUCA 272 " --> pdb=" O SERCA 268 " (cutoff:3.500A) Processing helix chain 'CB' and resid 242 through 256 removed outlier: 3.580A pdb=" N GLUCB 251 " --> pdb=" O LEUCB 247 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEUCB 252 " --> pdb=" O ARGCB 248 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N METCB 253 " --> pdb=" O LYSCB 249 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSCB 254 " --> pdb=" O LYSCB 250 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARGCB 255 " --> pdb=" O GLUCB 251 " (cutoff:3.500A) Processing helix chain 'CC' and resid 23 through 32 removed outlier: 3.611A pdb=" N ARGCC 29 " --> pdb=" O GLYCC 25 " (cutoff:3.500A) Processing helix chain 'CC' and resid 50 through 70 Processing helix chain 'CC' and resid 96 through 107 removed outlier: 4.298A pdb=" N CYSCC 107 " --> pdb=" O LYSCC 103 " (cutoff:3.500A) Processing helix chain 'CC' and resid 111 through 118 Processing helix chain 'CC' and resid 144 through 155 Processing helix chain 'CC' and resid 172 through 184 removed outlier: 3.531A pdb=" N ILECC 176 " --> pdb=" O PHECC 172 " (cutoff:3.500A) Processing helix chain 'CC' and resid 194 through 197 Processing helix chain 'CC' and resid 201 through 220 removed outlier: 3.778A pdb=" N GLNCC 205 " --> pdb=" O LYSCC 201 " (cutoff:3.500A) Processing helix chain 'CC' and resid 231 through 245 removed outlier: 3.968A pdb=" N ALACC 235 " --> pdb=" O LYSCC 231 " (cutoff:3.500A) Processing helix chain 'CC' and resid 250 through 255 removed outlier: 3.605A pdb=" N ASNCC 255 " --> pdb=" O ASNCC 251 " (cutoff:3.500A) Processing helix chain 'CC' and resid 350 through 354 removed outlier: 3.578A pdb=" N GLYCC 353 " --> pdb=" O ALACC 350 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THRCC 354 " --> pdb=" O PROCC 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 350 through 354' Processing helix chain 'CC' and resid 462 through 482 Processing helix chain 'CC' and resid 522 through 528 removed outlier: 3.727A pdb=" N LEUCC 528 " --> pdb=" O TRPCC 525 " (cutoff:3.500A) Processing helix chain 'CC' and resid 534 through 548 Processing helix chain 'CC' and resid 566 through 569 Processing helix chain 'CC' and resid 723 through 730 removed outlier: 3.765A pdb=" N VALCC 727 " --> pdb=" O ARGCC 723 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SB' and resid 44 through 49 removed outlier: 8.707A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N THRSB 98 " --> pdb=" O ASPSB 31 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LYSSB 33 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N PHESB 100 " --> pdb=" O LYSSB 33 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASNSB 99 " --> pdb=" O VALSB 88 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VALSB 88 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HISSB 101 " --> pdb=" O LEUSB 86 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEUSB 86 " --> pdb=" O HISSB 101 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N METSB 103 " --> pdb=" O ILESB 84 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILESB 84 " --> pdb=" O METSB 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SB' and resid 44 through 49 removed outlier: 8.707A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N THRSB 98 " --> pdb=" O ASPSB 31 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LYSSB 33 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N PHESB 100 " --> pdb=" O LYSSB 33 " (cutoff:3.500A) removed outlier: 13.745A pdb=" N ASNSB 99 " --> pdb=" O LYSSB 219 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N LYSSB 219 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHESB 138 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VALSB 215 " --> pdb=" O ARGSB 136 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARGSB 136 " --> pdb=" O VALSB 215 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEUSB 217 " --> pdb=" O VALSB 134 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VALSB 134 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SC' and resid 78 through 89 removed outlier: 5.548A pdb=" N VALSC 80 " --> pdb=" O VALSC 103 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VALSC 103 " --> pdb=" O VALSC 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SC' and resid 158 through 161 Processing sheet with id=AA5, first strand: chain 'SE' and resid 75 through 76 removed outlier: 4.246A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HISSE 112 " --> pdb=" O ARGSE 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SE' and resid 146 through 148 Processing sheet with id=AA7, first strand: chain 'SE' and resid 217 through 221 removed outlier: 7.111A pdb=" N LEUSE 207 " --> pdb=" O LYSSE 198 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYSSE 198 " --> pdb=" O LEUSE 207 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HISSE 209 " --> pdb=" O VALSE 196 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYSSE 179 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLYSE 229 " --> pdb=" O LEUSE 180 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYRSE 182 " --> pdb=" O VALSE 227 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VALSE 227 " --> pdb=" O TYRSE 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'SG' and resid 12 through 17 removed outlier: 6.445A pdb=" N LYSSG 2 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEUSG 111 " --> pdb=" O LYSSG 2 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASNSG 4 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILESG 113 " --> pdb=" O ASNSG 4 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SERSG 6 " --> pdb=" O ILESG 113 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYSSG 115 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VALSG 112 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILESG 52 " --> pdb=" O VALSG 112 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VALSG 114 " --> pdb=" O PHESG 50 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHESG 50 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SG' and resid 63 through 64 Processing sheet with id=AB1, first strand: chain 'SG' and resid 160 through 163 Processing sheet with id=AB2, first strand: chain 'SH' and resid 45 through 50 Processing sheet with id=AB3, first strand: chain 'SH' and resid 180 through 184 removed outlier: 6.846A pdb=" N LYSSH 148 " --> pdb=" O GLNSH 180 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VALSH 182 " --> pdb=" O LYSSH 148 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLNSH 150 " --> pdb=" O VALSH 182 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLUSH 184 " --> pdb=" O GLNSH 150 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VALSH 152 " --> pdb=" O GLUSH 184 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYSSH 138 " --> pdb=" O ASPSW 54 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHESW 50 " --> pdb=" O TYRSH 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SI' and resid 3 through 4 removed outlier: 3.720A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SI' and resid 42 through 47 removed outlier: 6.740A pdb=" N HISSI 44 " --> pdb=" O ALASI 57 