Starting phenix.real_space_refine on Tue Jul 7 07:20:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtn_32792/07_2026/7wtn_32792.cif" } resolution = 3.4 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= 0.008 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 39 5.16 5 C 24634 2.51 5 N 8489 2.21 5 O 12064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46427 Number of models: 1 Model: "" Number of chains: 19 Chain: "C2" Number of atoms: 25592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 25592 Classifications: {'RNA': 1200} Modifications used: {'rna2p_pur': 99, 'rna2p_pyr': 86, 'rna3p_pur': 549, 'rna3p_pyr': 466} Link IDs: {'rna2p': 185, 'rna3p': 1014} 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: "SC" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "SE" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "SG" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "SH" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 171} Chain: "SI" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "SJ" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "SL" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "SN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "SO" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "SW" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "SX" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SY" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Sb" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Se" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 313 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "CA" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "CB" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 302 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "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: 9.39, per 1000 atoms: 0.20 Number of scatterers: 46427 At special positions: 0 Unit cell: (168.381, 226.626, 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 39 16.00 P 1200 15.00 O 12064 8.00 N 8489 7.00 C 24634 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: 3.90 Conformation dependent library (CDL) restraints added in 1.0 seconds 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4878 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 29 sheets defined 35.1% alpha, 20.8% beta 399 base pairs and 639 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'SB' and resid 70 through 75 Processing helix chain 'SB' and resid 106 through 114 Processing helix chain 'SB' and resid 157 through 178 Processing helix chain 'SB' and resid 180 through 189 Processing helix chain 'SB' and resid 191 through 202 removed outlier: 3.889A pdb=" N LYSSB 195 " --> pdb=" O GLUSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 232 removed outlier: 3.784A pdb=" N LEUSB 228 " --> pdb=" O ASPSB 224 " (cutoff:3.500A) Processing helix chain 'SC' and resid 39 through 47 removed outlier: 3.823A pdb=" N ALASC 47 " --> pdb=" O ARGSC 43 " (cutoff:3.500A) Processing helix chain 'SC' and resid 66 through 73 removed outlier: 3.643A pdb=" N ASPSC 70 " --> pdb=" O PHESC 66 " (cutoff:3.500A) Processing helix chain 'SC' and resid 120 through 135 Processing helix chain 'SC' and resid 181 through 192 Processing helix chain 'SC' and resid 206 through 224 Processing helix chain 'SC' and resid 226 through 231 removed outlier: 4.253A pdb=" N ALASC 231 " --> pdb=" O ASNSC 228 " (cutoff:3.500A) Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 37 through 41 removed outlier: 3.692A pdb=" N SERSE 41 " --> pdb=" O LEUSE 38 " (cutoff:3.500A) Processing helix chain 'SE' and resid 43 through 51 removed outlier: 3.677A pdb=" N ARGSE 51 " --> pdb=" O PHESE 47 " (cutoff:3.500A) 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 258 Processing helix chain 'SG' and resid 21 through 28 removed outlier: 3.604A pdb=" N ARGSG 25 " --> pdb=" O HISSG 22 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VALSG 26 " --> pdb=" O ARGSG 23 " (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 217 removed outlier: 4.058A pdb=" N SERSG 217 " --> pdb=" O ALASG 213 " (cutoff:3.500A) Processing helix chain 'SH' and resid 14 through 29 Processing helix chain 'SH' and resid 31 through 38 Processing helix chain 'SH' and resid 66 through 74 removed outlier: 4.186A 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 117 through 130 removed outlier: 3.698A 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 88 through 94 removed outlier: 3.935A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 118 Processing helix chain 'SI' and resid 136 through 146 removed outlier: 3.861A pdb=" N GLUSI 140 " --> pdb=" O SERSI 136 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 163 Processing helix chain 'SI' and resid 172 through 177 Processing helix chain 'SI' and resid 186 through 200 removed outlier: 3.509A pdb=" N LYSSI 200 " --> pdb=" O LEUSI 196 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 20 through 35 Processing helix chain 'SJ' and resid 39 through 61 Processing helix chain 'SJ' and resid 66 through 83 Processing helix chain 'SJ' and resid 92 through 97 Processing helix chain 'SJ' and resid 100 through 107 removed outlier: 3.576A pdb=" N PHESJ 104 " --> pdb=" O LYSSJ 100 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARGSJ 107 " --> pdb=" O ASPSJ 103 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 108 through 116 Processing helix chain 'SJ' and resid 121 through 131 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 51 removed outlier: 3.819A pdb=" N ILESL 49 " --> pdb=" O PROSL 45 " (cutoff:3.500A) Processing helix chain 'SN' and resid 31 through 44 Processing helix chain 'SN' and resid 46 through 58 Processing helix chain 'SN' and resid 62 through 67 removed outlier: 3.599A 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: 4.202A 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: 3.505A pdb=" N GLNSO 99 " --> pdb=" O GLYSO 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SERSO 108 " --> pdb=" O ALASO 104 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 21 removed outlier: 3.718A pdb=" N ASPSW 9 " --> pdb=" O SERSW 5 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 45 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 120 Processing helix chain 'SX' and resid 11 through 25 removed outlier: 3.972A pdb=" N LEUSX 15 " --> pdb=" O SERSX 11 " (cutoff:3.500A) Processing helix chain 'SX' and resid 27 through 34 Processing helix chain 'SX' and resid 35 through 40 removed outlier: 3.575A 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: 3.865A 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 78 through 86 removed outlier: 3.629A pdb=" N ALASY 82 " --> pdb=" O SERSY 78 " (cutoff:3.500A) Processing helix chain 'SY' and resid 87 through 95 Processing helix chain 'SY' and resid 104 through 116 Processing helix chain 'SY' and resid 122 through 135 Processing helix chain 'Sb' and resid 11 through 18 removed outlier: 3.848A pdb=" N LYSSb 18 " --> pdb=" O SERSb 14 " (cutoff:3.500A) Processing helix chain 'Se' and resid 32 through 44 Processing helix chain 'CA' and resid 102 through 112 removed outlier: 3.747A pdb=" N THRCA 107 " --> pdb=" O PROCA 103 " (cutoff:3.500A) Proline residue: CA 108 - end of helix removed outlier: 3.548A pdb=" N ASNCA 111 " --> pdb=" O THRCA 107 " (cutoff:3.500A) Processing helix chain 'CA' and resid 113 through 115 No H-bonds generated for 'chain 'CA' and resid 113 through 115' Processing helix chain 'CA' and resid 116 through 123 removed