Starting phenix.real_space_refine on Tue Sep 15 19:32:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wto_32793/09_2026/7wto_32793.map" } resolution = 3.5 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 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 1200 5.49 5 S 36 5.16 5 C 23398 2.51 5 N 8131 2.21 5 O 11724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44490 Number of models: 1 Model: "" Number of chains: 17 Chain: "C2" Number of atoms: 25592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 25592 Classifications: {'RNAv2': 1200} Modifications used: {'rna2p_pur': 100, 'rna2p_pyr': 86, 'rna3p_pur': 548, 'rna3p_pyr': 466} Link IDs: {'rna2p': 186, 'rna3p': 1013} Chain breaks: 9 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: "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: "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: 9.34, per 1000 atoms: 0.21 Number of scatterers: 44490 At special positions: 0 Unit cell: (167.322, 225.567, 172.617, 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 36 16.00 P 1200 15.00 O 11724 8.00 N 8131 7.00 C 23398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 25 sheets defined 35.3% alpha, 17.9% beta 398 base pairs and 630 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'SB' and resid 22 through 26 Processing helix chain 'SB' and resid 70 through 75 Processing helix chain 'SB' and resid 76 through 80 removed outlier: 3.953A pdb=" N HISSB 79 " --> pdb=" O SERSB 76 " (cutoff:3.500A) Processing helix chain 'SB' and resid 106 through 114 Processing helix chain 'SB' and resid 157 through 178 removed outlier: 3.910A 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 202 removed outlier: 4.010A pdb=" N LYSSB 195 " --> pdb=" O GLUSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 232 removed outlier: 3.808A pdb=" N LEUSB 228 " --> pdb=" O ASPSB 224 " (cutoff:3.500A) Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 37 through 41 removed outlier: 3.536A pdb=" N SERSE 41 " --> pdb=" O LEUSE 38 " (cutoff:3.500A) Processing helix chain 'SE' and resid 44 through 50 Processing helix chain 'SE' and resid 57 through 66 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 21 through 25 removed outlier: 3.503A pdb=" N ARGSG 25 " --> pdb=" O HISSG 22 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 152 through 156 Processing helix chain 'SG' and resid 180 through 216 Processing helix chain 'SH' and resid 14 through 29 Processing helix chain 'SH' and resid 31 through 39 removed outlier: 3.662A pdb=" N ARGSH 39 " --> pdb=" O LYSSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 66 through 74 removed outlier: 4.135A 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 116 Processing helix chain 'SH' and resid 117 through 130 removed outlier: 3.759A pdb=" N VALSH 121 " --> pdb=" O THRSH 117 " (cutoff:3.500A) removed outlier: 3.629A 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 25 through 27 No H-bonds generated for 'chain 'SI' and resid 25 through 27' Processing helix chain 'SI' and resid 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 88 through 93 removed outlier: 3.960A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THRSI 93 " --> pdb=" O GLUSI 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 88 through 93' Processing helix chain 'SI' and resid 106 through 117 Processing helix chain 'SI' and resid 136 through 146 removed outlier: 3.935A pdb=" N GLUSI 140 " --> pdb=" O SERSI 136 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 163 removed outlier: 3.558A 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 185 through 200 removed outlier: 3.728A pdb=" N LEUSI 189 " --> pdb=" O GLUSI 185 " (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 84 Processing helix chain 'SJ' and resid 92 through 97 Processing helix chain 'SJ' and resid 100 through 106 removed outlier: 3.759A pdb=" N PHESJ 104 " --> pdb=" O LYSSJ 100 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 108 through 116 Processing helix chain 'SJ' and resid 121 through 131 removed outlier: 3.717A pdb=" N GLNSJ 131 " --> pdb=" O VALSJ 127 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 162 through 166 Processing helix chain 'SJ' and resid 170 through 184 Processing helix chain 'SL' and resid 45 through 50 removed outlier: 3.827A 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 68 removed outlier: 3.729A 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 132 Processing helix chain 'SN' and resid 144 through 151 removed outlier: 4.039A pdb=" N ALASN 148 " --> pdb=" O ALASN 144 " (cutoff:3.500A) Processing helix chain 'SO' and resid 56 through 75 Processing helix chain 'SO' and resid 95 through 108 removed outlier: 3.611A pdb=" N GLNSO 99 " --> pdb=" O GLYSO 95 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 21 removed outlier: 3.591A 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 removed outlier: 3.855A pdb=" N LEUSX 15 " --> pdb=" O SERSX 11 " (cutoff:3.500A) Processing helix chain 'SX' and resid 27 through 33 Processing helix chain 'SX' and resid 35 through 40 removed outlier: 3.687A pdb=" N LYSSX 39 " --> pdb=" O GLYSX 35 " (cutoff:3.500A) Processing helix chain 'SX' and resid 132 through 137 Processing helix chain 'SY' and resid 36 through 48 removed outlier: 4.108A pdb=" N TYRSY 48 " --> pdb=" O LEUSY 44 " (cutoff:3.500A) 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 79 through 86 Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 104 through 116 Processing helix chain 'SY' and resid 122 through 135 removed outlier: 4.097A pdb=" N ASPSY 135 " --> pdb=" O ARGSY 131 " (cutoff:3.500A) Processing helix chain 'Se' and resid 32 through 44 Processing helix chain 'CA' and resid 102 through 104 No H-bonds generated for 'chain 'CA' and resid 102 through 104' Processing helix chain 'CA' and resid 105 through 112 Processing helix chain 'CA' and resid 112 through 123 Proline residue: CA 118 - end of helix Processing helix chain 'CA' and resid 148 through 163 removed outlier: 3.879A 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 195 through 207 Processing helix chain 'CA' and resid 210 through 220 Processing helix chain 'CA' and resid 236 through 253 removed outlier: 3.692A pdb=" N GLYCA 253 " --> pdb=" O SERCA 249 " (cutoff:3.500A) Processing helix chain 'CA' and resid 255 through 272 removed outlier: 3.682A pdb=" N VALCA 259 " --> pdb=" O PROCA 255 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLUCA 272 " --> pdb=" O SERCA 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SB' and resid 42 through 48 removed outlier: 8.331A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SB' and resid 66 through 69 removed outlier: 8.444A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHESB 105 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N ARGSB 213 " --> pdb=" O PHESB 