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALASI 57 " --> pdb=" O HISSI 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VALSI 46 " --> pdb=" O TYRSI 55 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYRSI 55 " --> pdb=" O VALSI 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 72 through 76 removed outlier: 6.837A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 181 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILESI 183 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SERSI 66 " --> pdb=" O ILESI 183 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILESI 101 " --> pdb=" O VALSI 82 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASPSI 105 " --> pdb=" O ILESI 78 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILESI 78 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SJ' and resid 139 through 141 removed outlier: 4.509A pdb=" N ILESJ 134 " --> pdb=" O VALSJ 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SL' and resid 70 through 77 removed outlier: 17.007A pdb=" N LEUSL 71 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 15.462A pdb=" N LEUSL 91 " --> pdb=" O LEUSL 71 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLYSL 73 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALASL 89 " --> pdb=" O GLYSL 73 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VALSL 75 " --> pdb=" O ARGSL 87 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARGSL 87 " --> pdb=" O VALSL 75 " (cutoff:3.500A) removed outlier: 10.784A pdb=" N PHESL 137 " --> pdb=" O ASNSL 106 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VALSL 139 " --> pdb=" O PROSL 108 " (cutoff:3.500A) removed outlier: 7.292A 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: 5.488A pdb=" N VALSL 139 " --> pdb=" O GLYSL 126 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLYSL 126 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILESL 122 " --> pdb=" O SERSL 143 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASPSL 121 " --> pdb=" O VALSL 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SO' and resid 38 through 43 removed outlier: 6.569A pdb=" N VALSO 30 " --> pdb=" O ILESO 39 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARGSO 41 " --> pdb=" O VALSO 28 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VALSO 28 " --> pdb=" O ARGSO 41 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SO' and resid 38 through 43 removed outlier: 6.569A pdb=" N VALSO 30 " --> pdb=" O ILESO 39 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARGSO 41 " --> pdb=" O VALSO 28 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VALSO 28 " --> pdb=" O ARGSO 41 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLUSO 116 " --> pdb=" O VALSO 79 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VALSO 81 " --> pdb=" O GLUSO 116 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SW' and resid 71 through 74 removed outlier: 6.847A pdb=" N ILESW 103 " --> pdb=" O LEUSW 126 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHESW 128 " --> pdb=" O TYRSW 101 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYRSW 101 " --> pdb=" O PHESW 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SX' and resid 82 through 84 removed outlier: 6.129A pdb=" N GLNSX 75 " --> pdb=" O VALSX 53 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VALSX 53 " --> pdb=" O GLNSX 75 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEUSX 103 " --> pdb=" O VALSX 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SY' and resid 6 through 15 removed outlier: 5.810A pdb=" N ILESY 7 " --> pdb=" O LEUSY 28 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEUSY 28 " --> pdb=" O ILESY 7 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THRSY 9 " --> pdb=" O ASPSY 26 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASPSY 26 " --> pdb=" O THRSY 9 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYSSY 11 " --> pdb=" O VALSY 24 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VALSY 24 " --> pdb=" O LYSSY 11 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLYSY 67 " --> pdb=" O HISSY 29 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VALSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHESY 60 " --> pdb=" O VALSY 70 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHESY 72 " --> pdb=" O PHESY 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Sb' and resid 43 through 47 Processing sheet with id=AC6, first strand: chain 'CA' and resid 95 through 100 Processing sheet with id=AC7, first strand: chain 'CA' and resid 181 through 186 Processing sheet with id=AC8, first strand: chain 'CC' and resid 123 through 128 removed outlier: 6.384A pdb=" N ILECC 86 " --> pdb=" O ILECC 138 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VALCC 158 " --> pdb=" O ILECC 189 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VALCC 191 " --> pdb=" O VALCC 158 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHECC 160 " --> pdb=" O VALCC 191 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'CC' and resid 336 through 338 removed outlier: 11.924A pdb=" N PHECC 301 " --> pdb=" O PROCC 564 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEUCC 303 " --> pdb=" O ARGCC 562 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARGCC 562 " --> pdb=" O LEUCC 303 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARGCC 556 " --> pdb=" O ILECC 309 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLUCC 279 " --> pdb=" O ASPCC 262 " (cutoff:3.500A) Processing sheet with id=AD1, 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 755 through 759 removed outlier: 6.899A pdb=" N LYSCC 756 " --> pdb=" O LYSCC 746 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HISCC 640 " --> pdb=" O ALACC 698 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARGCC 700 " --> pdb=" O HISCC 640 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYRCC 642 " --> pdb=" O ARGCC 700 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N ILECC 702 " --> pdb=" O TYRCC 642 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYSCC 641 " --> pdb=" O GLNCC 631 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLNCC 631 " --> pdb=" O LYSCC 641 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHECC 629 " --> pdb=" O GLUCC 643 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASNCC 595 " --> pdb=" O LEUCC 689 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THRCC 687 " --> pdb=" O SERCC 597 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 2898 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 999 hydrogen bonds 1558 hydrogen bond angles 0 basepair planarities 416 basepair parallelities 654 stacking parallelities Total time for adding SS restraints: 31.71 Time building geometry restraints manager: 23.