outlier: 3.885A pdb=" N LEUCA 120 " --> pdb=" O ILECA 116 " (cutoff:3.500A) Processing helix chain 'CA' and resid 148 through 163 removed outlier: 3.691A 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 removed outlier: 3.540A pdb=" N SERCA 199 " --> pdb=" O GLYCA 195 " (cutoff:3.500A) Processing helix chain 'CA' and resid 210 through 220 removed outlier: 3.932A pdb=" N THRCA 220 " --> pdb=" O ILECA 216 " (cutoff:3.500A) Processing helix chain 'CA' and resid 236 through 252 Processing helix chain 'CA' and resid 255 through 272 removed outlier: 3.650A pdb=" N VALCA 259 " --> pdb=" O PROCA 255 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLUCA 272 " --> pdb=" O SERCA 268 " (cutoff:3.500A) Processing helix chain 'CB' and resid 242 through 251 removed outlier: 3.618A pdb=" N GLUCB 251 " --> pdb=" O LEUCB 247 " (cutoff:3.500A) Processing helix chain 'CB' and resid 251 through 256 Processing sheet with id=AA1, first strand: chain 'SB' and resid 44 through 48 removed outlier: 8.606A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THRSB 98 " --> pdb=" O ASPSB 31 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYSSB 33 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N PHESB 100 " --> pdb=" O LYSSB 33 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASNSB 99 " --> pdb=" O VALSB 88 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VALSB 88 " --> pdb=" O ASNSB 99 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HISSB 101 " --> pdb=" O LEUSB 86 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEUSB 86 " --> pdb=" O HISSB 101 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N METSB 103 " --> pdb=" O ILESB 84 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILESB 84 " --> pdb=" O METSB 103 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHESB 105 " --> pdb=" O ARGSB 82 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARGSB 82 " --> pdb=" O PHESB 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SB' and resid 44 through 48 removed outlier: 8.606A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THRSB 98 " --> pdb=" O ASPSB 31 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYSSB 33 " --> pdb=" O THRSB 98 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N PHESB 100 " --> pdb=" O LYSSB 33 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ARGSB 213 " --> pdb=" O PHESB 105 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHESB 138 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VALSB 215 " --> pdb=" O ARGSB 136 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARGSB 136 " --> pdb=" O VALSB 215 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEUSB 217 " --> pdb=" O VALSB 134 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VALSB 134 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SC' and resid 77 through 89 removed outlier: 5.346A pdb=" N ASPSC 78 " --> pdb=" O GLYSC 105 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLYSC 105 " --> pdb=" O ASPSC 78 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VALSC 80 " --> pdb=" O VALSC 103 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VALSC 103 " --> pdb=" O VALSC 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SC' and resid 141 through 142 Processing sheet with id=AA5, first strand: chain 'SC' and resid 158 through 161 Processing sheet with id=AA6, first strand: chain 'SC' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'SE' and resid 75 through 76 removed outlier: 3.643A pdb=" N GLUSE 97 " --> pdb=" O LEUSE 92 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'SE' and resid 146 through 148 Processing sheet with id=AA9, first strand: chain 'SE' and resid 218 through 221 removed outlier: 3.572A pdb=" N HISSE 197 " --> pdb=" O HISSE 209 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYSSE 211 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILESE 195 " --> pdb=" O LYSSE 211 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEUSE 180 " --> pdb=" O ILESE 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SG' and resid 12 through 17 removed outlier: 6.400A pdb=" N LEUSG 106 " --> pdb=" O ASPSG 57 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASPSG 57 " --> pdb=" O LEUSG 106 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VALSG 108 " --> pdb=" O GLYSG 55 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYSG 55 " --> pdb=" O VALSG 108 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALASG 110 " --> pdb=" O SERSG 53 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VALSG 49 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'SG' and resid 72 through 77 Processing sheet with id=AB3, first strand: chain 'SG' and resid 160 through 163 Processing sheet with id=AB4, first strand: chain 'SH' and resid 45 through 50 Processing sheet with id=AB5, first strand: chain 'SH' and resid 181 through 184 removed outlier: 8.366A pdb=" N VALSH 182 " --> pdb=" O LYSSH 148 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLNSH 150 " --> pdb=" O VALSH 182 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLUSH 184 " --> pdb=" O GLNSH 150 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VALSH 152 " --> pdb=" O GLUSH 184 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYSSH 138 " --> pdb=" O ASPSW 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHESW 50 " --> pdb=" O TYRSH 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 3 through 4 removed outlier: 4.065A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SI' and resid 37 through 38 removed outlier: 3.579A pdb=" N ILESI 60 " --> pdb=" O LYSSI 37 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARGSI 42 " --> pdb=" O LEUSI 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SI' and resid 72 through 76 removed outlier: 6.137A pdb=" N GLNSI 103 " --> pdb=" O VALSI 81 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VALSI 81 " --> pdb=" O GLNSI 103 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ASPSI 105 " --> pdb=" O ALASI 79 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALASI 79 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SJ' and resid 139 through 141 removed outlier: 4.574A pdb=" N ILESJ 134 " --> pdb=" O VALSJ 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SL' and resid 70 through 77 removed outlier: 16.656A pdb=" N LEUSL 71 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 15.625A pdb=" N LEUSL 91 " --> pdb=" O LEUSL 71 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N GLYSL 73 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ALASL 89 " --> pdb=" O GLYSL 73 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VALSL 75 " --> pdb=" O ARGSL 87 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARGSL 87 " --> pdb=" O VALSL 75 " (cutoff:3.500A) removed outlier: 16.246A pdb=" N VALSL 135 " --> pdb=" O HISSL 104 " (cutoff:3.500A) removed outlier: 13.862A pdb=" N ASNSL 106 " --> pdb=" O VALSL 135 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N PHESL 137 " --> pdb=" O ASNSL 106 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VALSL 139 " --> pdb=" O PROSL 108 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N HISSL 110 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LYSSL 141 " --> pdb=" O HISSL 110 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARGSL 136 " --> pdb=" O CYSSL 128 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THRSL 124 " --> pdb=" O VALSL 140 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VALSL 142 " --> pdb=" O ILESL 122 