105 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASNSB 209 " --> pdb=" O PHESB 142 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHESB 142 " --> pdb=" O ASNSB 209 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHESB 138 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VALSB 215 " --> pdb=" O ARGSB 136 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARGSB 136 " --> pdb=" O VALSB 215 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEUSB 217 " --> pdb=" O VALSB 134 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VALSB 134 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SE' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'SE' and resid 75 through 76 removed outlier: 4.031A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'SE' and resid 102 through 103 removed outlier: 4.335A pdb=" N VALSE 102 " --> pdb=" O ALASE 110 " (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 218 through 221 removed outlier: 3.504A pdb=" N HISSE 197 " --> pdb=" O HISSE 209 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYSSE 211 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILESE 195 " --> pdb=" O LYSSE 211 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYSSE 179 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLYSE 229 " --> pdb=" O LEUSE 180 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYRSE 182 " --> pdb=" O VALSE 227 " (cutoff:3.500A) removed outlier: 5.077A 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: 6.354A pdb=" N LEUSG 106 " --> pdb=" O ASPSG 57 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASPSG 57 " --> pdb=" O LEUSG 106 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VALSG 108 " --> pdb=" O GLYSG 55 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLYSG 55 " --> pdb=" O VALSG 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALASG 110 " --> pdb=" O SERSG 53 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VALSG 49 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SG' and resid 72 through 76 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 removed outlier: 6.681A pdb=" N LYSSH 56 " --> pdb=" O HISSH 89 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILESH 91 " --> pdb=" O LYSSH 56 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEUSH 58 " --> pdb=" O ILESH 91 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEUSH 93 " --> pdb=" O LEUSH 58 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILESH 60 " --> pdb=" O LEUSH 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SH' and resid 181 through 184 removed outlier: 8.149A pdb=" N VALSH 182 " --> pdb=" O LYSSH 148 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLNSH 150 " --> pdb=" O VALSH 182 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLUSH 184 " --> pdb=" O GLNSH 150 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VALSH 152 " --> pdb=" O GLUSH 184 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYSSH 138 " --> pdb=" O ASPSW 54 " (cutoff:3.500A) removed outlier: 4.247A 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: 3.888A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SI' and resid 37 through 38 removed outlier: 6.204A pdb=" N LYSSI 37 " --> pdb=" O ILESI 60 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 72 through 75 removed outlier: 6.938A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 181 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILESI 183 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SERSI 66 " --> pdb=" O ILESI 183 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILESI 101 " --> pdb=" O VALSI 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASPSI 105 " --> pdb=" O ILESI 78 " (cutoff:3.500A) removed outlier: 6.579A 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 Processing sheet with id=AB8, first strand: chain 'SL' and resid 70 through 77 removed outlier: 16.880A pdb=" N LEUSL 71 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 15.658A pdb=" N LEUSL 91 " --> pdb=" O LEUSL 71 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLYSL 73 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALASL 89 " --> pdb=" O GLYSL 73 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VALSL 75 " --> pdb=" O ARGSL 87 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARGSL 87 " --> pdb=" O VALSL 75 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHESL 137 " --> pdb=" O PROSL 108 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VALSL 139 " --> pdb=" O GLYSL 126 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLYSL 126 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASPSL 121 " --> pdb=" O VALSL 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SO' and resid 38 through 42 removed outlier: 6.499A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VALSO 81 " --> pdb=" O GLYSO 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SW' and resid 71 through 74 removed outlier: 5.408A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SX' and resid 82 through 84 removed outlier: 3.565A pdb=" N CYSSX 71 " --> pdb=" O LEUSX 57 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLNSX 75 " --> pdb=" O VALSX 53 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VALSX 53 " --> pdb=" O GLNSX 75 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEUSX 103 " --> pdb=" O VALSX 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SY' and resid 6 through 15 removed outlier: 4.258A pdb=" N VALSY 12 " --> pdb=" O GLNSY 22 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLNSY 22 " --> pdb=" O VALSY 12 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SERSY 14 " --> pdb=" O ARGSY 20 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARGSY 20 " --> pdb=" O SERSY 14 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLYSY 67 " --> pdb=" O HISSY 29 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VALSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHESY 60 " --> pdb=" O VALSY 70 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHESY 72 " --> pdb=" O PHESY 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Sb' and resid 43 through 47 Processing sheet with id=AC5, first strand: chain 'Sb' and resid 64 through 65 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 186 768 hydrogen bonds defined for protein. 