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 5444 1.25 - 1.39: 16137 1.39 - 1.53: 31500 1.53 - 1.67: 3428 1.67 - 1.82: 84 Bond restraints: 56593 Sorted by residual: bond pdb=" CG PROSC 37 " pdb=" CD PROSC 37 " ideal model delta sigma weight residual 1.503 1.111 0.392 3.40e-02 8.65e+02 1.33e+02 bond pdb=" CG PROSC 62 " pdb=" CD PROSC 62 " ideal model delta sigma weight residual 1.503 1.204 0.299 3.40e-02 8.65e+02 7.76e+01 bond pdb=" N PROSC 37 " pdb=" CD PROSC 37 " ideal model delta sigma weight residual 1.473 1.552 -0.079 1.40e-02 5.10e+03 3.22e+01 bond pdb=" N PROSC 62 " pdb=" CD PROSC 62 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" C LEUSN 45 " pdb=" N THRSN 46 " ideal model delta sigma weight residual 1.330 1.277 0.053 1.47e-02 4.63e+03 1.28e+01 ... (remaining 56588 not shown) Histogram of bond angle deviations from ideal: 83.08 - 93.92: 4 93.92 - 104.76: 5898 104.76 - 115.60: 39562 115.60 - 126.44: 33060 126.44 - 137.27: 3946 Bond angle restraints: 82470 Sorted by residual: angle pdb=" N PROSC 37 " pdb=" CD PROSC 37 " pdb=" CG PROSC 37 " ideal model delta sigma weight residual 103.20 83.08 20.12 1.50e+00 4.44e-01 1.80e+02 angle pdb=" CA PROSC 37 " pdb=" N PROSC 37 " pdb=" CD PROSC 37 " ideal model delta sigma weight residual 112.00 95.14 16.86 1.40e+00 5.10e-01 1.45e+02 angle pdb=" N PROSC 62 " pdb=" CD PROSC 62 " pdb=" CG PROSC 62 " ideal model delta sigma weight residual 103.20 86.63 16.57 1.50e+00 4.44e-01 1.22e+02 angle pdb=" CA PROSC 62 " pdb=" N PROSC 62 " pdb=" CD PROSC 62 " ideal model delta sigma weight residual 112.00 97.70 14.30 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PROSC 37 " pdb=" CB PROSC 37 " pdb=" CG PROSC 37 " ideal model delta sigma weight residual 104.50 88.46 16.04 1.90e+00 2.77e-01 7.13e+01 ... (remaining 82465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 32177 35.89 - 71.78: 3094 71.78 - 107.66: 321 107.66 - 143.55: 10 143.55 - 179.44: 19 Dihedral angle restraints: 35621 sinusoidal: 26134 harmonic: 9487 Sorted by residual: dihedral pdb=" CA LEUSH 9 " pdb=" C LEUSH 9 " pdb=" N SERSH 10 " pdb=" CA SERSH 10 " ideal model delta harmonic sigma weight residual 180.00 127.31 52.69 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA VALSH 64 " pdb=" C VALSH 64 " pdb=" N PROSH 65 " pdb=" CA PROSH 65 " ideal model delta harmonic sigma weight residual 180.00 133.17 46.83 0 5.00e+00 4.00e-02 8.77e+01 dihedral pdb=" O4' UC2 864 " pdb=" C1' UC2 864 " pdb=" N1 UC2 864 " pdb=" C2 UC2 864 " ideal model delta sinusoidal sigma weight residual 200.00 31.88 168.12 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 35618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 9140 0.079 - 0.158: 993 0.158 - 0.237: 97 0.237 - 0.316: 17 0.316 - 0.395: 7 Chirality restraints: 10254 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 2.25 0.39 2.00e-01 2.50e+01 3.89e+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 2.08 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C1' CC2 191 " pdb=" O4' CC2 191 " pdb=" C2' CC2 191 " pdb=" N1 CC2 191 " both_signs ideal model delta sigma weight residual False 2.45 2.07 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 10251 not shown) Planarity restraints: 5849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALSC 36 " -0.116 5.00e-02 4.00e+02 1.59e-01 4.04e+01 pdb=" N PROSC 37 " 0.274 5.00e-02 4.00e+02 pdb=" CA PROSC 37 " -0.081 5.00e-02 4.00e+02 pdb=" CD PROSC 37 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GC21141 " -0.037 2.00e-02 2.50e+03 3.28e-02 3.23e+01 pdb=" N9 GC21141 " 0.026 2.00e-02 2.50e+03 pdb=" C8 GC21141 " 0.001 2.00e-02 2.50e+03 pdb=" N7 GC21141 " -0.007 2.00e-02 2.50e+03 pdb=" C5 GC21141 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GC21141 " 0.021 2.00e-02 2.50e+03 pdb=" O6 GC21141 " -0.031 2.00e-02 2.50e+03 pdb=" N1 GC21141 " -0.009 2.00e-02 2.50e+03 pdb=" C2 GC21141 " 0.080 2.00e-02 2.50e+03 pdb=" N2 GC21141 " -0.054 2.00e-02 2.50e+03 pdb=" N3 GC21141 " 0.005 2.00e-02 2.50e+03 pdb=" C4 GC21141 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CC21121 " 0.010 2.00e-02 2.50e+03 3.52e-02 2.79e+01 pdb=" N1 CC21121 " 0.007 2.00e-02 2.50e+03 pdb=" C2 CC21121 " -0.087 2.00e-02 2.50e+03 pdb=" O2 CC21121 " 0.047 2.00e-02 2.50e+03 pdb=" N3 CC21121 " 0.009 2.00e-02 2.50e+03 pdb=" C4 CC21121 " -0.021 2.00e-02 2.50e+03 pdb=" N4 CC21121 " 0.022 2.00e-02 2.50e+03 pdb=" C5 CC21121 " 0.009 2.00e-02 2.50e+03 pdb=" C6 CC21121 " 0.004 2.00e-02 2.50e+03 ... (remaining 5846 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 2455 2.66 - 3.22: 45187 3.22 - 3.78: 99312 3.78 - 4.34: 126766 4.34 - 4.90: 180044 Nonbonded interactions: 453764 Sorted by model distance: nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.103 3.040 nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.116 3.040 nonbonded pdb=" N THRSb 61 " pdb="ZN ZNSb 101 " model vdw 2.142 2.310 nonbonded pdb=" O2 UC2 231 " pdb=" O6 GC2 234 " model vdw 2.181 2.432 nonbonded pdb=" N ILESb 62 " pdb="ZN ZNSb 101 " model vdw 2.189 2.310 ... (remaining 453759 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: 1.980 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: 10.970 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 136.050 Find NCS groups from input model: 0.990 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.007 0.392 56593 Z= 0.463 Angle : 0.965 20.116 82470 Z= 0.489 Chirality : 0.051 0.395 10254 Planarity : 0.008 0.159 5849 Dihedral : 22.218 179.440 29495 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.73 % Favored : 91.14 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 2.10 % 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: -2.27 (0.14), residues: 3252 helix: -0.71 (0.15), residues: 991 sheet: -1.31 (0.19), residues: 711 loop : -2.11 (0.14), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRPSC 144 HIS 0.023 0.002 HISSE 197 PHE 0.051 0.003 PHESX 95 TYR 0.043 0.003 TYRSY 94 ARG 0.022 0.001 ARGSe 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 478 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SH 166 LEU cc_start: 0.8749 (mm) cc_final: 0.8507 (mm) REVERT: SJ 139 GLN cc_start: 0.8011 (tp40) cc_final: 0.7714 (tp40) REVERT: Sb 8 LEU cc_start: 0.9279 (mt) cc_final: 0.8995 (mt) REVERT: Sb 79 PHE cc_start: 0.8787 (p90) cc_final: 0.8317 (p90) REVERT: CA 153 GLN cc_start: 0.8732 (tp40) cc_final: 0.8476 (tp40) REVERT: CA 216 ILE cc_start: 0.8716 (mm) cc_final: 0.8512 (mm) REVERT: CC 114 MET cc_start: 0.0661 (mtm) cc_final: -0.0694 (mmt) REVERT: CC 160 PHE cc_start: 0.8161 (m-80) cc_final: 0.7921 (m-80) outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.5195 time to fit residues: 417.6308 Evaluate side-chains 359 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 3.050 ------------------------------------------------------------------------------- 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: 5.9990 chunk 338 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 115 optimal weight: 50.0000 chunk 228 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 349 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 405 optimal weight: 50.