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILESL 122 " --> pdb=" O VALSL 142 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASPSL 121 " --> pdb=" O VALSL 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SO' and resid 38 through 42 removed outlier: 6.805A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SO' and resid 38 through 42 removed outlier: 6.805A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N GLUSO 116 " --> pdb=" O VALSO 79 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VALSO 81 " --> pdb=" O GLUSO 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SW' and resid 71 through 74 removed outlier: 3.645A pdb=" N GLYSW 123 " --> pdb=" O VALSW 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'SW' and resid 71 through 74 removed outlier: 5.520A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'SX' and resid 49 through 57 removed outlier: 6.822A pdb=" N ARGSX 73 " --> pdb=" O LEUSX 54 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYSSX 56 " --> pdb=" O CYSSX 71 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N CYSSX 71 " --> pdb=" O LYSSX 56 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHESX 122 " --> pdb=" O THRSX 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALSX 124 " --> pdb=" O PHESX 86 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VALSX 124 " --> pdb=" O ALASX 105 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALASX 105 " --> pdb=" O VALSX 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'SY' and resid 6 through 15 removed outlier: 5.738A pdb=" N ILESY 7 " --> pdb=" O LEUSY 28 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEUSY 28 " --> pdb=" O ILESY 7 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THRSY 9 " --> pdb=" O ASPSY 26 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASPSY 26 " --> pdb=" O THRSY 9 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYSSY 11 " --> pdb=" O VALSY 24 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VALSY 24 " --> pdb=" O LYSSY 11 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VALSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHESY 60 " --> pdb=" O VALSY 70 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHESY 72 " --> pdb=" O PHESY 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Sb' and resid 43 through 47 Processing sheet with id=AC9, first strand: chain 'Sb' and resid 64 through 65 Processing sheet with id=AD1, first strand: chain 'CA' and resid 95 through 100 Processing sheet with id=AD2, first strand: chain 'CA' and resid 181 through 186 879 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 954 hydrogen bonds 1470 hydrogen bond angles 0 basepair planarities 399 basepair parallelities 639 stacking parallelities Total time for adding SS restraints: 18.02 Time building geometry restraints manager: 5.38 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: 8398 1.33 - 1.45: 18727 1.45 - 1.58: 20238 1.58 - 1.70: 2390 1.70 - 1.82: 61 Bond restraints: 49814 Sorted by residual: bond pdb=" C GLNSX 63 " pdb=" N PROSX 64 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.42e+00 bond pdb=" C SERSH 31 " pdb=" N PROSH 32 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 6.99e+00 bond pdb=" C ARGSI 31 " pdb=" N GLNSI 32 " ideal model delta sigma weight residual 1.330 1.304 0.027 1.37e-02 5.33e+03 3.74e+00 bond pdb=" CG1 ILESJ 143 " pdb=" CD1 ILESJ 143 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.72e+00 bond pdb=" CB ASPSY 38 " pdb=" CG ASPSY 38 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.48e+00 ... (remaining 49809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 72442 3.55 - 7.09: 546 7.09 - 10.64: 47 10.64 - 14.18: 7 14.18 - 17.73: 1 Bond angle restraints: 73043 Sorted by residual: angle pdb=" N ILESH 162 " pdb=" CA ILESH 162 " pdb=" C ILESH 162 " ideal model delta sigma weight residual 112.43 106.86 5.57 9.20e-01 1.18e+00 3.66e+01 angle pdb=" C SERSH 30 " pdb=" N SERSH 31 " pdb=" CA SERSH 31 " ideal model delta sigma weight residual 121.70 132.59 -10.89 1.80e+00 3.09e-01 3.66e+01 angle pdb=" C PROSH 63 " pdb=" N VALSH 64 " pdb=" CA VALSH 64 " ideal model delta sigma weight residual 122.13 132.35 -10.22 1.85e+00 2.92e-01 3.05e+01 angle pdb=" C ARGSI 31 " pdb=" N GLNSI 32 " pdb=" CA GLNSI 32 " ideal model delta sigma weight residual 120.60 128.34 -7.74 1.53e+00 4.27e-01 2.56e+01 angle pdb=" C SERSb 58 " pdb=" N CYSSb 59 " pdb=" CA CYSSb 59 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 ... (remaining 73038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 26396 35.84 - 71.68: 967 71.68 - 107.52: 80 107.52 - 143.36: 10 143.36 - 179.20: 17 Dihedral angle restraints: 27470 sinusoidal: 19910 harmonic: 7560 Sorted by residual: dihedral pdb=" CA VALSH 64 " pdb=" C VALSH 64 " pdb=" N PROSH 65 " pdb=" CA PROSH 65 " ideal model delta harmonic sigma weight residual 180.00 130.67 49.33 0 5.00e+00 4.00e-02 9.73e+01 dihedral pdb=" CA GLNSX 63 " pdb=" C GLNSX 63 " pdb=" N PROSX 64 " pdb=" CA PROSX 64 " ideal model delta harmonic sigma weight residual 180.00 -132.93 -47.07 0 5.00e+00 4.00e-02 8.86e+01 dihedral pdb=" CA LEUSH 9 " pdb=" C LEUSH 9 " pdb=" N SERSH 10 " pdb=" CA SERSH 10 " ideal model delta harmonic sigma weight residual 180.00 133.63 46.37 0 5.00e+00 4.00e-02 8.60e+01 ... (remaining 27467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 8872 0.107 - 0.215: 293 0.215 - 0.322: 23 0.322 - 0.429: 3 0.429 - 0.537: 1 Chirality restraints: 9192 Sorted by residual: chirality pdb=" CG LEUSE 164 " pdb=" CB LEUSE 164 " pdb=" CD1 LEUSE 164 " pdb=" CD2 LEUSE 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" CB VALSH 64 " pdb=" CA VALSH 64 " pdb=" CG1 VALSH 64 " pdb=" CG2 VALSH 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB ILECA 224 " pdb=" CA ILECA 224 " pdb=" CG1 ILECA 224 " pdb=" CG2 ILECA 224 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 9189 not shown) Planarity restraints: 4828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALSH 64 " -0.124 5.00e-02 4.00e+02 1.89e-01 5.70e+01 pdb=" N PROSH 65 " 0.326 5.00e-02 4.00e+02 pdb=" CA PROSH 65 " -0.110 5.00e-02 4.00e+02 pdb=" CD PROSH 65 " -0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' CC2 14 " 0.017 2.00e-02 2.50e+03 3.47e-02 2.71e+01 pdb=" N1 CC2 14 " -0.011 2.00e-02 2.50e+03 pdb=" C2 CC2 14 " -0.083 2.00e-02 2.50e+03 pdb=" O2 CC2 14 " 0.047 2.00e-02 2.50e+03 pdb=" N3 CC2 14 " 0.011 2.00e-02 2.50e+03 pdb=" C4 CC2 14 " -0.024 2.00e-02 2.50e+03 pdb=" N4 CC2 14 " 0.023 2.00e-02 2.50e+03 pdb=" C5 CC2 14 " 0.008 2.00e-02 2.50e+03 pdb=" C6 CC2 14 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC21141 " -0.033 2.00e-02 2.50e+03 2.84e-02 2.43e+01 pdb=" N9 GC21141 " 0.021 2.00e-02 2.50e+03 pdb=" C8 GC21141 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GC21141 " -0.003 2.00e-02 2.50e+03 pdb=" C5 GC21141 " -0.002 2.00e-02 2.50e+03 pdb=" C6 GC21141 " 0.020 2.00e-02 2.50e+03 pdb=" O6 GC21141 " -0.030 2.00e-02 2.50e+03 pdb=" N1 GC21141 " -0.009 2.00e-02 2.50e+03 pdb=" C2 GC21141 " 0.070 2.00e-02 2.50e+03 pdb=" N2 GC21141 " -0.043 2.00e-02 2.50e+03 pdb=" N3 GC21141 " 0.003 2.00e-02 2.50e+03 pdb=" C4 GC21141 " 0.000 2.00e-02 2.50e+03 ... (remaining 4825 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 2263 2.67 - 3.23: 38366 3.23 - 3.79: 85462 3.79 - 4.34: 112675 4.34 - 4.90: 158731 Nonbonded interactions: 397497 Sorted by model distance: nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.114 3.040 nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.148 3.040 nonbonded pdb=" OP1 AC2 475 " pdb=" OG1 THRSJ 