2151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 954 hydrogen bonds 1478 hydrogen bond angles 0 basepair planarities 398 basepair parallelities 630 stacking parallelities Total time for adding SS restraints: 17.68 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6539 1.33 - 1.45: 18606 1.45 - 1.57: 20253 1.57 - 1.69: 2390 1.69 - 1.81: 56 Bond restraints: 47844 Sorted by residual: bond pdb=" C GLNSX 63 " pdb=" N PROSX 64 " ideal model delta sigma weight residual 1.334 1.398 -0.065 2.34e-02 1.83e+03 7.60e+00 bond pdb=" C PHESH 131 " pdb=" N PROSH 132 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.22e-02 6.72e+03 5.64e+00 bond pdb=" C3' UC2 272 " pdb=" O3' UC2 272 " ideal model delta sigma weight residual 1.415 1.452 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C3' CC2 136 " pdb=" O3' CC2 136 " ideal model delta sigma weight residual 1.415 1.451 -0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C THRSI 107 " pdb=" N PROSI 108 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 3.02e+00 ... (remaining 47839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 69349 3.74 - 7.47: 997 7.47 - 11.21: 36 11.21 - 14.94: 3 14.94 - 18.68: 1 Bond angle restraints: 70386 Sorted by residual: angle pdb=" C3' UC2 272 " pdb=" O3' UC2 272 " pdb=" P GC2 273 " ideal model delta sigma weight residual 119.70 127.11 -7.41 1.20e+00 6.94e-01 3.81e+01 angle pdb=" C SERSH 30 " pdb=" N SERSH 31 " pdb=" CA SERSH 31 " ideal model delta sigma weight residual 121.70 132.58 -10.88 1.80e+00 3.09e-01 3.65e+01 angle pdb=" C3' CC2 136 " pdb=" O3' CC2 136 " pdb=" P UC2 137 " ideal model delta sigma weight residual 119.70 126.12 -6.42 1.20e+00 6.94e-01 2.86e+01 angle pdb=" CA LEUSG 69 " pdb=" CB LEUSG 69 " pdb=" CG LEUSG 69 " ideal model delta sigma weight residual 116.30 134.98 -18.68 3.50e+00 8.16e-02 2.85e+01 angle pdb=" C3' AC2 417 " pdb=" O3' AC2 417 " pdb=" P GC2 418 " ideal model delta sigma weight residual 119.70 126.05 -6.35 1.20e+00 6.94e-01 2.80e+01 ... (remaining 70381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 23692 35.38 - 70.75: 2420 70.75 - 106.13: 143 106.13 - 141.51: 4 141.51 - 176.89: 6 Dihedral angle restraints: 26265 sinusoidal: 19415 harmonic: 6850 Sorted by residual: dihedral pdb=" C4' AC2 93 " pdb=" C3' AC2 93 " pdb=" C2' AC2 93 " pdb=" C1' AC2 93 " ideal model delta sinusoidal sigma weight residual 36.35 -40.02 76.37 1 3.10e+00 1.04e-01 7.64e+02 dihedral pdb=" C4' UC21031 " pdb=" C3' UC21031 " pdb=" C2' UC21031 " pdb=" C1' UC21031 " ideal model delta sinusoidal sigma weight residual 36.34 -39.09 75.44 1 3.10e+00 1.04e-01 7.48e+02 dihedral pdb=" C4' CC2 500 " pdb=" C3' CC2 500 " pdb=" C2' CC2 500 " pdb=" C1' CC2 500 " ideal model delta sinusoidal sigma weight residual 36.34 -39.05 75.40 1 3.10e+00 1.04e-01 7.47e+02 ... (remaining 26262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 6716 0.083 - 0.166: 554 0.166 - 0.249: 1220 0.249 - 0.332: 382 0.332 - 0.415: 10 Chirality restraints: 8882 Sorted by residual: chirality pdb=" P UC2 794 " pdb=" OP1 UC2 794 " pdb=" OP2 UC2 794 " pdb=" O5' UC2 794 " both_signs ideal model delta sigma weight residual True 2.17 -2.59 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" P GC2 418 " pdb=" OP1 GC2 418 " pdb=" OP2 GC2 418 " pdb=" O5' GC2 418 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" P UC21098 " pdb=" OP1 UC21098 " pdb=" OP2 UC21098 " pdb=" O5' UC21098 " both_signs ideal model delta sigma weight residual True 2.17 -2.55 -0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 8879 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CC2 962 " 0.024 2.00e-02 2.50e+03 3.19e-02 2.28e+01 pdb=" N1 CC2 962 " -0.024 2.00e-02 2.50e+03 pdb=" C2 CC2 962 " -0.075 2.00e-02 2.50e+03 pdb=" O2 CC2 962 " 0.046 2.00e-02 2.50e+03 pdb=" N3 CC2 962 " -0.001 2.00e-02 2.50e+03 pdb=" C4 CC2 962 " 0.000 2.00e-02 2.50e+03 pdb=" N4 CC2 962 " 0.015 2.00e-02 2.50e+03 pdb=" C5 CC2 962 " 0.010 2.00e-02 2.50e+03 pdb=" C6 CC2 962 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC2 867 " 0.011 2.00e-02 2.50e+03 2.44e-02 1.79e+01 pdb=" N9 GC2 867 " -0.012 2.00e-02 2.50e+03 pdb=" C8 GC2 867 " -0.004 2.00e-02 2.50e+03 pdb=" N7 GC2 867 " -0.009 2.00e-02 2.50e+03 pdb=" C5 GC2 867 " -0.003 2.00e-02 2.50e+03 pdb=" C6 GC2 867 " 0.008 2.00e-02 2.50e+03 pdb=" O6 GC2 867 " -0.005 2.00e-02 2.50e+03 pdb=" N1 GC2 867 " 0.006 2.00e-02 2.50e+03 pdb=" C2 GC2 867 " 0.064 2.00e-02 2.50e+03 pdb=" N2 GC2 867 " -0.051 2.00e-02 2.50e+03 pdb=" N3 GC2 867 " -0.001 2.00e-02 2.50e+03 pdb=" C4 GC2 867 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CC2 224 " 0.010 2.00e-02 2.50e+03 2.70e-02 1.64e+01 pdb=" N1 CC2 224 " 0.002 2.00e-02 2.50e+03 pdb=" C2 CC2 224 " -0.067 2.00e-02 2.50e+03 pdb=" O2 CC2 224 " 0.037 2.00e-02 2.50e+03 pdb=" N3 CC2 224 " 0.007 2.00e-02 2.50e+03 pdb=" C4 CC2 224 " -0.015 2.00e-02 2.50e+03 pdb=" N4 CC2 224 " 0.015 2.00e-02 2.50e+03 pdb=" C5 CC2 224 " 0.013 2.00e-02 2.50e+03 pdb=" C6 CC2 224 " -0.002 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 2053 2.66 - 3.22: 36645 3.22 - 3.78: 82845 3.78 - 4.34: 108455 4.34 - 4.90: 151675 Nonbonded interactions: 381673 Sorted by model distance: nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.105 3.040 nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.114 3.040 nonbonded pdb=" O2' UC2 8 " pdb=" OP2 AC21139 " model vdw 2.189 3.040 nonbonded pdb=" OH TYRSY 76 " pdb=" OE2 GLUSY 86 " model vdw 2.205 3.040 nonbonded pdb=" O2 UC2 231 " pdb=" O6 GC2 234 " model vdw 2.221 3.040 ... (remaining 381668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.160 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 51.200 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 47844 Z= 0.255 Angle : 1.093 18.679 70386 Z= 0.478 Chirality : 0.108 0.415 8882 Planarity : 0.007 0.080 4494 Dihedral : 20.927 176.887 21843 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.87 % Favored : 92.05 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 3.06 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.16), residues: 2351 helix: -0.43 (0.18), residues: 739 sheet: -0.90 (0.24), residues: 454 loop : -2.17 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARGSW 57 TYR 0.026 0.002 TYRSJ 12 PHE 0.042 0.002 PHESe 44 TRP 0.022 0.002 TRPSB 29 HIS 0.012 0.001 HISSN 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.26 (47844) covalent geometry : angle 1.09312 / 0.48 (70386) hydrogen bonds : bond 0.12235 / 6.36 ( 1722) hydrogen bonds : angle 5.55216 / 2.16 ( 3629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: SE 240 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7598 (pttp) REVERT: SJ 17 ARG cc_start: 0.8028 (mtt90) cc_final: 0.7776 (mtt90) REVERT: SL 21 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8792 (p0) REVERT: SW 114 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7857 (mt-10) REVERT: SX 137 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7786 (mttp) REVERT: SY 8 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: Sb 31 TYR cc_start: 0.8718 (p90) cc_final: 0.8509 (p90) REVERT: Se 42 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7676 (ttp80) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.2785 time to fit residues: 172.9313 Evaluate side-chains 317 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SL residue 21 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 69 HIS SE 209 HIS SG 10 ASN SG 197 ASN ** SI 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 48 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 58 HIS SN 101 HIS SN 105 ASN SW 24 GLN SY 22 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078461 restraints weight = 100767.