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 199 GLN SC 201 ASN ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 42 GLN ** SH 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 35 ASN SL 110 HIS SL 138 ASN SW 15 ASN SX 22 ASN Sb 51 GLN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 218 ASN CA 239 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 56593 Z= 0.179 Angle : 0.628 9.359 82470 Z= 0.320 Chirality : 0.038 0.314 10254 Planarity : 0.005 0.075 5849 Dihedral : 23.046 179.165 22852 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.65 % Rotamer: Outliers : 1.32 % Allowed : 10.03 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 2.10 % Twisted General : 0.06 % 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: -1.69 (0.14), residues: 3252 helix: 0.09 (0.16), residues: 1014 sheet: -0.96 (0.20), residues: 644 loop : -2.01 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPSB 29 HIS 0.005 0.001 HISSW 56 PHE 0.031 0.002 PHESX 86 TYR 0.019 0.001 TYRSJ 19 ARG 0.005 0.000 ARGSW 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 420 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 92 GLN cc_start: 0.7763 (pm20) cc_final: 0.7381 (pm20) REVERT: SB 122 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7634 (tm-30) REVERT: SB 207 LEU cc_start: 0.8637 (mp) cc_final: 0.8311 (mp) REVERT: SC 81 MET cc_start: 0.7880 (mmm) cc_final: 0.7610 (mmm) REVERT: SG 156 PHE cc_start: 0.8023 (m-80) cc_final: 0.7642 (t80) REVERT: SH 43 PHE cc_start: 0.6488 (p90) cc_final: 0.6250 (p90) REVERT: SI 76 THR cc_start: 0.9149 (t) cc_final: 0.8852 (p) REVERT: SJ 42 ILE cc_start: 0.8826 (mt) cc_final: 0.8572 (mt) REVERT: SO 38 THR cc_start: 0.9101 (p) cc_final: 0.8871 (p) REVERT: SO 46 MET cc_start: 0.8357 (ptm) cc_final: 0.8051 (ptm) REVERT: SW 49 GLU cc_start: 0.8436 (pp20) cc_final: 0.8065 (pp20) REVERT: SW 51 GLU cc_start: 0.7290 (tt0) cc_final: 0.7048 (tt0) REVERT: SX 3 LYS cc_start: 0.7406 (mtpp) cc_final: 0.7143 (mtpt) REVERT: SY 86 GLU cc_start: 0.8396 (tp30) cc_final: 0.7635 (tp30) REVERT: Sb 8 LEU cc_start: 0.9173 (mt) cc_final: 0.8958 (mt) REVERT: CB 245 PHE cc_start: 0.7947 (m-80) cc_final: 0.7691 (m-80) REVERT: CC 114 MET cc_start: 0.0948 (mtm) cc_final: -0.0528 (mmt) REVERT: CC 160 PHE cc_start: 0.8137 (m-80) cc_final: 0.7920 (m-80) outliers start: 37 outliers final: 27 residues processed: 433 average time/residue: 0.4999 time to fit residues: 365.2869 Evaluate side-chains 387 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 360 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SE residue 116 ASP Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 56 ASN Chi-restraints excluded: chain SG residue 89 ASP Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SI residue 189 LEU Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 77 ILE Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 239 HIS Chi-restraints excluded: chain CC residue 204 PHE Chi-restraints excluded: chain CC residue 249 SER Chi-restraints excluded: chain CC residue 482 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 225 optimal weight: 6.9990 chunk 125 optimal weight: 0.0270 chunk 337 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 438 optimal weight: 9.9990 chunk 361 optimal weight: 2.9990 chunk 402 optimal weight: 0.0770 chunk 138 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 201 ASN ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 13 GLN SJ 139 GLN ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 113 ASN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 56593 Z= 0.286 Angle : 0.661 13.394 82470 Z= 0.334 Chirality : 0.039 0.330 10254 Planarity : 0.005 0.077 5849 Dihedral : 22.974 179.090 22852 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.46 % Favored : 91.48 % Rotamer: Outliers : 2.13 % Allowed : 13.73 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -1.56 (0.14), residues: 3252 helix: 0.32 (0.16), residues: 1025 sheet: -0.97 (0.20), residues: 671 loop : -2.02 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPSC 144 HIS 0.006 0.001 HISCA 239 PHE 0.024 0.002 PHESX 86 TYR 0.018 0.001 TYRSX 29 ARG 0.007 0.000 ARGSG 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 386 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 92 GLN cc_start: 0.7711 (pm20) cc_final: 0.7406 (pm20) REVERT: SB 122 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7682 (tm-30) REVERT: SC 81 MET cc_start: 0.7912 (mmm) cc_final: 0.7667 (mmm) REVERT: SG 156 PHE cc_start: 0.8096 (m-80) cc_final: 0.7728 (t80) REVERT: SH 9 LEU cc_start: 0.6448 (pt) cc_final: 0.6170 (pt) REVERT: SH 43 PHE cc_start: 0.6605 (p90) cc_final: 0.6243 (p90) REVERT: SI 76 THR cc_start: 0.9169 (t) cc_final: 0.8853 (p) REVERT: SW 51 GLU cc_start: 0.7361 (tt0) cc_final: 0.7155 (tt0) REVERT: SX 3 LYS cc_start: 0.7352 (mtpp) cc_final: 0.7018 (mtpt) REVERT: SY 86 GLU cc_start: 0.8505 (tp30) cc_final: 0.7775 (tp30) REVERT: Sb 7 LEU cc_start: 0.9181 (mt) cc_final: 0.8928 (mp) REVERT: Sb 8 LEU cc_start: 0.9207 (mt) cc_final: 0.8963 (mt) REVERT: Sb 43 ILE cc_start: 0.9313 (mp) cc_final: 0.9062 (tp) REVERT: CB 245 PHE cc_start: 0.7820 (m-80) cc_final: 0.7597 (m-80) REVERT: CC 114 MET cc_start: 0.1020 (mtm) cc_final: -0.0489 (mmt) REVERT: CC 160 PHE cc_start: 0.8181 (m-80) cc_final: 0.7894 (m-80) outliers start: 60 outliers final: 37 residues processed: 422 average time/residue: 0.4973 time to fit residues: 358.9206 Evaluate side-chains 396 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 359 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 124 ASN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SE residue 116 ASP Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 56 ASN Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 89 THR Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 58 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain Sb residue 78 SER Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 246 SER Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 204 PHE Chi-restraints excluded: chain CC residue 249 SER Chi-restraints excluded: chain CC residue 482 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 400 optimal weight: 0.0570 chunk 305 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 407 optimal weight: 8.9990 chunk 431 optimal weight: 50.0000 chunk 212 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 116 optimal weight: 40.0000 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 201 ASN ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 13 GLN SH 74 GLN ** SO 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 56593 Z= 0.265 Angle : 0.641 14.216 82470 Z= 0.325 Chirality : 0.038 0.330 10254 Planarity : 0.005 0.078 5849 Dihedral : 22.928 178.586 22852 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.93 % Favored : 92.00 % Rotamer: Outliers : 2.88 % Allowed : 15.26 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -1.43 (0.15), residues: 3252 helix: 0.53 (0.16), residues: 1020 sheet: -0.93 (0.20), residues: 665 loop : -1.99 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPSC 144 HIS 0.005 0.001 HISSB 211 PHE 0.043 0.002 PHESH 24 TYR 0.018 0.001 TYRCA 117 ARG 0.009 0.000 ARGSI 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 381 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 92 GLN cc_start: 0.7749 (pm20) cc_final: 0.7501 (pm20) REVERT: SB 122 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7816 (tm-30) REVERT: SB 207 LEU cc_start: 0.8580 (mp) cc_final: 0.8362 (mp) REVERT: SC 81 MET cc_start: 0.7969 (mmm) cc_final: 0.7647 (mmm) REVERT: SG 156 PHE