Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:43:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/02_2023/7wtp_32794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/02_2023/7wtp_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_32794/02_2023/7wtp_32794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/02_2023/7wtp_32794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/02_2023/7wtp_32794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtp_32794/02_2023/7wtp_32794.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 21.20, per 1000 atoms: 0.40 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: 19.36 Conformation dependent library (CDL) restraints added in 3.2 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: 14.52 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: 29.10 Time building geometry restraints manager: 21.00 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: 30099 35.89 - 71.78: 1197 71.78 - 107.66: 114 107.66 - 143.55: 10 143.55 - 179.44: 19 Dihedral angle restraints: 31439 sinusoidal: 21952 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 31436 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 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. 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: 1.930 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: 0.040 Extract box with map and model: 12.150 Check model and map are aligned: 0.570 Process input model: 122.320 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.360 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.964 20.116 82470 Z= 0.489 Chirality : 0.051 0.395 10254 Planarity : 0.008 0.159 5849 Dihedral : 16.685 179.440 25313 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 % 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 *********************** 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 : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.5291 time to fit residues: 426.7002 Evaluate side-chains 356 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 2.951 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5675 ------------------------------------------------------------------------------- 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: 6.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 218 ASN CA 239 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 56593 Z= 0.180 Angle : 0.626 11.806 82470 Z= 0.320 Chirality : 0.038 0.313 10254 Planarity : 0.005 0.077 5849 Dihedral : 15.983 179.022 18670 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.80 % Rotamer Outliers : 1.35 % 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: -1.70 (0.14), residues: 3252 helix: 0.08 (0.16), residues: 1014 sheet: -0.98 (0.20), residues: 650 loop : -2.02 (0.14), residues: 1588 *********************** 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 452 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 414 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 428 average time/residue: 0.5084 time to fit residues: 369.3226 Evaluate side-chains 380 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 353 time to evaluate : 2.994 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3786 time to fit residues: 23.0465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 225 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 337 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 405 optimal weight: 20.0000 chunk 438 optimal weight: 20.0000 chunk 361 optimal weight: 5.9990 chunk 402 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN ** SB 208 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** SY 113 ASN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.203 56593 Z= 0.388 Angle : 0.733 16.159 82470 Z= 0.369 Chirality : 0.042 0.347 10254 Planarity : 0.006 0.077 5849 Dihedral : 16.158 179.883 18670 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.98 % Favored : 90.96 % Rotamer Outliers : 1.42 % 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: -1.70 (0.14), residues: 3252 helix: 0.22 (0.16), residues: 1031 sheet: -1.10 (0.20), residues: 689 loop : -2.10 (0.15), residues: 1532 *********************** 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 420 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 380 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 408 average time/residue: 0.5268 time to fit residues: 368.1979 Evaluate side-chains 369 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 347 time to evaluate : 2.999 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3957 time to fit residues: 20.2789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 400 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 407 optimal weight: 0.9980 chunk 431 optimal weight: 30.0000 chunk 212 optimal weight: 4.9990 chunk 385 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 26 GLN Sb 51 GLN ** 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: 0.8166 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.149 56593 Z= 0.322 Angle : 0.680 17.701 82470 Z= 0.343 Chirality : 0.040 0.341 10254 Planarity : 0.005 0.074 5849 Dihedral : 16.092 178.606 18670 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.33 % Favored : 91.61 % Rotamer Outliers : 2.24 % 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: -1.60 (0.14), residues: 3252 helix: 0.37 (0.16), residues: 1025 sheet: -1.09 (0.20), residues: 671 loop : -2.06 (0.15), residues: 1556 *********************** 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 434 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 371 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 33 residues processed: 410 average time/residue: 0.4982 time to fit residues: 351.3062 Evaluate side-chains 375 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 342 time to evaluate : 3.001 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4007 time to fit residues: 28.7430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 359 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 367 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 386 optimal weight: 30.0000 chunk 108 optimal weight: 40.0000 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 124 ASN ** SB 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** SH 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN SH 170 GLN ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 105 ASN SW 113 HIS Sb 26 GLN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.135 56593 Z= 0.443 Angle : 0.770 17.453 82470 Z= 0.385 Chirality : 0.044 0.356 10254 Planarity : 0.006 0.077 5849 Dihedral : 16.276 179.531 18670 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.02 % Favored : 89.91 % Rotamer Outliers : 2.06 % 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: -1.73 (0.14), residues: 3252 helix: 0.24 (0.16), residues: 1029 sheet: -1.14 (0.20), residues: 671 loop : -2.14 (0.15), residues: 1552 *********************** 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 435 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 377 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 33 residues processed: 417 average time/residue: 0.5063 time to fit residues: 361.6593 Evaluate side-chains 367 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 334 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4100 time to fit residues: 28.6677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 145 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 431 optimal weight: 50.0000 chunk 358 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 0.0070 chunk 226 optimal weight: 2.9990 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 153 HIS ** SB 208 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** SO 12 GLN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 57 ASN CA 239 HIS ** CC 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.139 56593 Z= 0.195 Angle : 0.629 16.831 82470 Z= 0.319 Chirality : 0.037 0.318 10254 Planarity : 0.005 0.075 5849 Dihedral : 15.973 178.350 18670 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.03 % Favored : 91.91 % Rotamer Outliers : 1.42 % 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: -1.47 (0.15), residues: 3252 helix: 0.48 (0.16), residues: 1022 sheet: -1.10 (0.20), residues: 654 loop : -1.93 (0.15), residues: 1576 *********************** 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 427 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 387 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 410 average time/residue: 0.5112 time to fit residues: 357.4752 Evaluate side-chains 363 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 342 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3919 time to fit residues: 18.9682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 416 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 245 optimal weight: 8.9990 chunk 315 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 363 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 429 optimal weight: 50.0000 chunk 269 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 11 GLN SH 108 GLN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.131 56593 Z= 0.169 Angle : 0.606 17.824 82470 Z= 0.306 Chirality : 0.036 0.305 10254 Planarity : 0.004 0.071 5849 Dihedral : 15.768 178.408 18670 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.16 % Rotamer Outliers : 1.07 % 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: 0.60 (0.17), residues: 1025 sheet: -0.98 (0.21), residues: 660 loop : -1.83 (0.15), residues: 1567 *********************** 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 431 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 401 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 413 average time/residue: 0.5240 time to fit residues: 368.8206 Evaluate side-chains 385 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 369 time to evaluate : 2.964 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4092 time to fit residues: 15.9659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 265 optimal weight: 0.0370 chunk 171 optimal weight: 0.5980 chunk 256 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 273 optimal weight: 0.0050 chunk 292 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 337 optimal weight: 0.8980 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 208 GLN ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 122 HIS SI 35 ASN SI 103 GLN ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Se 57 ASN CA 239 HIS CC 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.121 56593 Z= 0.138 Angle : 0.583 16.849 82470 Z= 0.293 Chirality : 0.035 0.303 10254 Planarity : 0.004 0.063 5849 Dihedral : 15.519 179.509 18670 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.95 % Favored : 92.99 % Rotamer Outliers : 0.60 % 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: -1.23 (0.15), residues: 3252 helix: 0.58 (0.16), residues: 1038 sheet: -0.92 (0.21), residues: 656 loop : -1.75 (0.16), residues: 1558 *********************** 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 427 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 410 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 419 average time/residue: 0.5187 time to fit residues: 368.6309 Evaluate side-chains 375 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 368 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3922 time to fit residues: 8.7694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 391 optimal weight: 9.9990 chunk 411 optimal weight: 7.9990 chunk 375 optimal weight: 2.9990 chunk 400 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 361 optimal weight: 1.9990 chunk 378 optimal weight: 0.0470 chunk 399 optimal weight: 6.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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 ** SB 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 20 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: 0.8133 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.145 56593 Z= 0.267 Angle : 0.645 16.809 82470 Z= 0.324 Chirality : 0.038 0.317 10254 Planarity : 0.005 0.066 5849 Dihedral : 15.638 178.718 18670 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer Outliers : 1.03 % 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: -1.24 (0.15), residues: 3252 helix: 0.60 (0.17), residues: 1032 sheet: -0.91 (0.20), residues: 664 loop : -1.78 (0.16), residues: 1556 *********************** 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 407 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 378 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 392 average time/residue: 0.5082 time to fit residues: 341.8116 Evaluate side-chains 376 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 359 time to evaluate : 2.978 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4229 time to fit residues: 16.7359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 263 optimal weight: 2.9990 chunk 423 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 444 optimal weight: 50.0000 chunk 408 optimal weight: 7.9990 chunk 353 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 273 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 183 GLN ** SB 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SI 20 GLN SI 35 ASN ** SL 138 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.127 56593 Z= 0.215 Angle : 0.620 17.863 82470 Z= 0.312 Chirality : 0.037 0.314 10254 Planarity : 0.005 0.067 5849 Dihedral : 15.584 178.752 18670 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer Outliers : 0.36 % 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: -1.19 (0.15), residues: 3252 helix: 0.64 (0.17), residues: 1033 sheet: -0.92 (0.20), residues: 666 loop : -1.73 (0.16), residues: 1553 ********************** 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 389 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 379 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 383 average time/residue: 0.5089 time to fit residues: 334.2542 Evaluate side-chains 370 residues out of total 2827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 361 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4204 time to fit residues: 10.5222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 446 random chunks: chunk 281 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 chunk 326 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 354 optimal weight: 0.0970 chunk 148 optimal weight: 9.9990 chunk 363 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 30.0000 overall best weight: 5.2186 ------------------------------------------------------------------------------- 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 ** SB 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SC 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 35 ASN SN 101 HIS Sb 26 GLN ** Se 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Se 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.112305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.075431 restraints weight = 149568.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.074664 restraints weight = 124723.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074593 restraints weight = 88668.376| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.147 56593 Z= 0.432 Angle : 0.771 16.401 82470 Z= 0.385 Chirality : 0.044 0.358 10254 Planarity : 0.006 0.067 5849 Dihedral : 15.979 179.203 18670 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.75 % Favored : 90.19 % Rotamer Outliers : 0.57 % 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: -1.46 (0.15), residues: 3252 helix: 0.43 (0.16), residues: 1034 sheet: -1.06 (0.20), residues: 675 loop : -1.92 (0.15), residues: 1543 =============================================================================== Job complete usr+sys time: 7025.25 seconds wall clock time: 127 minutes 56.33 seconds (7676.33 seconds total)