130 " model vdw 2.202 3.040 nonbonded pdb=" O2 UC2 231 " pdb=" O6 GC2 234 " model vdw 2.204 3.040 nonbonded pdb=" O6 GC21658 " pdb=" O4 UC21743 " model vdw 2.209 2.432 ... (remaining 397492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 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: 0.940 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 53.210 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 0.075 49814 Z= 0.228 Angle : 0.830 17.728 73043 Z= 0.422 Chirality : 0.045 0.537 9192 Planarity : 0.008 0.189 4828 Dihedral : 15.923 179.202 22592 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.27 % Favored : 91.65 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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: -1.93 (0.15), residues: 2599 helix: -0.45 (0.17), residues: 832 sheet: -0.55 (0.24), residues: 468 loop : -2.16 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGSW 23 TYR 0.022 0.002 TYRSe 35 PHE 0.034 0.002 PHESe 44 TRP 0.024 0.002 TRPCA 113 HIS 0.009 0.001 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.23 (49814) covalent geometry : angle 0.82991 / 0.42 (73043) hydrogen bonds : bond 0.12314 / 7.28 ( 1809) hydrogen bonds : angle 5.50028 / 3.17 ( 3936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 452 time to evaluate : 1.052 Fit side-chains REVERT: SB 103 MET cc_start: 0.8190 (tmm) cc_final: 0.7645 (ttp) REVERT: SH 125 ILE cc_start: 0.8601 (mm) cc_final: 0.8321 (mm) REVERT: SN 116 ILE cc_start: 0.8754 (mm) cc_final: 0.8540 (mt) REVERT: SO 46 MET cc_start: 0.8629 (mtp) cc_final: 0.8049 (mpp) REVERT: SX 52 ILE cc_start: 0.8853 (mm) cc_final: 0.8465 (mm) REVERT: SX 132 LEU cc_start: 0.7754 (mm) cc_final: 0.7482 (mt) REVERT: CA 269 ARG cc_start: 0.7221 (ttp-170) cc_final: 0.6135 (ptt90) outliers start: 2 outliers final: 0 residues processed: 453 average time/residue: 0.3034 time to fit residues: 222.3117 Evaluate side-chains 385 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 199 ASN SE 130 GLN SE 157 ASN SE 201 HIS SG 197 ASN SH 89 HIS SH 110 GLN SI 20 GLN SI 111 GLN SN 62 GLN SN 101 HIS SO 12 GLN SW 64 GLN SY 22 GLN ** Sb 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090390 restraints weight = 88156.347| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.61 r_work: 0.2810 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49814 Z= 0.180 Angle : 0.625 9.699 73043 Z= 0.321 Chirality : 0.037 0.357 9192 Planarity : 0.006 0.130 4828 Dihedral : 15.183 178.765 17287 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.58 % Favored : 92.38 % Rotamer: Outliers : 1.70 % Allowed : 9.35 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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: -1.36 (0.16), residues: 2599 helix: 0.42 (0.18), residues: 851 sheet: -0.58 (0.23), residues: 503 loop : -2.03 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGSC 140 TYR 0.013 0.001 TYRSG 169 PHE 0.024 0.002 PHESX 86 TRP 0.011 0.001 TRPSX 24 HIS 0.003 0.001 HISSX 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (49814) covalent geometry : angle 0.62464 / 0.32 (73043) hydrogen bonds : bond 0.07150 / 4.34 ( 1809) hydrogen bonds : angle 4.34436 / 2.48 ( 3936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 444 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 103 MET cc_start: 0.8820 (tmm) cc_final: 0.8316 (ttp) REVERT: SC 181 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7741 (m) REVERT: SE 66 MET cc_start: 0.9032 (tpp) cc_final: 0.8576 (tpp) REVERT: SL 42 PHE cc_start: 0.7434 (m-10) cc_final: 0.7031 (m-10) REVERT: SN 116 ILE cc_start: 0.8843 (mm) cc_final: 0.8574 (mt) REVERT: SN 138 ASN cc_start: 0.7150 (p0) cc_final: 0.6899 (p0) REVERT: SO 46 MET cc_start: 0.8761 (mtp) cc_final: 0.8204 (mpp) REVERT: SY 26 ASP cc_start: 0.8650 (p0) cc_final: 0.8388 (p0) REVERT: CA 209 ASP cc_start: 0.8528 (m-30) cc_final: 0.8313 (m-30) outliers start: 38 outliers final: 34 residues processed: 457 average time/residue: 0.2943 time to fit residues: 218.6901 Evaluate side-chains 427 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 392 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SC residue 221 THR Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 157 ASN Chi-restraints excluded: chain SG residue 22 HIS Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 69 LEU Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 141 ARG Chi-restraints excluded: chain SI residue 193 LEU Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 62 GLN Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 93 LEU Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 41 THR Chi-restraints excluded: chain CA residue 101 VAL Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 208 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 276 optimal weight: 0.1980 chunk 346 optimal weight: 0.0770 chunk 223 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 GLN SG 197 ASN SG 201 GLN SH 89 HIS SI 20 GLN SI 111 GLN SL 21 ASN SN 62 GLN SY 22 GLN ** Sb 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 153 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088774 restraints weight = 88004.518| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.43 r_work: 0.2875 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49814 Z= 0.196 Angle : 0.620 9.295 73043 Z= 0.318 Chirality : 0.037 0.337 9192 Planarity : 0.005 0.104 4828 Dihedral : 15.146 179.178 17287 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.08 % Favored : 91.88 % Rotamer: Outliers : 2.10 % Allowed : 13.46 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.04 % 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: -1.16 (0.16), residues: 2599 helix: 0.72 (0.18), residues: 864 sheet: -0.66 (0.23), residues: 498 loop : -1.95 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGSY 8 TYR 0.012 0.001 TYRSG 169 PHE 0.023 0.002 PHESG 144 TRP 0.010 0.001 TRPSX 24 HIS 0.004 0.001 HISCA 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (49814) covalent geometry : angle 0.61996 / 0.32 (73043) hydrogen bonds : bond 0.07211 / 4.38 ( 1809) hydrogen bonds : angle 4.20225 / 2.39 ( 3936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 423 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: SC 181 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7732 (m) REVERT: SE 66 MET cc_start: 0.9190 (tpp) cc_final: 0.8713 (tpp) REVERT: SE 250 GLU cc_start: 0.7604 (pm20) cc_final: 0.7391 (pm20) REVERT: SI 140 GLU cc_start: 0.8697 (mp0) cc_final: 0.8429 (mp0) REVERT: SL 42 PHE cc_start: 0.7548 (m-10) cc_final: 0.7130 (m-10) REVERT: SL 58 CYS cc_start: 0.8992 (t) cc_final: 0.8166 (m) REVERT: SN 116 ILE cc_start: 0.8991 (mm) cc_final: 0.8744 (mt) REVERT: SN 138 ASN cc_start: 0.7315 (p0) cc_final: 0.6843 (p0) REVERT: SO 46 MET cc_start: 0.8815 (mtp) cc_final: 0.8215 (mpp) REVERT: SO 92 LYS cc_start: 0.8479 (ptpp) cc_final: 0.8230 (ptpp) REVERT: SX 139 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7661 (mtpt) REVERT: CA 153 GLN cc_start: 0.8193 (tp40) cc_final: 0.7887 (tp-100) REVERT: CA 157 ASP cc_start: 0.8705 (m-30) cc_final: 0.8451 (m-30) REVERT: CA 209 ASP cc_start: 0.8663 (m-30) cc_final: 0.8435 (m-30) outliers start: 47 outliers final: 37 residues processed: 447 average time/residue: 0.2621 time to fit residues: 192.4639 Evaluate side-chains 428 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 390 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 164 LEU Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 69 LEU Chi-restraints excluded: chain SG residue 96 