cc_start: 0.8111 (m-80) cc_final: 0.7768 (t80) REVERT: SH 9 LEU cc_start: 0.6502 (pt) cc_final: 0.6190 (pt) REVERT: SH 158 ASP cc_start: 0.7367 (t0) cc_final: 0.7053 (t70) REVERT: SI 29 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8035 (pt) REVERT: SI 76 THR cc_start: 0.9144 (t) cc_final: 0.8809 (p) REVERT: SJ 58 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7200 (p0) REVERT: SJ 139 GLN cc_start: 0.7965 (tp40) cc_final: 0.7736 (tp-100) REVERT: SO 36 LYS cc_start: 0.7340 (tmtt) cc_final: 0.6706 (tmtt) REVERT: SW 51 GLU cc_start: 0.7362 (tt0) cc_final: 0.7152 (tt0) REVERT: SX 3 LYS cc_start: 0.7248 (mtpp) cc_final: 0.6939 (mtpt) REVERT: SX 94 ASN cc_start: 0.9179 (p0) cc_final: 0.8869 (p0) REVERT: SY 86 GLU cc_start: 0.8537 (tp30) cc_final: 0.8009 (tp30) REVERT: Sb 7 LEU cc_start: 0.9158 (mt) cc_final: 0.8949 (mp) REVERT: Sb 8 LEU cc_start: 0.9186 (mt) cc_final: 0.8910 (mt) REVERT: Sb 43 ILE cc_start: 0.9294 (mp) cc_final: 0.9056 (tp) REVERT: CB 245 PHE cc_start: 0.7802 (m-80) cc_final: 0.7560 (m-80) REVERT: CC 114 MET cc_start: 0.1249 (mtm) cc_final: -0.0612 (mmt) outliers start: 81 outliers final: 56 residues processed: 429 average time/residue: 0.4846 time to fit residues: 359.3733 Evaluate side-chains 407 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 349 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 124 ASN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 116 ASP Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SG residue 32 ILE Chi-restraints excluded: chain SG residue 41 VAL Chi-restraints excluded: chain SG residue 56 ASN Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 101 ILE Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 58 ASP Chi-restraints excluded: chain SJ residue 103 ASP Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 79 VAL Chi-restraints excluded: chain SO residue 89 THR Chi-restraints excluded: chain SO residue 115 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 58 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 77 ILE Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 78 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 183 GLU Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 246 SER Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 204 PHE Chi-restraints excluded: chain CC residue 229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 359 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 367 optimal weight: 0.3980 chunk 297 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 386 optimal weight: 30.0000 chunk 108 optimal weight: 40.0000 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN SB 220 GLN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 201 ASN ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 170 GLN ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 26 GLN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 56593 Z= 0.387 Angle : 0.723 14.369 82470 Z= 0.363 Chirality : 0.042 0.350 10254 Planarity : 0.005 0.083 5849 Dihedral : 22.962 179.767 22852 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.16 % Favored : 90.77 % Rotamer: Outliers : 3.06 % Allowed : 17.15 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -1.52 (0.15), residues: 3252 helix: 0.47 (0.16), residues: 1020 sheet: -1.12 (0.20), residues: 679 loop : -1.99 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPSC 144 HIS 0.008 0.001 HISSB 211 PHE 0.021 0.002 PHESE 226 TYR 0.021 0.002 TYRSX 29 ARG 0.011 0.001 ARGSI 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 373 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 122 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7710 (tm-30) REVERT: SE 195 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8635 (mt) REVERT: SG 156 PHE cc_start: 0.8189 (m-80) cc_final: 0.7770 (t80) REVERT: SH 158 ASP cc_start: 0.7294 (t0) cc_final: 0.6971 (t70) REVERT: SI 29 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8083 (pt) REVERT: SO 46 MET cc_start: 0.8502 (ptm) cc_final: 0.8210 (ptm) REVERT: SX 94 ASN cc_start: 0.9193 (p0) cc_final: 0.8928 (p0) REVERT: SY 86 GLU cc_start: 0.8529 (tp30) cc_final: 0.7954 (tp30) REVERT: Sb 7 LEU cc_start: 0.9195 (mt) cc_final: 0.8976 (mp) REVERT: Sb 8 LEU cc_start: 0.9220 (mt) cc_final: 0.8935 (mt) REVERT: CA 214 PHE cc_start: 0.8262 (t80) cc_final: 0.7800 (t80) REVERT: CB 245 PHE cc_start: 0.7847 (m-80) cc_final: 0.7572 (m-80) REVERT: CC 114 MET cc_start: 0.1257 (mtm) cc_final: -0.0611 (mmt) outliers start: 86 outliers final: 67 residues processed: 430 average time/residue: 0.4983 time to fit residues: 366.9961 Evaluate side-chains 412 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 343 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 68 VAL Chi-restraints excluded: chain SB residue 137 ILE Chi-restraints excluded: chain SB residue 203 ASP Chi-restraints excluded: chain SB residue 208 GLN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SC residue 167 VAL Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 146 THR Chi-restraints excluded: chain SE residue 195 ILE Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SE residue 256 ARG Chi-restraints excluded: chain SG residue 32 ILE Chi-restraints excluded: chain SG residue 41 VAL Chi-restraints excluded: chain SG residue 56 ASN Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 101 ILE Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 58 ASP Chi-restraints excluded: chain SJ residue 103 ASP Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 123 VAL Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SN residue 138 ASN Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 79 VAL Chi-restraints excluded: chain SO residue 89 THR Chi-restraints excluded: chain SO residue 115 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 58 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 75 VAL Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 246 SER Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 102 TYR Chi-restraints excluded: chain CC residue 204 PHE Chi-restraints excluded: chain CC residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 145 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 431 optimal weight: 40.0000 chunk 358 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN ** SC 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 201 ASN ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 56593 Z= 0.237 Angle : 0.634 14.580 82470 Z= 0.321 Chirality : 0.038 0.326 10254 Planarity : 0.005 0.071 5849 Dihedral : 22.885 178.296 22852 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 3.02 % Allowed : 18.78 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: 3252 helix: 0.58 (0.17), residues: 1018 sheet: -1.03 (0.21), residues: 653 loop : -1.85 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPSC 144 HIS 0.004 0.001 HISSB 211 PHE 0.037 0.001 PHECC 482 TYR 0.014 0.001 TYRSX 29 ARG 0.011 0.000 ARGSI 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 388 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 122 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7680 (tm-30) REVERT: SC 81 MET cc_start: 0.7680 (mmm) cc_final: 