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081056 restraints weight = 51486.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081070 restraints weight = 38263.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081063 restraints weight = 33168.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081184 restraints weight = 34115.445| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 47844 Z= 0.245 Angle : 1.397 22.429 70386 Z= 0.556 Chirality : 0.123 2.321 8882 Planarity : 0.005 0.067 4494 Dihedral : 19.177 175.690 17017 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.78 % Favored : 92.17 % Rotamer: Outliers : 1.33 % Allowed : 8.43 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 2.04 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2351 helix: 0.30 (0.19), residues: 772 sheet: -0.81 (0.24), residues: 451 loop : -2.20 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSb 80 TYR 0.020 0.001 TYRSW 101 PHE 0.016 0.001 PHECA 158 TRP 0.011 0.001 TRPSI 112 HIS 0.008 0.001 HISSN 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.25 (47844) covalent geometry : angle 1.39697 / 0.56 (70386) hydrogen bonds : bond 0.08148 / 4.21 ( 1722) hydrogen bonds : angle 4.47179 / 1.73 ( 3629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 339 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SE 242 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7933 (mmtt) REVERT: SI 111 GLN cc_start: 0.7893 (mp10) cc_final: 0.7675 (mp10) REVERT: SN 110 ASP cc_start: 0.7032 (t0) cc_final: 0.6815 (t0) REVERT: SO 37 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7343 (tm-30) REVERT: SO 72 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8719 (mttt) REVERT: SO 77 THR cc_start: 0.8205 (p) cc_final: 0.7912 (p) REVERT: SY 39 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7987 (tm-30) REVERT: SY 63 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7284 (tm-30) REVERT: SY 81 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7424 (mt-10) REVERT: SY 86 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8281 (mm-30) REVERT: Sb 31 TYR cc_start: 0.8832 (p90) cc_final: 0.8306 (p90) REVERT: Se 42 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7714 (ttp80) outliers start: 27 outliers final: 19 residues processed: 352 average time/residue: 0.2562 time to fit residues: 148.6100 Evaluate side-chains 334 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 315 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 78 ASP Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 193 LEU Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SW residue 106 THR Chi-restraints excluded: chain SW residue 117 ARG Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 41 THR Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 291 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 153 optimal weight: 2.9990 chunk 339 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS ** SI 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 48 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 105 ASN SW 24 GLN SX 65 ASN SX 75 GLN Sb 19 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.113764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076841 restraints weight = 100876.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079490 restraints weight = 51665.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079030 restraints weight = 38825.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079358 restraints weight = 34944.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079414 restraints weight = 34397.370| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 47844 Z= 0.256 Angle : 1.170 16.943 70386 Z= 0.475 Chirality : 0.098 1.835 8882 Planarity : 0.005 0.065 4494 Dihedral : 19.214 171.375 17015 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.59 % Favored : 91.37 % Rotamer: Outliers : 1.72 % Allowed : 11.83 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.17), residues: 2351 helix: 0.66 (0.19), residues: 765 sheet: -0.88 (0.24), residues: 442 loop : -2.15 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGSI 194 TYR 0.025 0.002 TYRSE 121 PHE 0.016 0.002 PHESH 43 TRP 0.011 0.001 TRPSX 24 HIS 0.006 0.001 HISSJ 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.26 (47844) covalent geometry : angle 1.16985 / 0.48 (70386) hydrogen bonds : bond 0.08574 / 4.46 ( 1722) hydrogen bonds : angle 4.35425 / 1.69 ( 3629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SI 105 ASP cc_start: 0.8090 (t0) cc_final: 0.7725 (m-30) REVERT: SI 141 ARG cc_start: 0.8851 (ptp-170) cc_final: 0.8622 (ptp-170) REVERT: SL 21 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8819 (p0) REVERT: SO 36 LYS cc_start: 0.8459 (tttp) cc_final: 0.8249 (tttp) REVERT: SO 37 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7254 (tm-30) REVERT: SO 72 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8630 (mttt) REVERT: SW 85 ASP cc_start: 0.8398 (m-30) cc_final: 0.8191 (m-30) REVERT: SY 39 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7897 (tm-30) REVERT: SY 63 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7665 (tm-30) REVERT: SY 81 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7651 (mt-10) REVERT: Sb 31 TYR cc_start: 0.8854 (p90) cc_final: 0.8314 (p90) REVERT: Sb 82 LYS cc_start: 0.7863 (tppt) cc_final: 0.7466 (mmtt) REVERT: Se 42 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.7953 (ttp80) outliers start: 35 outliers final: 27 residues processed: 364 average time/residue: 0.2677 time to fit residues: 162.1611 Evaluate side-chains 343 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 315 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 193 LEU Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SW residue 101 TYR Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SY residue 42 GLU Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 41 THR Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 169 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 103 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 286 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS SI 159 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN SN 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.113654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076366 restraints weight = 100849.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078341 restraints weight = 49597.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079410 restraints weight = 36627.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.079892 restraints weight = 32262.