SER Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 61 THR Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 62 GLN Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SO residue 124 ASP Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 57 LEU Chi-restraints excluded: chain SX residue 93 LEU Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain CA residue 101 VAL Chi-restraints excluded: chain CA residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 179 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 161 optimal weight: 40.0000 chunk 185 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN SG 56 ASN SG 197 ASN SH 89 HIS SI 20 GLN SI 111 GLN ** SI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 112 GLN SJ 133 HIS SL 21 ASN ** SW 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 127 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.124635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.085224 restraints weight = 88496.075| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.52 r_work: 0.2734 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 49814 Z= 0.376 Angle : 0.768 9.630 73043 Z= 0.388 Chirality : 0.045 0.361 9192 Planarity : 0.006 0.087 4828 Dihedral : 15.513 178.624 17287 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.12 % Favored : 90.80 % Rotamer: Outliers : 3.26 % Allowed : 15.34 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.08 % 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: -1.42 (0.16), residues: 2599 helix: 0.57 (0.18), residues: 869 sheet: -0.89 (0.23), residues: 504 loop : -2.12 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGSX 20 TYR 0.016 0.002 TYRSL 93 PHE 0.021 0.002 PHESI 21 TRP 0.012 0.002 TRPSX 24 HIS 0.008 0.001 HISSX 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.38 (49814) covalent geometry : angle 0.76777 / 0.39 (73043) hydrogen bonds : bond 0.09166 / 5.59 ( 1809) hydrogen bonds : angle 4.42218 / 2.52 ( 3936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 423 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: SC 181 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7632 (m) REVERT: SE 66 MET cc_start: 0.9262 (tpp) cc_final: 0.8819 (tpp) REVERT: SE 164 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7064 (mm) REVERT: SE 250 GLU cc_start: 0.7591 (pm20) cc_final: 0.6963 (pm20) REVERT: SI 29 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.7864 (pt) REVERT: SI 140 GLU cc_start: 0.8665 (mp0) cc_final: 0.8454 (mp0) REVERT: SL 42 PHE cc_start: 0.7867 (m-10) cc_final: 0.7492 (m-10) REVERT: SN 115 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8920 (tt) REVERT: SO 46 MET cc_start: 0.8824 (mtp) cc_final: 0.8191 (mpp) REVERT: SO 92 LYS cc_start: 0.8548 (ptpp) cc_final: 0.8319 (ptpp) REVERT: SO 99 GLN cc_start: 0.8658 (mp10) cc_final: 0.8354 (mp10) REVERT: SX 139 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7916 (mtpt) REVERT: CA 157 ASP cc_start: 0.8757 (m-30) cc_final: 0.8509 (m-30) outliers start: 73 outliers final: 50 residues processed: 463 average time/residue: 0.2663 time to fit residues: 202.9504 Evaluate side-chains 431 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 377 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 164 LEU Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SG residue 37 ASP Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 69 LEU Chi-restraints excluded: chain SG residue 96 SER Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SG residue 170 THR Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 61 THR Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 123 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SN residue 115 LEU Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 83 ILE Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SO residue 124 ASP Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain Se residue 42 ARG Chi-restraints excluded: chain CA residue 101 VAL Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 266 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 10.0000 chunk 285 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 331 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 GLN SC 147 ASN SE 130 GLN SE 157 ASN SH 89 HIS SI 20 GLN SI 116 HIS SL 21 ASN SW 15 ASN CA 218 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090009 restraints weight = 87774.737| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.39 r_work: 0.2844 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 49814 Z= 0.133 Angle : 0.595 9.029 73043 Z= 0.307 Chirality : 0.036 0.333 9192 Planarity : 0.005 0.103 4828 Dihedral : 15.151 178.446 17287 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.73 % Favored : 92.23 % Rotamer: Outliers : 2.82 % Allowed : 17.22 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.08 % 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: -1.06 (0.17), residues: 2599 helix: 0.95 (0.18), residues: 864 sheet: -0.85 (0.23), residues: 504 loop : -1.89 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGSC 140 TYR 0.020 0.001 TYRSJ 114 PHE 0.019 0.001 PHESX 86 TRP 0.011 0.001 TRPSI 112 HIS 0.004 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (49814) covalent geometry : angle 0.59507 / 0.31 (73043) hydrogen bonds : bond 0.06874 / 4.18 ( 1809) hydrogen bonds : angle 4.09093 / 2.33 ( 3936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 439 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SC 116 LYS cc_start: 0.7786 (tppp) cc_final: 0.7354 (tptt) REVERT: SC 181 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7621 (m) REVERT: SE 66 MET cc_start: 0.9126 (tpp) cc_final: 0.8764 (tpp) REVERT: SG 149 LYS cc_start: 0.8407 (mmtm) cc_final: 0.7968 (mmtp) REVERT: SH 142 TYR cc_start: 0.8904 (m-80) cc_final: 0.8613 (m-80) REVERT: SL 42 PHE cc_start: 0.7478 (m-10) cc_final: 0.7208 (m-10) REVERT: SN 116 ILE cc_start: 0.8918 (mm) cc_final: 0.8693 (mt) REVERT: SO 46 MET cc_start: 0.8785 (mtp) cc_final: 0.8157 (mpp) REVERT: SO 92 LYS cc_start: 0.8289 (ptpp) cc_final: 0.8050 (ptpp) REVERT: Se 39 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8227 (mt) REVERT: CA 153 GLN cc_start: 0.8131 (tp40) cc_final: 0.7810 (tp-100) REVERT: CA 157 ASP cc_start: 0.8639 (m-30) cc_final: 0.8382 (m-30) REVERT: CA 167 ASP cc_start: 0.7617 (t0) cc_final: 0.7286 (t0) outliers start: 63 outliers final: 41 residues processed: 470 average time/residue: 0.2890 time to fit residues: 221.6256 Evaluate side-chains 444 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 401 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 43 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 180 THR Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SG residue 69 LEU Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SG residue 170 THR Chi-restraints excluded: chain SH residue 10 SER Chi-restraints excluded: chain SH residue 30 SER Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SH residue 117 THR Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 83 ILE Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SW residue 104 LEU Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 266 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 326 optimal weight: 0.9980 chunk 149 optimal weight: 30.0000 chunk 279 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 317 optimal weight: 0.9980 chunk 260 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 371 optimal weight: 7.9990 chunk 335 optimal weight: 5.9990 chunk 138 optimal weight: 0.0570 chunk 163 optimal weight: 