0.7322 (mmm) REVERT: SE 195 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8558 (mt) REVERT: SG 156 PHE cc_start: 0.8138 (m-80) cc_final: 0.7752 (t80) REVERT: SH 158 ASP cc_start: 0.7332 (t0) cc_final: 0.7039 (t70) REVERT: SI 29 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.7992 (pt) REVERT: SI 76 THR cc_start: 0.9128 (t) cc_final: 0.8845 (p) REVERT: SJ 104 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7619 (t80) REVERT: SN 35 GLU cc_start: 0.8338 (mp0) cc_final: 0.8086 (mp0) REVERT: SO 46 MET cc_start: 0.8405 (ptm) cc_final: 0.8015 (ptm) REVERT: SX 3 LYS cc_start: 0.7456 (mttt) cc_final: 0.6945 (mtpt) REVERT: SX 94 ASN cc_start: 0.9219 (p0) cc_final: 0.8916 (p0) REVERT: SY 86 GLU cc_start: 0.8597 (tp30) cc_final: 0.8075 (tp30) REVERT: Sb 7 LEU cc_start: 0.9130 (mt) cc_final: 0.8928 (mp) REVERT: Sb 8 LEU cc_start: 0.9185 (mt) cc_final: 0.8889 (mt) REVERT: CB 245 PHE cc_start: 0.7815 (m-80) cc_final: 0.7531 (m-80) REVERT: CC 114 MET cc_start: 0.1272 (mtm) cc_final: -0.0680 (mmt) outliers start: 85 outliers final: 65 residues processed: 439 average time/residue: 0.4876 time to fit residues: 367.1980 Evaluate side-chains 422 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 354 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 47 LEU Chi-restraints excluded: chain SB residue 68 VAL Chi-restraints excluded: chain SB residue 119 THR Chi-restraints excluded: chain SB residue 124 ASN Chi-restraints excluded: chain SB residue 203 ASP Chi-restraints excluded: chain SB residue 208 GLN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SC residue 167 VAL Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 173 ILE Chi-restraints excluded: chain SE residue 195 ILE Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SE residue 256 ARG Chi-restraints excluded: chain SG residue 32 ILE Chi-restraints excluded: chain SG residue 41 VAL Chi-restraints excluded: chain SG residue 56 ASN Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 101 ILE Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 58 ASP Chi-restraints excluded: chain SJ residue 104 PHE Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 23 PHE Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 79 VAL Chi-restraints excluded: chain SO residue 115 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 77 ILE Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 102 TYR Chi-restraints excluded: chain CC residue 204 PHE Chi-restraints excluded: chain CC residue 229 LEU Chi-restraints excluded: chain CC residue 720 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 416 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 315 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 363 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 chunk 429 optimal weight: 30.0000 chunk 269 optimal weight: 7.9990 chunk 262 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN SB 153 HIS ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 11 GLN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 56593 Z= 0.247 Angle : 0.641 14.366 82470 Z= 0.323 Chirality : 0.038 0.326 10254 Planarity : 0.005 0.065 5849 Dihedral : 22.832 178.326 22852 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.73 % Favored : 91.21 % Rotamer: Outliers : 3.20 % Allowed : 19.60 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -1.31 (0.15), residues: 3252 helix: 0.62 (0.17), residues: 1020 sheet: -1.02 (0.21), residues: 652 loop : -1.83 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPSC 144 HIS 0.004 0.001 HISSW 113 PHE 0.043 0.001 PHESH 24 TYR 0.015 0.001 TYRSJ 19 ARG 0.014 0.000 ARGSI 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 380 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 41 ARG cc_start: 0.7028 (ptm160) cc_final: 0.6759 (ttt90) REVERT: SB 72 ASP cc_start: 0.8766 (t0) cc_final: 0.8551 (t0) REVERT: SB 144 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7657 (ptt90) REVERT: SC 81 MET cc_start: 0.7887 (mmm) cc_final: 0.7542 (mmm) REVERT: SG 156 PHE cc_start: 0.8139 (m-80) cc_final: 0.7766 (t80) REVERT: SH 158 ASP cc_start: 0.7314 (t0) cc_final: 0.7086 (t70) REVERT: SI 29 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8023 (pt) REVERT: SJ 104 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7608 (t80) REVERT: SO 46 MET cc_start: 0.8353 (ptm) cc_final: 0.8100 (ptm) REVERT: SX 3 LYS cc_start: 0.7506 (mttt) cc_final: 0.6980 (mtpt) REVERT: SX 94 ASN cc_start: 0.9210 (p0) cc_final: 0.8926 (p0) REVERT: SY 86 GLU cc_start: 0.8569 (tp30) cc_final: 0.8104 (tp30) REVERT: Sb 7 LEU cc_start: 0.9122 (mt) cc_final: 0.8917 (mp) REVERT: Sb 8 LEU cc_start: 0.9184 (mt) cc_final: 0.8861 (mt) REVERT: CB 245 PHE cc_start: 0.7831 (m-80) cc_final: 0.7535 (m-80) outliers start: 90 outliers final: 72 residues processed: 431 average time/residue: 0.4922 time to fit residues: 363.0530 Evaluate side-chains 435 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 360 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 68 VAL Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 119 THR Chi-restraints excluded: chain SB residue 137 ILE Chi-restraints excluded: chain SB residue 140 ILE Chi-restraints excluded: chain SB residue 144 ARG Chi-restraints excluded: chain SB residue 203 ASP Chi-restraints excluded: chain SB residue 208 GLN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 167 VAL Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 146 THR Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SE residue 256 ARG Chi-restraints excluded: chain SG residue 32 ILE Chi-restraints excluded: chain SG residue 41 VAL Chi-restraints excluded: chain SG residue 56 ASN Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 58 ASP Chi-restraints excluded: chain SJ residue 94 ASP Chi-restraints excluded: chain SJ residue 104 PHE Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 23 PHE Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 89 THR Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SO residue 115 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SW residue 110 ILE Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 77 ILE Chi-restraints excluded: chain SX residue 79 ASN Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 75 VAL Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 102 TYR Chi-restraints excluded: chain CC residue 204 PHE Chi-restraints excluded: chain CC residue 216 PHE Chi-restraints excluded: chain CC residue 229 LEU Chi-restraints excluded: chain CC residue 620 VAL Chi-restraints excluded: chain CC residue 720 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 265 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 256 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 292 optimal weight: 7.9990 chunk 212 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 337 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 108 GLN SH 122 HIS SI 103 GLN ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56593 Z= 0.205 Angle : 0.616 14.605 82470 Z= 0.310 Chirality : 0.037 0.318 10254 Planarity : 0.005 0.075 5849 Dihedral : 22.741 178.456 22852 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.87 % Favored : 