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080046 restraints weight = 30596.233| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 47844 Z= 0.241 Angle : 1.120 16.577 70386 Z= 0.454 Chirality : 0.092 1.738 8882 Planarity : 0.005 0.061 4494 Dihedral : 19.199 177.694 17015 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.34 % Favored : 91.62 % Rotamer: Outliers : 2.61 % Allowed : 14.34 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.17), residues: 2351 helix: 0.88 (0.19), residues: 756 sheet: -0.96 (0.24), residues: 440 loop : -2.09 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGSb 80 TYR 0.015 0.002 TYRSe 40 PHE 0.016 0.002 PHESH 85 TRP 0.011 0.001 TRPSX 24 HIS 0.008 0.001 HISSG 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.24 (47844) covalent geometry : angle 1.12014 / 0.45 (70386) hydrogen bonds : bond 0.08311 / 4.32 ( 1722) hydrogen bonds : angle 4.24381 / 1.65 ( 3629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SE 164 LEU cc_start: 0.6659 (mt) cc_final: 0.6378 (pt) REVERT: SI 29 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8481 (pt) REVERT: SI 141 ARG cc_start: 0.8796 (ptp-170) cc_final: 0.8538 (ptp-170) REVERT: SJ 143 ILE cc_start: 0.9023 (mm) cc_final: 0.8601 (tp) REVERT: SL 21 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8806 (p0) REVERT: SO 72 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8696 (mttt) REVERT: SX 57 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8421 (pp) REVERT: SX 101 GLU cc_start: 0.8002 (pm20) cc_final: 0.7695 (pm20) REVERT: SY 39 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7796 (tm-30) REVERT: SY 46 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8060 (tp30) REVERT: SY 63 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7713 (tm-30) REVERT: Sb 31 TYR cc_start: 0.8861 (p90) cc_final: 0.8403 (p90) REVERT: Se 42 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.7812 (ttp80) outliers start: 53 outliers final: 36 residues processed: 373 average time/residue: 0.2626 time to fit residues: 163.2703 Evaluate side-chains 352 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 207 LEU Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SH residue 31 SER Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 193 LEU Chi-restraints excluded: chain SJ residue 25 ASP Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 52 VAL Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 39 ILE Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 101 TYR Chi-restraints excluded: chain SW residue 106 THR Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SX residue 57 LEU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 42 GLU Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 169 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 332 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS SH 5 GLN SI 159 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075539 restraints weight = 100691.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077468 restraints weight = 49743.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078512 restraints weight = 36941.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079000 restraints weight = 32551.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079159 restraints weight = 30872.539| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 47844 Z= 0.268 Angle : 1.129 16.790 70386 Z= 0.459 Chirality : 0.092 1.569 8882 Planarity : 0.005 0.065 4494 Dihedral : 19.271 178.058 17015 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.51 % Favored : 91.45 % Rotamer: Outliers : 2.61 % Allowed : 15.92 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.17), residues: 2351 helix: 0.93 (0.19), residues: 760 sheet: -1.05 (0.24), residues: 441 loop : -2.05 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGSE 3 TYR 0.029 0.002 TYRSE 121 PHE 0.018 0.002 PHESb 79 TRP 0.012 0.001 TRPSX 24 HIS 0.011 0.001 HISSG 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.27 (47844) covalent geometry : angle 1.12891 / 0.46 (70386) hydrogen bonds : bond 0.08707 / 4.54 ( 1722) hydrogen bonds : angle 4.26704 / 1.66 ( 3629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: SE 164 LEU cc_start: 0.6702 (mt) cc_final: 0.6476 (pt) REVERT: SE 242 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8234 (mmtt) REVERT: SI 29 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8484 (pt) REVERT: SI 105 ASP cc_start: 0.8106 (t0) cc_final: 0.7878 (m-30) REVERT: SJ 143 ILE cc_start: 0.9056 (mm) cc_final: 0.8583 (tp) REVERT: SL 21 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8781 (p0) REVERT: SO 36 LYS cc_start: 0.8564 (tttp) cc_final: 0.8228 (tttp) REVERT: SO 72 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8667 (mttt) REVERT: SX 57 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8496 (pp) REVERT: SX 75 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8330 (tp40) REVERT: SY 38 ASP cc_start: 0.7598 (p0) cc_final: 0.6927 (p0) REVERT: SY 46 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7897 (tp30) REVERT: SY 63 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7722 (tm-30) REVERT: Sb 31 TYR cc_start: 0.8886 (p90) cc_final: 0.8430 (p90) REVERT: Se 42 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.7773 (ttp80) outliers start: 53 outliers final: 39 residues processed: 362 average time/residue: 0.2681 time to fit residues: 161.3003 Evaluate side-chains 344 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 301 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SH residue 31 SER Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SJ residue 25 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 52 VAL Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SW residue 101 TYR Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SX residue 57 LEU Chi-restraints excluded: chain SX residue 75 GLN Chi-restraints excluded: chain SX residue 127 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Se residue 41 THR Chi-restraints excluded: chain CA residue 94 PHE Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 169 ASP Chi-restraints excluded: chain CA residue 254 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 281 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 294 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS SI 159 GLN SJ 48 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN SN 36 GLN ** SN 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.074102 restraints weight = 101548.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.076328 restraints weight = 55827.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.076050 restraints weight = 41521.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.076109 restraints weight = 39016.