0.6980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 GLN SC 147 ASN SE 157 ASN SG 197 ASN SH 89 HIS SI 20 GLN SI 111 GLN SL 21 ASN ** SO 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SW 15 ASN SW 70 ASN CA 218 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.091447 restraints weight = 88185.838| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.45 r_work: 0.2928 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 49814 Z= 0.118 Angle : 0.567 8.938 73043 Z= 0.292 Chirality : 0.035 0.326 9192 Planarity : 0.005 0.103 4828 Dihedral : 14.979 177.908 17287 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.58 % Favored : 92.38 % Rotamer: Outliers : 2.86 % Allowed : 18.16 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.08 % 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: -0.84 (0.17), residues: 2599 helix: 1.13 (0.18), residues: 868 sheet: -0.60 (0.23), residues: 490 loop : -1.82 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSC 95 TYR 0.020 0.001 TYRSJ 114 PHE 0.019 0.001 PHESX 86 TRP 0.011 0.001 TRPCA 113 HIS 0.003 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (49814) covalent geometry : angle 0.56704 / 0.29 (73043) hydrogen bonds : bond 0.06525 / 3.97 ( 1809) hydrogen bonds : angle 3.96661 / 2.26 ( 3936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 425 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 103 MET cc_start: 0.8869 (tmm) cc_final: 0.8503 (tmm) REVERT: SB 146 GLN cc_start: 0.7205 (pt0) cc_final: 0.6818 (pt0) REVERT: SC 116 LYS cc_start: 0.7787 (tppp) cc_final: 0.7357 (tptt) REVERT: SC 181 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7648 (m) REVERT: SE 66 MET cc_start: 0.9126 (tpp) cc_final: 0.8709 (tpp) REVERT: SG 149 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8033 (mmtp) REVERT: SH 142 TYR cc_start: 0.8904 (m-80) cc_final: 0.8592 (m-80) REVERT: SI 29 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7711 (pt) REVERT: SL 42 PHE cc_start: 0.7442 (m-10) cc_final: 0.7150 (m-10) REVERT: SO 46 MET cc_start: 0.8796 (mtp) cc_final: 0.8082 (mpp) REVERT: SO 92 LYS cc_start: 0.8281 (ptpp) cc_final: 0.7932 (ptpp) REVERT: Sb 79 PHE cc_start: 0.8846 (p90) cc_final: 0.8378 (p90) REVERT: CA 153 GLN cc_start: 0.8129 (tp40) cc_final: 0.7670 (tp-100) REVERT: CA 157 ASP cc_start: 0.8681 (m-30) cc_final: 0.8435 (m-30) REVERT: CA 167 ASP cc_start: 0.7536 (t0) cc_final: 0.7292 (t0) REVERT: CB 243 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7493 (tttt) REVERT: CB 249 LYS cc_start: 0.8431 (mmtt) cc_final: 0.6931 (tttt) REVERT: CB 251 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7824 (pm20) outliers start: 64 outliers final: 42 residues processed: 459 average time/residue: 0.2235 time to fit residues: 167.5123 Evaluate side-chains 440 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 395 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 43 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 131 ASP Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 180 THR Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 117 THR Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SG residue 15 THR Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 145 PHE Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SG residue 170 THR Chi-restraints excluded: chain SH residue 30 SER Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 61 GLU Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SN residue 19 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SO residue 83 ILE Chi-restraints excluded: chain SO residue 124 ASP Chi-restraints excluded: chain SW residue 104 LEU Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 266 VAL Chi-restraints excluded: chain CB residue 251 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 344 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 348 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 218 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 GLN SC 147 ASN SE 157 ASN SG 197 ASN SH 89 HIS SI 20 GLN SI 111 GLN SL 21 ASN SW 12 ASN SW 15 ASN ** SW 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 218 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.085438 restraints weight = 87925.555| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.65 r_work: 0.2744 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 49814 Z= 0.326 Angle : 0.707 12.233 73043 Z= 0.358 Chirality : 0.042 0.353 9192 Planarity : 0.006 0.110 4828 Dihedral : 15.231 179.739 17287 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.85 % Favored : 91.11 % Rotamer: Outliers : 3.53 % Allowed : 18.02 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.08 % 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: -1.07 (0.16), residues: 2599 helix: 0.94 (0.18), residues: 871 sheet: -0.69 (0.23), residues: 495 loop : -1.99 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGSI 141 TYR 0.034 0.002 TYRSJ 19 PHE 0.018 0.002 PHESX 86 TRP 0.011 0.002 TRPCA 113 HIS 0.007 0.001 HISSX 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.33 (49814) covalent geometry : angle 0.70717 / 0.36 (73043) hydrogen bonds : bond 0.08332 / 5.08 ( 1809) hydrogen bonds : angle 4.21437 / 2.39 ( 3936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 392 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: SC 116 LYS cc_start: 0.7764 (tppp) cc_final: 0.7363 (tptt) REVERT: SC 137 ILE cc_start: 0.8792 (tp) cc_final: 0.8519 (mp) REVERT: SC 181 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7589 (m) REVERT: SE 66 MET cc_start: 0.9088 (tpp) cc_final: 0.8694 (tpp) REVERT: SH 47 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8722 (tpp80) REVERT: SH 133 THR cc_start: 0.8116 (p) cc_final: 0.7863 (t) REVERT: SH 142 TYR cc_start: 0.8850 (m-80) cc_final: 0.8523 (m-80) REVERT: SI 29 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7791 (pt) REVERT: SI 141 ARG cc_start: 0.9338 (ptt-90) cc_final: 0.8732 (ptp90) REVERT: SL 58 CYS cc_start: 0.8817 (t) cc_final: 0.8236 (m) REVERT: SO 46 MET cc_start: 0.8800 (mtp) cc_final: 0.8124 (mpp) REVERT: SO 92 LYS cc_start: 0.8328 (ptpp) cc_final: 0.8114 (ptpp) REVERT: SW 15 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8817 (t160) REVERT: SX 139 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7769 (mtpt) REVERT: Sb 6 ASP cc_start: 0.7710 (t0) cc_final: 0.7510 (t70) REVERT: Se 39 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8280 (mt) REVERT: CA 157 ASP cc_start: 0.8649 (m-30) cc_final: 0.8363 (m-30) REVERT: CA 167 ASP cc_start: 0.7676 (t0) cc_final: 0.7398 (t0) REVERT: CA 263 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (mp) outliers start: 79 outliers final: 55 residues processed: 440 average time/residue: 0.2054 time to fit residues: 147.9670 Evaluate side-chains 437 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 43 VAL Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 180 THR Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 117 THR Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 157 ASN Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SG residue 15 THR Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SG residue 170 THR Chi-restraints excluded: chain SG residue 212 LEU Chi-restraints excluded: chain SH residue 30 SER Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 61 THR Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 113 VAL Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SN residue 19 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 83 ILE Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SO