92.07 % Rotamer: Outliers : 3.02 % Allowed : 20.78 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3252 helix: 0.68 (0.17), residues: 1020 sheet: -0.98 (0.20), residues: 662 loop : -1.80 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPSC 144 HIS 0.005 0.001 HISSW 113 PHE 0.044 0.001 PHESH 24 TYR 0.040 0.001 TYRSJ 19 ARG 0.016 0.000 ARGSI 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 391 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 41 ARG cc_start: 0.6920 (ptm160) cc_final: 0.6670 (ttt90) REVERT: SB 72 ASP cc_start: 0.8748 (t0) cc_final: 0.8529 (t0) REVERT: SB 144 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7571 (ptt90) REVERT: SB 207 LEU cc_start: 0.8581 (mp) cc_final: 0.8312 (mp) REVERT: SC 81 MET cc_start: 0.7872 (mmm) cc_final: 0.7575 (mmm) REVERT: SG 156 PHE cc_start: 0.8134 (m-80) cc_final: 0.7768 (t80) REVERT: SH 158 ASP cc_start: 0.7373 (t0) cc_final: 0.7137 (t70) REVERT: SI 29 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8003 (pt) REVERT: SJ 19 TYR cc_start: 0.7296 (m-10) cc_final: 0.6965 (m-10) REVERT: SJ 104 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7598 (t80) REVERT: SO 46 MET cc_start: 0.8301 (ptm) cc_final: 0.7845 (ptm) REVERT: SX 3 LYS cc_start: 0.7550 (mttt) cc_final: 0.7018 (mtpt) REVERT: SX 94 ASN cc_start: 0.9204 (p0) cc_final: 0.8914 (p0) REVERT: SY 86 GLU cc_start: 0.8566 (tp30) cc_final: 0.8032 (tp30) REVERT: Sb 7 LEU cc_start: 0.9093 (mt) cc_final: 0.8877 (mp) REVERT: Sb 33 LEU cc_start: 0.8492 (mt) cc_final: 0.8279 (mt) REVERT: CA 214 PHE cc_start: 0.8297 (t80) cc_final: 0.7887 (t80) REVERT: CB 245 PHE cc_start: 0.7813 (m-80) cc_final: 0.7523 (m-80) REVERT: CC 114 MET cc_start: 0.0662 (mtm) cc_final: -0.0395 (mmt) outliers start: 85 outliers final: 72 residues processed: 439 average time/residue: 0.5059 time to fit residues: 379.1906 Evaluate side-chains 440 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 365 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 68 VAL Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 119 THR Chi-restraints excluded: chain SB residue 124 ASN Chi-restraints excluded: chain SB residue 144 ARG Chi-restraints excluded: chain SB residue 208 GLN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 167 VAL Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 146 THR Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SE residue 248 ILE Chi-restraints excluded: chain SE residue 256 ARG Chi-restraints excluded: chain SG residue 32 ILE Chi-restraints excluded: chain SG residue 41 VAL Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 58 ASP Chi-restraints excluded: chain SJ residue 94 ASP Chi-restraints excluded: chain SJ residue 104 PHE Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 23 PHE Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 79 VAL Chi-restraints excluded: chain SO residue 89 THR Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SO residue 115 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 58 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 77 ILE Chi-restraints excluded: chain SX residue 79 ASN Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 75 VAL Chi-restraints excluded: chain SY residue 88 THR Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 78 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 102 TYR Chi-restraints excluded: chain CC residue 204 PHE Chi-restraints excluded: chain CC residue 216 PHE Chi-restraints excluded: chain CC residue 229 LEU Chi-restraints excluded: chain CC residue 720 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 391 optimal weight: 5.9990 chunk 411 optimal weight: 50.0000 chunk 375 optimal weight: 5.9990 chunk 400 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 314 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 361 optimal weight: 1.9990 chunk 378 optimal weight: 0.7980 chunk 399 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 56593 Z= 0.184 Angle : 0.610 14.544 82470 Z= 0.307 Chirality : 0.036 0.311 10254 Planarity : 0.005 0.077 5849 Dihedral : 22.676 178.717 22852 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.04 % Rotamer: Outliers : 2.81 % Allowed : 21.38 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.22 (0.15), residues: 3252 helix: 0.67 (0.17), residues: 1022 sheet: -0.97 (0.20), residues: 662 loop : -1.77 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPSC 144 HIS 0.005 0.001 HISSW 113 PHE 0.045 0.001 PHESH 24 TYR 0.031 0.001 TYRSJ 19 ARG 0.016 0.000 ARGSI 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 387 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 41 ARG cc_start: 0.6838 (ptm160) cc_final: 0.6604 (ttt90) REVERT: SB 144 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7503 (ptt90) REVERT: SC 81 MET cc_start: 0.7894 (mmm) cc_final: 0.7596 (mmm) REVERT: SE 157 ASN cc_start: 0.8712 (m-40) cc_final: 0.8495 (m-40) REVERT: SG 156 PHE cc_start: 0.8130 (m-80) cc_final: 0.7772 (t80) REVERT: SH 158 ASP cc_start: 0.7335 (t0) cc_final: 0.7129 (t70) REVERT: SI 29 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7998 (pt) REVERT: SI 76 THR cc_start: 0.9142 (t) cc_final: 0.8876 (p) REVERT: SJ 19 TYR cc_start: 0.7211 (m-10) cc_final: 0.6950 (m-10) REVERT: SJ 104 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7617 (t80) REVERT: SO 46 MET cc_start: 0.8184 (ptm) cc_final: 0.7727 (ptm) REVERT: SX 3 LYS cc_start: 0.7459 (mttt) cc_final: 0.6922 (mtpt) REVERT: SX 18 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.7028 (m90) REVERT: SX 94 ASN cc_start: 0.9229 (p0) cc_final: 0.8928 (p0) REVERT: Sb 7 LEU cc_start: 0.9058 (mt) cc_final: 0.8851 (mp) REVERT: CA 214 PHE cc_start: 0.8321 (t80) cc_final: 0.8041 (t80) REVERT: CA 218 ASN cc_start: 0.8613 (m110) cc_final: 0.8350 (p0) REVERT: CB 245 PHE cc_start: 0.7794 (m-80) cc_final: 0.7498 (m-80) REVERT: CC 114 MET cc_start: 0.0599 (mtm) cc_final: -0.0506 (mmt) outliers start: 79 outliers final: 68 residues processed: 436 average time/residue: 0.4963 time to fit residues: 370.9335 Evaluate side-chains 438 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 366 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 68 VAL Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 119 THR Chi-restraints excluded: chain SB residue 124 ASN Chi-restraints excluded: chain SB residue 137 ILE Chi-restraints excluded: chain SB residue 140 ILE Chi-restraints excluded: chain SB residue 144 ARG Chi-restraints excluded: chain SB residue 203 ASP Chi-restraints excluded: chain SB residue 208 GLN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 167 VAL Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SE residue 248 ILE Chi-restraints excluded: chain SE residue 256 ARG Chi-restraints excluded: chain SG residue 32 ILE Chi-restraints excluded: chain SG residue 41 VAL Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 184 LEU Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 58 ASP Chi-restraints excluded: chain SJ residue 94 ASP Chi-restraints excluded: chain SJ residue 104 PHE Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 123 VAL Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 23 