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076239 restraints weight = 39039.005| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 47844 Z= 0.362 Angle : 1.219 17.642 70386 Z= 0.496 Chirality : 0.098 1.592 8882 Planarity : 0.006 0.068 4494 Dihedral : 19.320 178.455 17015 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.66 % Favored : 90.30 % Rotamer: Outliers : 3.15 % Allowed : 16.41 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.17), residues: 2351 helix: 0.90 (0.19), residues: 758 sheet: -1.13 (0.24), residues: 439 loop : -2.13 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGSE 3 TYR 0.019 0.002 TYRSW 101 PHE 0.025 0.002 PHESH 43 TRP 0.016 0.002 TRPSX 24 HIS 0.007 0.001 HISSN 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.36 (47844) covalent geometry : angle 1.21864 / 0.50 (70386) hydrogen bonds : bond 0.09473 / 4.94 ( 1722) hydrogen bonds : angle 4.39432 / 1.70 ( 3629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SE 164 LEU cc_start: 0.7020 (mt) cc_final: 0.6480 (pt) REVERT: SI 29 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8497 (pt) REVERT: SI 105 ASP cc_start: 0.8194 (t0) cc_final: 0.7967 (m-30) REVERT: SI 140 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: SJ 134 ILE cc_start: 0.7833 (mm) cc_final: 0.7418 (mm) REVERT: SJ 143 ILE cc_start: 0.9116 (mm) cc_final: 0.8672 (tp) REVERT: SL 21 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8769 (p0) REVERT: SN 64 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8551 (ttt90) REVERT: SO 36 LYS cc_start: 0.8728 (tttp) cc_final: 0.8431 (tttp) REVERT: SX 75 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8291 (tp40) REVERT: SY 63 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7818 (tm-30) REVERT: Sb 31 TYR cc_start: 0.8899 (p90) cc_final: 0.8517 (p90) REVERT: Sb 59 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.7021 (p) REVERT: Se 42 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.7760 (ttp80) outliers start: 64 outliers final: 54 residues processed: 355 average time/residue: 0.2657 time to fit residues: 158.1293 Evaluate side-chains 358 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 207 LEU Chi-restraints excluded: chain SE residue 38 LEU Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 131 LEU Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 108 VAL Chi-restraints excluded: chain SH residue 31 SER Chi-restraints excluded: chain SH residue 103 SER Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 140 GLU Chi-restraints excluded: chain SI residue 158 SER Chi-restraints excluded: chain SJ residue 25 ASP Chi-restraints excluded: chain SJ residue 113 VAL Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 52 VAL Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 39 ILE Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SO residue 126 THR Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SW residue 101 TYR Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SX residue 75 GLN Chi-restraints excluded: chain SX residue 76 LEU Chi-restraints excluded: chain SX residue 127 VAL Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 75 VAL Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 59 CYS Chi-restraints excluded: chain Se residue 41 THR Chi-restraints excluded: chain CA residue 94 PHE Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 163 THR Chi-restraints excluded: chain CA residue 169 ASP Chi-restraints excluded: chain CA residue 254 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 275 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 242 optimal weight: 0.0980 chunk 113 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS SG 139 ASN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN ** SN 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.114058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077556 restraints weight = 100927.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.079860 restraints weight = 52929.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079711 restraints weight = 39631.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080047 restraints weight = 36909.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080073 restraints weight = 33850.787| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 47844 Z= 0.200 Angle : 1.070 17.125 70386 Z= 0.435 Chirality : 0.087 1.500 8882 Planarity : 0.005 0.063 4494 Dihedral : 19.278 178.588 17015 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.68 % Favored : 91.28 % Rotamer: Outliers : 2.56 % Allowed : 17.74 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.17), residues: 2351 helix: 1.04 (0.19), residues: 759 sheet: -1.04 (0.24), residues: 425 loop : -2.06 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGSE 3 TYR 0.018 0.001 TYRSW 101 PHE 0.016 0.001 PHECA 158 TRP 0.011 0.001 TRPSX 24 HIS 0.006 0.001 HISSN 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (47844) covalent geometry : angle 1.07004 / 0.44 (70386) hydrogen bonds : bond 0.08199 / 4.27 ( 1722) hydrogen bonds : angle 4.22526 / 1.64 ( 3629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 325 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: SE 164 LEU cc_start: 0.6748 (mt) cc_final: 0.6438 (pt) REVERT: SI 29 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8468 (pt) REVERT: SJ 134 ILE cc_start: 0.7618 (mm) cc_final: 0.7258 (mm) REVERT: SJ 143 ILE cc_start: 0.8972 (mm) cc_final: 0.8541 (tp) REVERT: SL 16 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8633 (mm-40) REVERT: SL 21 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8773 (p0) REVERT: SL 60 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: SN 64 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8509 (ttt90) REVERT: SO 36 LYS cc_start: 0.8640 (tttp) cc_final: 0.8436 (tttp) REVERT: SX 101 GLU cc_start: 0.8064 (pm20) cc_final: 0.7753 (pm20) REVERT: SY 46 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7902 (tp30) REVERT: Sb 31 TYR cc_start: 0.8857 (p90) cc_final: 0.8485 (p90) REVERT: Se 42 ARG cc_start: 0.8259 (ttp-170) cc_final: 0.7910 (ttp80) outliers start: 52 outliers final: 42 residues processed: 362 average time/residue: 0.2649 time to fit residues: 159.9517 Evaluate side-chains 354 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 207 LEU Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR 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 213 SER Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SH residue 31 SER Chi-restraints excluded: chain SH residue 103 SER Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SJ residue 25 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 16 GLN Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 25 VAL Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SO residue 39 ILE Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SW residue 101 TYR Chi-restraints excluded: chain SW residue 106 THR Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SX residue 127 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 100 VAL Chi-restraints excluded: chain CA residue 94 PHE Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 163 THR Chi-restraints excluded: chain CA residue 169 ASP Chi-restraints excluded: chain CA residue 254 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 80 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 328 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 321 optimal weight: 7.9990 chunk 346 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 208 GLN SE 209 HIS SG 139 ASN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 138 ASN SN 36 GLN ** SN 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.076729 restraints weight = 101276.