residue 124 ASP Chi-restraints excluded: chain SW residue 15 ASN Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SX residue 132 LEU Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain Se residue 42 ARG Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 101 VAL Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CA residue 266 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 116 optimal weight: 40.0000 chunk 175 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 302 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 312 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 130 GLN SE 157 ASN SH 89 HIS SL 21 ASN SW 15 ASN SW 64 GLN CA 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.128315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089559 restraints weight = 87800.602| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.40 r_work: 0.2840 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49814 Z= 0.164 Angle : 0.610 16.360 73043 Z= 0.312 Chirality : 0.037 0.335 9192 Planarity : 0.005 0.112 4828 Dihedral : 15.071 178.799 17287 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.85 % Favored : 92.11 % Rotamer: Outliers : 3.09 % Allowed : 18.96 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.08 % 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: -0.94 (0.17), residues: 2599 helix: 1.10 (0.18), residues: 862 sheet: -0.79 (0.23), residues: 505 loop : -1.85 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGSC 140 TYR 0.016 0.001 TYRSJ 114 PHE 0.020 0.001 PHESX 86 TRP 0.012 0.001 TRPCA 113 HIS 0.005 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (49814) covalent geometry : angle 0.61033 / 0.31 (73043) hydrogen bonds : bond 0.06994 / 4.25 ( 1809) hydrogen bonds : angle 4.07748 / 2.32 ( 3936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 396 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: SB 183 GLN cc_start: 0.8247 (mp10) cc_final: 0.7970 (mp10) REVERT: SC 116 LYS cc_start: 0.7706 (tppp) cc_final: 0.7450 (tptt) REVERT: SC 137 ILE cc_start: 0.8840 (tp) cc_final: 0.8545 (mt) REVERT: SC 181 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7648 (m) REVERT: SE 66 MET cc_start: 0.9035 (tpp) cc_final: 0.8671 (tpp) REVERT: SG 97 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8954 (m) REVERT: SG 149 LYS cc_start: 0.8313 (mmtm) cc_final: 0.7822 (mmtp) REVERT: SH 47 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8679 (tpp80) REVERT: SH 142 TYR cc_start: 0.8798 (m-80) cc_final: 0.8494 (m-80) REVERT: SI 29 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7742 (pt) REVERT: SI 141 ARG cc_start: 0.9276 (ptt-90) cc_final: 0.8881 (ptt-90) REVERT: SJ 8 TYR cc_start: 0.7987 (p90) cc_final: 0.7760 (p90) REVERT: SL 42 PHE cc_start: 0.7254 (m-10) cc_final: 0.7008 (m-10) REVERT: SL 58 CYS cc_start: 0.8754 (t) cc_final: 0.8339 (m) REVERT: SO 46 MET cc_start: 0.8732 (mtp) cc_final: 0.8112 (mpp) REVERT: Sb 6 ASP cc_start: 0.7569 (t0) cc_final: 0.7350 (t70) REVERT: Se 39 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8146 (mt) REVERT: CA 157 ASP cc_start: 0.8578 (m-30) cc_final: 0.8298 (m-30) REVERT: CA 263 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8360 (mp) outliers start: 69 outliers final: 52 residues processed: 436 average time/residue: 0.1953 time to fit residues: 139.5241 Evaluate side-chains 453 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 396 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 43 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 131 ASP Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 180 THR Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 139 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 157 ASN Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 248 ILE Chi-restraints excluded: chain SG residue 15 THR Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SG residue 170 THR Chi-restraints excluded: chain SH residue 30 SER Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 61 GLU Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 19 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 83 ILE Chi-restraints excluded: chain SO residue 124 ASP Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CA residue 266 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 22 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 374 optimal weight: 5.9990 chunk 338 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 147 ASN SE 130 GLN SE 157 ASN SG 197 ASN SH 89 HIS SL 21 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088043 restraints weight = 87406.344| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.36 r_work: 0.2803 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 49814 Z= 0.221 Angle : 0.641 15.995 73043 Z= 0.327 Chirality : 0.038 0.347 9192 Planarity : 0.005 0.116 4828 Dihedral : 15.090 179.281 17287 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.42 % Rotamer: Outliers : 3.35 % Allowed : 18.92 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.08 % 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: -0.96 (0.17), residues: 2599 helix: 1.07 (0.18), residues: 866 sheet: -0.73 (0.23), residues: 486 loop : -1.89 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSC 140 TYR 0.018 0.001 TYRSJ 114 PHE 0.019 0.001 PHESX 86 TRP 0.012 0.001 TRPCA 113 HIS 0.004 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (49814) covalent geometry : angle 0.64120 / 0.33 (73043) hydrogen bonds : bond 0.07402 / 4.50 ( 1809) hydrogen bonds : angle 4.10889 / 2.34 ( 3936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 392 time to evaluate : 0.641 Fit side-chains REVERT: SB 183 GLN cc_start: 0.8339 (mp10) cc_final: 0.8071 (mp10) REVERT: SC 116 LYS cc_start: 0.7793 (tppp) cc_final: 0.7538 (tptt) REVERT: SC 137 ILE cc_start: 0.8890 (tp) cc_final: 0.8592 (mt) REVERT: SC 181 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7649 (m) REVERT: SE 66 MET cc_start: 0.9156 (tpp) cc_final: 0.8793 (tpp) REVERT: SG 97 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.9015 (m) REVERT: SG 149 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8017 (mmtp) REVERT: SH 47 ARG cc_start: 0.8837 (tpp80) cc_final: 0.8614 (tpp80) REVERT: SH 133 THR cc_start: 0.8090 (p) cc_final: 0.7745 (t) REVERT: SH 142 TYR cc_start: 0.8934 (m-80) cc_final: 0.8564 (m-80) REVERT: SI 29 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7742 (pt) REVERT: SI 141 ARG cc_start: 0.9240 (ptt-90) cc_final: 0.8844 (ptt-90) REVERT: SJ 19 TYR cc_start: 0.9366 (m-80) cc_final: 0.9139 (m-80) REVERT: SL 58 CYS cc_start: 0.9049 (t) cc_final: 0.8474 (m) REVERT: SO 24 ASN cc_start: 0.8137 (t0) cc_final: 0.7837 (t0) REVERT: SO 99 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: Se 39 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8229 (mt) REVERT: CA 157 ASP cc_start: 0.8681 (m-30) cc_final: 0.8414 (m-30) REVERT: CA 167 ASP cc_start: 0.7555 (t0) cc_final: 0.7248 (t0) REVERT: CA 263 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8355 (mp) outliers start: 75 outliers final: 56 residues processed: 437 average time/residue: 0.1815 time to fit residues: 130.2486 Evaluate side-chains 452 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 390 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 43 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 180 THR Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 139 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 157 ASN Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 248 ILE