PHE Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 79 VAL Chi-restraints excluded: chain SO residue 89 THR Chi-restraints excluded: chain SO residue 115 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 58 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 77 ILE Chi-restraints excluded: chain SX residue 79 ASN Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 75 VAL Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 251 ILE Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 102 TYR Chi-restraints excluded: chain CC residue 216 PHE Chi-restraints excluded: chain CC residue 229 LEU Chi-restraints excluded: chain CC residue 720 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 263 optimal weight: 0.9980 chunk 423 optimal weight: 9.9990 chunk 258 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 294 optimal weight: 0.9990 chunk 444 optimal weight: 50.0000 chunk 408 optimal weight: 20.0000 chunk 353 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 183 GLN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 35 ASN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 56593 Z= 0.312 Angle : 0.676 14.924 82470 Z= 0.339 Chirality : 0.039 0.336 10254 Planarity : 0.005 0.080 5849 Dihedral : 22.707 178.716 22852 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.61 % Favored : 91.33 % Rotamer: Outliers : 2.88 % Allowed : 21.56 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.29 (0.15), residues: 3252 helix: 0.66 (0.17), residues: 1016 sheet: -1.00 (0.20), residues: 674 loop : -1.83 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPSC 144 HIS 0.007 0.001 HISSB 211 PHE 0.045 0.002 PHESH 24 TYR 0.031 0.001 TYRSJ 19 ARG 0.017 0.001 ARGSI 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 366 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 41 ARG cc_start: 0.6963 (ptm160) cc_final: 0.6721 (ttt90) REVERT: SB 144 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7566 (ptt90) REVERT: SB 207 LEU cc_start: 0.8560 (mp) cc_final: 0.8296 (mp) REVERT: SC 81 MET cc_start: 0.7937 (mmm) cc_final: 0.7656 (mmm) REVERT: SG 29 ASP cc_start: 0.8371 (p0) cc_final: 0.8009 (p0) REVERT: SH 158 ASP cc_start: 0.7324 (t0) cc_final: 0.7066 (t70) REVERT: SI 29 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8050 (pt) REVERT: SJ 19 TYR cc_start: 0.7381 (m-10) cc_final: 0.7144 (m-10) REVERT: SN 36 GLN cc_start: 0.7747 (mp10) cc_final: 0.7513 (mp10) REVERT: SO 46 MET cc_start: 0.8299 (ptm) cc_final: 0.7978 (ptm) REVERT: SX 3 LYS cc_start: 0.7441 (mttt) cc_final: 0.6893 (mtpt) REVERT: SX 94 ASN cc_start: 0.9147 (p0) cc_final: 0.8866 (p0) REVERT: Sb 7 LEU cc_start: 0.9115 (mt) cc_final: 0.8869 (mp) REVERT: Sb 8 LEU cc_start: 0.9172 (mt) cc_final: 0.8869 (mt) REVERT: CA 214 PHE cc_start: 0.8334 (t80) cc_final: 0.8060 (t80) REVERT: CA 218 ASN cc_start: 0.8704 (m110) cc_final: 0.8434 (p0) REVERT: CB 245 PHE cc_start: 0.7806 (m-80) cc_final: 0.7503 (m-80) REVERT: CC 114 MET cc_start: 0.0592 (mtm) cc_final: -0.0531 (mmt) outliers start: 81 outliers final: 76 residues processed: 414 average time/residue: 0.4963 time to fit residues: 352.8374 Evaluate side-chains 437 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 359 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 47 LEU Chi-restraints excluded: chain SB residue 68 VAL Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 119 THR Chi-restraints excluded: chain SB residue 124 ASN Chi-restraints excluded: chain SB residue 137 ILE Chi-restraints excluded: chain SB residue 140 ILE Chi-restraints excluded: chain SB residue 143 THR Chi-restraints excluded: chain SB residue 144 ARG Chi-restraints excluded: chain SB residue 208 GLN Chi-restraints excluded: chain SC residue 36 VAL Chi-restraints excluded: chain SC residue 137 ILE Chi-restraints excluded: chain SC residue 156 THR Chi-restraints excluded: chain SC residue 158 THR Chi-restraints excluded: chain SC residue 167 VAL Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 146 THR Chi-restraints excluded: chain SE residue 216 ASN Chi-restraints excluded: chain SE residue 223 ASN Chi-restraints excluded: chain SE residue 248 ILE Chi-restraints excluded: chain SG residue 32 ILE Chi-restraints excluded: chain SG residue 41 VAL Chi-restraints excluded: chain SG residue 56 ASN Chi-restraints excluded: chain SG residue 114 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 184 LEU Chi-restraints excluded: chain SJ residue 7 THR Chi-restraints excluded: chain SJ residue 58 ASP Chi-restraints excluded: chain SJ residue 94 ASP Chi-restraints excluded: chain SJ residue 103 ASP Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SL residue 31 THR Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 65 SER Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 123 VAL Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 23 PHE Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 79 VAL Chi-restraints excluded: chain SO residue 89 THR Chi-restraints excluded: chain SO residue 115 ILE Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 58 SER Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 18 HIS Chi-restraints excluded: chain SX residue 40 SER Chi-restraints excluded: chain SX residue 77 ILE Chi-restraints excluded: chain SX residue 79 ASN Chi-restraints excluded: chain SX residue 84 THR Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 51 GLU Chi-restraints excluded: chain SY residue 75 VAL Chi-restraints excluded: chain SY residue 92 VAL Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 130 MET Chi-restraints excluded: chain CA residue 186 GLU Chi-restraints excluded: chain CA residue 251 ILE Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CC residue 75 LEU Chi-restraints excluded: chain CC residue 102 TYR Chi-restraints excluded: chain CC residue 229 LEU Chi-restraints excluded: chain CC residue 720 MET 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: 0.2980 chunk 108 optimal weight: 40.0000 chunk 326 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 354 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 363 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN SB 183 GLN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077040 restraints weight = 148999.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076037 restraints weight = 113962.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076413 restraints weight = 82022.869| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 56593 Z= 0.280 Angle : 0.664 15.206 82470 Z= 0.333 Chirality : 0.039 0.334 10254 Planarity : 0.005 0.079 5849 Dihedral : 22.721 178.730 22852 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.52 % Favored : 91.42 % Rotamer: Outliers : 2.95 % Allowed : 21.95 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.27 (0.15), residues: 3252 helix: 0.67 (0.17), residues: 1017 sheet: -0.98 (0.20), residues: 657 loop : -1.82 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPSC 144 HIS 0.005 0.001 HISSB 211 PHE 0.046 0.001 PHESH 24 TYR 0.030 0.001 TYRSJ 19 ARG 0.017 0.000 ARGSI 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7395.06 seconds wall clock time: 133 minutes 52.28 seconds (8032.28 seconds total)