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078682 restraints weight = 49719.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079750 restraints weight = 36707.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080262 restraints weight = 32160.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080416 restraints weight = 30486.326| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 47844 Z= 0.221 Angle : 1.079 16.909 70386 Z= 0.440 Chirality : 0.087 1.476 8882 Planarity : 0.005 0.064 4494 Dihedral : 19.214 179.066 17015 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.97 % Favored : 90.98 % Rotamer: Outliers : 2.71 % Allowed : 18.14 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2351 helix: 1.05 (0.19), residues: 760 sheet: -0.99 (0.25), residues: 418 loop : -2.07 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGSE 3 TYR 0.023 0.002 TYRSJ 12 PHE 0.026 0.002 PHESH 43 TRP 0.013 0.001 TRPSI 112 HIS 0.007 0.001 HISSJ 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (47844) covalent geometry : angle 1.07898 / 0.44 (70386) hydrogen bonds : bond 0.08370 / 4.37 ( 1722) hydrogen bonds : angle 4.23554 / 1.64 ( 3629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: SE 164 LEU cc_start: 0.6643 (mt) cc_final: 0.6372 (pt) REVERT: SE 182 TYR cc_start: 0.8907 (t80) cc_final: 0.8293 (t80) REVERT: SI 29 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8464 (pt) REVERT: SI 140 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: SJ 134 ILE cc_start: 0.7794 (mm) cc_final: 0.7410 (mm) REVERT: SJ 143 ILE cc_start: 0.9003 (mm) cc_final: 0.8595 (tp) REVERT: SL 60 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8626 (m-80) REVERT: SN 64 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8498 (ttt90) REVERT: SW 68 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7395 (ptp90) REVERT: SX 101 GLU cc_start: 0.7972 (pm20) cc_final: 0.7699 (pm20) REVERT: SY 46 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7982 (tp30) REVERT: Sb 31 TYR cc_start: 0.8873 (p90) cc_final: 0.8498 (p90) REVERT: Se 42 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7938 (ttp80) outliers start: 55 outliers final: 43 residues processed: 355 average time/residue: 0.2670 time to fit residues: 158.4218 Evaluate side-chains 355 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 66 VAL Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 207 LEU Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 108 VAL Chi-restraints excluded: chain SH residue 31 SER Chi-restraints excluded: chain SH residue 103 SER Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 140 GLU Chi-restraints excluded: chain SJ residue 25 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 25 VAL Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 39 ILE Chi-restraints excluded: chain SO residue 46 MET Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SX residue 127 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 100 VAL Chi-restraints excluded: chain CA residue 94 PHE Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 163 THR Chi-restraints excluded: chain CA residue 169 ASP Chi-restraints excluded: chain CA residue 254 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 137 optimal weight: 1.9990 chunk 257 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 285 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS SE 231 GLN SH 71 HIS ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN ** SN 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078906 restraints weight = 101074.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.080804 restraints weight = 54245.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080700 restraints weight = 41435.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081260 restraints weight = 39252.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081156 restraints weight = 35384.974| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 47844 Z= 0.184 Angle : 1.041 17.152 70386 Z= 0.424 Chirality : 0.085 1.447 8882 Planarity : 0.005 0.063 4494 Dihedral : 19.191 179.650 17015 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.76 % Favored : 91.20 % Rotamer: Outliers : 2.46 % Allowed : 18.14 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2351 helix: 1.12 (0.19), residues: 758 sheet: -0.96 (0.25), residues: 418 loop : -2.06 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGSE 3 TYR 0.020 0.001 TYRSJ 12 PHE 0.026 0.001 PHESH 85 TRP 0.012 0.001 TRPSI 112 HIS 0.007 0.001 HISSN 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (47844) covalent geometry : angle 1.04071 / 0.42 (70386) hydrogen bonds : bond 0.08052 / 4.20 ( 1722) hydrogen bonds : angle 4.17792 / 1.62 ( 3629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: SE 182 TYR cc_start: 0.8842 (t80) cc_final: 0.8303 (t80) REVERT: SI 29 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8438 (pt) REVERT: SI 140 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: SJ 134 ILE cc_start: 0.7651 (mm) cc_final: 0.7296 (mm) REVERT: SJ 143 ILE cc_start: 0.8986 (mm) cc_final: 0.8553 (tp) REVERT: SL 60 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: SL 138 ASN cc_start: 0.8404 (m-40) cc_final: 0.8072 (m-40) REVERT: SN 64 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8477 (ttt90) REVERT: SO 36 LYS cc_start: 0.8599 (tttm) cc_final: 0.8396 (tttp) REVERT: SW 68 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7326 (ptp90) REVERT: SX 55 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7680 (pp20) REVERT: SY 39 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7660 (tm-30) REVERT: SY 43 LYS cc_start: 0.9069 (tppt) cc_final: 0.8767 (ttmm) REVERT: Sb 31 TYR cc_start: 0.8823 (p90) cc_final: 0.8491 (p90) REVERT: Se 42 ARG cc_start: 0.8217 (ttp-170) cc_final: 0.7874 (ttp80) REVERT: CA 117 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7757 (p90) outliers start: 50 outliers final: 39 residues processed: 363 average time/residue: 0.2748 time to fit residues: 165.2576 