Chi-restraints excluded: chain SG residue 15 THR Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SG residue 170 THR Chi-restraints excluded: chain SH residue 10 SER Chi-restraints excluded: chain SH residue 30 SER Chi-restraints excluded: chain SH residue 31 SER Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 113 VAL Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 19 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 83 ILE Chi-restraints excluded: chain SO residue 99 GLN Chi-restraints excluded: chain SO residue 124 ASP Chi-restraints excluded: chain SW residue 104 LEU Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SX residue 132 LEU Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CA residue 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 341 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 222 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 234 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 147 ASN SE 130 GLN SE 157 ASN SH 89 HIS SL 21 ASN ** SL 110 HIS ** 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 = 0.3784 r_free = 0.3784 target = 0.129823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.090640 restraints weight = 88188.630| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.36 r_work: 0.2884 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 49814 Z= 0.131 Angle : 0.590 16.431 73043 Z= 0.302 Chirality : 0.035 0.333 9192 Planarity : 0.005 0.114 4828 Dihedral : 14.957 178.052 17287 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.31 % Favored : 92.65 % Rotamer: Outliers : 3.00 % Allowed : 19.10 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 1.80 % Twisted General : 0.08 % 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: -0.86 (0.17), residues: 2599 helix: 1.18 (0.18), residues: 866 sheet: -0.78 (0.23), residues: 499 loop : -1.80 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSC 140 TYR 0.034 0.001 TYRSC 143 PHE 0.021 0.001 PHESX 86 TRP 0.014 0.001 TRPCA 113 HIS 0.005 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (49814) covalent geometry : angle 0.59045 / 0.30 (73043) hydrogen bonds : bond 0.06612 / 4.02 ( 1809) hydrogen bonds : angle 3.98308 / 2.26 ( 3936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5198 Ramachandran restraints generated. 2599 Oldfield, 0 Emsley, 2599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 401 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: SB 103 MET cc_start: 0.8646 (tmm) cc_final: 0.8238 (tmm) REVERT: SB 183 GLN cc_start: 0.8158 (mp10) cc_final: 0.7914 (mp10) REVERT: SC 116 LYS cc_start: 0.7833 (tppp) cc_final: 0.7611 (tptt) REVERT: SC 137 ILE cc_start: 0.8872 (tp) cc_final: 0.8575 (mt) REVERT: SC 181 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7711 (m) REVERT: SE 66 MET cc_start: 0.8958 (tpp) cc_final: 0.8609 (tpp) REVERT: SG 97 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8987 (m) REVERT: SH 47 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8647 (tpp80) REVERT: SH 142 TYR cc_start: 0.8777 (m-80) cc_final: 0.8496 (m-80) REVERT: SI 6 ASP cc_start: 0.8180 (p0) cc_final: 0.7883 (p0) REVERT: SI 29 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7695 (pt) REVERT: SI 151 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8625 (mppt) REVERT: SJ 8 TYR cc_start: 0.7949 (p90) cc_final: 0.7733 (p90) REVERT: SL 58 CYS cc_start: 0.8707 (t) cc_final: 0.8302 (m) REVERT: SO 99 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8040 (mp10) REVERT: Sb 79 PHE cc_start: 0.8728 (p90) cc_final: 0.8330 (p90) REVERT: Se 39 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8099 (mt) REVERT: CA 157 ASP cc_start: 0.8527 (m-30) cc_final: 0.8240 (m-30) REVERT: CA 263 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8344 (mp) REVERT: CB 251 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7961 (pm20) outliers start: 67 outliers final: 56 residues processed: 439 average time/residue: 0.1924 time to fit residues: 139.2916 Evaluate side-chains 445 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 382 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 43 VAL Chi-restraints excluded: chain SB residue 126 THR Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 180 THR Chi-restraints excluded: chain SC residue 111 VAL Chi-restraints excluded: chain SC residue 181 SER Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 139 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 157 ASN Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 248 ILE Chi-restraints excluded: chain SG residue 15 THR Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SG residue 170 THR Chi-restraints excluded: chain SG residue 212 LEU Chi-restraints excluded: chain SH residue 9 LEU Chi-restraints excluded: chain SH residue 10 SER Chi-restraints excluded: chain SH residue 30 SER Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 SER Chi-restraints excluded: chain SH residue 136 VAL Chi-restraints excluded: chain SI residue 7 SER Chi-restraints excluded: chain SI residue 14 THR Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 196 LEU Chi-restraints excluded: chain SJ residue 77 ILE Chi-restraints excluded: chain SJ residue 128 LEU Chi-restraints excluded: chain SJ residue 143 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 74 THR Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 19 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 103 GLU Chi-restraints excluded: chain SO residue 83 ILE Chi-restraints excluded: chain SO residue 99 GLN Chi-restraints excluded: chain SO residue 124 ASP Chi-restraints excluded: chain SW residue 104 LEU Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 46 SER Chi-restraints excluded: chain SX residue 117 ILE Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Se residue 39 LEU Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 250 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 263 LEU Chi-restraints excluded: chain CA residue 266 VAL Chi-restraints excluded: chain CB residue 251 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 302 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 214 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 335 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 130 GLN SE 157 ASN SG 197 ASN SH 89 HIS SL 21 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088407 restraints weight = 87656.421| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.52 r_work: 0.2781 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 49814 Z= 0.232 Angle : 0.643 16.172 73043 Z= 0.327 Chirality : 0.038 0.347 9192 Planarity : 0.005 0.115 4828 Dihedral : 15.023 179.160 17287 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.62 % Favored : 91.30 % Rotamer: Outliers : 3.22 % Allowed : 19.23 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.08 % Twisted Proline : 0.90 % Twisted General : 0.08 % 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: -0.91 (0.17), residues: 2599 helix: 1.13 (0.18), residues: 867 sheet: -0.77 (0.23), residues: 489 loop : -1.84 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSC 140 TYR 0.026 0.002 TYRSC 143 PHE 0.020 0.002 PHESX 86 TRP 0.013 0.001 TRPCA 113 HIS 0.005 0.001 HISSX 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (49814) covalent geometry : angle 0.64314 / 0.33 (73043) hydrogen bonds : bond 0.07397 / 4.50 ( 1809) hydrogen bonds : angle 4.07066 / 2.31 ( 3936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9872.05 seconds wall clock time: 169 minutes 51.78 seconds (10191.78 seconds total)