Evaluate side-chains 357 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 207 LEU Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 108 VAL Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 140 GLU Chi-restraints excluded: chain SJ residue 25 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 25 VAL Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SW residue 106 THR Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SX residue 76 LEU Chi-restraints excluded: chain SX residue 127 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 100 VAL Chi-restraints excluded: chain CA residue 94 PHE Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 163 THR Chi-restraints excluded: chain CA residue 169 ASP Chi-restraints excluded: chain CA residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 200 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 287 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS SG 139 ASN ** SH 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 138 ASN SN 36 GLN ** SN 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076862 restraints weight = 101498.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078835 restraints weight = 54193.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078403 restraints weight = 42636.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079283 restraints weight = 40232.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078873 restraints weight = 35662.093| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 47844 Z= 0.257 Angle : 1.106 16.967 70386 Z= 0.452 Chirality : 0.088 1.428 8882 Planarity : 0.005 0.065 4494 Dihedral : 19.188 179.748 17015 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.60 % Rotamer: Outliers : 2.32 % Allowed : 18.43 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.17), residues: 2351 helix: 1.05 (0.19), residues: 760 sheet: -1.04 (0.24), residues: 426 loop : -2.07 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGSE 3 TYR 0.020 0.002 TYRSJ 12 PHE 0.025 0.002 PHESH 85 TRP 0.013 0.001 TRPSX 24 HIS 0.007 0.001 HISSN 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 (47844) covalent geometry : angle 1.10593 / 0.45 (70386) hydrogen bonds : bond 0.08657 / 4.52 ( 1722) hydrogen bonds : angle 4.26616 / 1.65 ( 3629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: SE 182 TYR cc_start: 0.8948 (t80) cc_final: 0.8424 (t80) REVERT: SI 29 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8475 (pt) REVERT: SI 140 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: SJ 134 ILE cc_start: 0.7742 (mm) cc_final: 0.7361 (mm) REVERT: SL 60 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: SN 64 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8512 (ttt90) REVERT: SW 68 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7120 (ptp90) REVERT: SY 43 LYS cc_start: 0.9141 (tppt) cc_final: 0.8805 (ttmm) REVERT: Se 42 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7738 (ttp80) REVERT: CA 117 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7885 (p90) outliers start: 47 outliers final: 42 residues processed: 344 average time/residue: 0.2660 time to fit residues: 153.8771 Evaluate side-chains 343 residues out of total 2029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 96 LEU Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 207 LEU Chi-restraints excluded: chain SB residue 208 GLN Chi-restraints excluded: chain SE residue 21 ASP Chi-restraints excluded: chain SE residue 61 VAL Chi-restraints excluded: chain SE residue 115 THR Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 213 SER Chi-restraints excluded: chain SG residue 63 MET Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 108 VAL Chi-restraints excluded: chain SH residue 51 VAL Chi-restraints excluded: chain SH residue 103 SER Chi-restraints excluded: chain SH residue 168 SER Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 140 GLU Chi-restraints excluded: chain SJ residue 25 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 25 VAL Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 86 ILE Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SL residue 143 SER Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 82 LYS Chi-restraints excluded: chain SO residue 91 THR Chi-restraints excluded: chain SW residue 33 VAL Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 54 LEU Chi-restraints excluded: chain SX residue 76 LEU Chi-restraints excluded: chain SX residue 127 VAL Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 75 VAL Chi-restraints excluded: chain SY residue 100 VAL Chi-restraints excluded: chain CA residue 94 PHE Chi-restraints excluded: chain CA residue 96 SER Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 128 VAL Chi-restraints excluded: chain CA residue 163 THR Chi-restraints excluded: chain CA residue 169 ASP Chi-restraints excluded: chain CA residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 42 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 264 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 179 optimal weight: 0.0970 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 95 ASN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 209 HIS SG 139 ASN ** SH 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 21 ASN SN 36 GLN ** SN 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.113815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.076993 restraints weight = 101133.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.079609 restraints weight = 51343.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079788 restraints weight = 37497.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079995 restraints weight = 33725.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079993 restraints weight = 31356.414| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 47844 Z= 0.227 Angle : 1.082 16.963 70386 Z= 0.442 Chirality : 0.087 1.413 8882 Planarity : 0.005 0.064 4494 Dihedral : 19.193 179.781 17015 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.97 % Favored : 90.98 % Rotamer: Outliers : 2.41 % Allowed : 18.63 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.09 % Twisted Proline : 1.02 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.17), residues: 2351 helix: 1.07 (0.19), residues: 759 sheet: -0.98 (0.24), residues: 420 loop : -2.08 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGSE 3 TYR 0.020 0.002 TYRSJ 12 PHE 0.026 0.002 PHESH 85 TRP 0.013 0.001 TRPSX 24 HIS 0.008 0.001 HISSN 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (47844) covalent geometry : angle 1.08159 / 0.44 (70386) hydrogen bonds : bond 0.08408 / 4.38 ( 1722) hydrogen bonds : angle 4.23362 / 1.63 ( 3629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8130.36 seconds wall clock time: 141 minutes 35.84 seconds (8495.84 seconds total)