Starting phenix.real_space_refine on Tue Sep 15 22:11:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wtn_32792/09_2026/7wtn_32792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtn_32792/09_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_32792/09_2026/7wtn_32792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtn_32792/09_2026/7wtn_32792.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtn_32792/09_2026/7wtn_32792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtn_32792/09_2026/7wtn_32792.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wtn_32792/09_2026/7wtn_32792.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wtn_32792/09_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-2.2.1-6174/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: {'RNAv2': 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: 8.98, per 1000 atoms: 0.19 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: 3.87 Conformation dependent library (CDL) restraints added in 1.2 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: 6.39 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: 18.79 Time building geometry restraints manager: 5.35 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: 71771 3.55 - 7.09: 1214 7.09 - 10.64: 50 10.64 - 14.18: 7 14.18 - 17.73: 1 Bond angle restraints: 73043 Sorted by residual: angle pdb=" C3' UC2 272 " pdb=" O3' UC2 272 " pdb=" P GC2 273 " ideal model delta sigma weight residual 119.70 127.24 -7.54 1.20e+00 6.94e-01 3.95e+01 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=" C3' UC21097 " pdb=" O3' UC21097 " pdb=" P UC21098 " ideal model delta sigma weight residual 119.70 126.40 -6.70 1.20e+00 6.94e-01 3.11e+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 ... (remaining 73038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 24919 35.79 - 71.58: 2423 71.58 - 107.37: 117 107.37 - 143.16: 5 143.16 - 178.95: 6 Dihedral angle restraints: 27470 sinusoidal: 19910 harmonic: 7560 Sorted by residual: dihedral pdb=" C4' CC2 191 " pdb=" C3' CC2 191 " pdb=" C2' CC2 191 " pdb=" C1' CC2 191 " ideal model delta sinusoidal sigma weight residual 36.34 -40.32 76.66 1 3.10e+00 1.04e-01 7.68e+02 dihedral pdb=" C4' AC2 93 " pdb=" C3' AC2 93 " pdb=" C2' AC2 93 " pdb=" C1' AC2 93 " ideal model delta sinusoidal sigma weight residual 36.34 -39.32 75.66 1 3.10e+00 1.04e-01 7.52e+02 dihedral pdb=" C4' AC2 26 " pdb=" C3' AC2 26 " pdb=" C2' AC2 26 " pdb=" C1' AC2 26 " ideal model delta sinusoidal sigma weight residual 36.34 -39.03 75.37 1 3.10e+00 1.04e-01 7.47e+02 ... (remaining 27467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 7326 0.107 - 0.215: 626 0.215 - 0.322: 1222 0.322 - 0.429: 17 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=" P GC2 418 " pdb=" OP1 GC2 418 " pdb=" OP2 GC2 418 " pdb=" O5' GC2 418 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.41 2.00e-01 2.50e+01 4.12e+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: 3.120 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: 0.060 Extract box with map and model: 1.030 Check model and map are aligned: 0.150 Set scattering table: 0.130 Process input model: 53.440 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.810 ------------------------------------------------------------------------------- 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= 0.240 Angle : 1.077 17.728 73043 Z= 0.473 Chirality : 0.107 0.537 9192 Planarity : 0.008 0.189 4828 Dihedral : 20.773 178.946 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 0.00495 / 0.24 (49814) covalent geometry : angle 1.07694 / 0.47 (73043) hydrogen bonds : bond 0.12314 / 6.30 ( 1809) hydrogen bonds : angle 5.50028 / 2.20 ( 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 : 1.160 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: 0.3104 time to fit residues: 227.8893 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 : 1.183 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.8980 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3807 r_free = 0.3807 target = 0.131402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093896 restraints weight = 88459.544| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.43 r_work: 0.2923 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 49814 Z= 0.237 Angle : 1.385 21.364 73043 Z= 0.551 Chirality : 0.119 2.313 9192 Planarity : 0.006 0.132 4828 Dihedral : 19.004 171.820 17287 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.73 % Favored : 92.23 % Rotamer: Outliers : 1.79 % Allowed : 8.94 % Favored : 89.27 % 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: -1.34 (0.16), residues: 2599 helix: 0.42 (0.18), residues: 851 sheet: -0.40 (0.24), residues: 472 loop : -2.05 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGSC 140 TYR 0.012 0.001 TYRSG 169 PHE 0.023 0.002 PHESX 86 TRP 0.010 0.001 TRPCA 113 HIS 0.004 0.001 HISSX 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 (49814) covalent geometry : angle 1.38498 / 0.55 (73043) hydrogen bonds : bond 0.07947 / 4.05 ( 1809) hydrogen bonds : angle 4.43433 / 1.74 ( 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 476 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 436 time to evaluate : 1.189 Fit side-chains REVERT: SE 66 MET cc_start: 0.8994 (tpp) cc_final: 0.8477 (tpp) REVERT: SL 42 PHE cc_start: 0.7385 (m-10) cc_final: 0.7041 (m-10) REVERT: SL 50 GLU cc_start: 0.8375 (pp20) cc_final: 0.7997 (pp20) REVERT: SN 116 ILE cc_start: 0.8847 (mm) cc_final: 0.8589 (mt) REVERT: SN 138 ASN cc_start: 0.7045 (p0) cc_final: 0.6839 (p0) REVERT: SO 46 MET cc_start: 0.8651 (mtp) cc_final: 0.8166 (mpp) REVERT: SY 26 ASP cc_start: 0.8597 (p0) cc_final: 0.8329 (p0) REVERT: CA 209 ASP cc_start: 0.8358 (m-30) cc_final: 0.8130 (m-30) REVERT: CB 249 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8082 (mmtt) outliers start: 40 outliers final: 34 residues processed: 450 average time/residue: 0.2986 time to fit residues: 218.4460 Evaluate side-chains 420 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 386 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain SI residue 196 LEU 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 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 57 LEU 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 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: 6.9990 chunk 30 optimal weight: 3.9990 chunk 276 optimal weight: 0.0980 chunk 346 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 330 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 SH 89 HIS SI 20 GLN SI 111 GLN SY 22 GLN CA 153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.131944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092330 restraints weight = 88279.813| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.60 r_work: 0.2959 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1926 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= 0.201 Angle : 1.102 15.723 73043 Z= 0.450 Chirality : 0.090 0.845 9192 Planarity : 0.005 0.103 4828 Dihedral : 19.088 178.662 17287 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.20 % Favored : 91.77 % Rotamer: Outliers : 1.92 % Allowed : 13.10 % Favored : 84.97 % 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: -1.15 (0.16), residues: 2599 helix: 0.70 (0.18), residues: 869 sheet: -0.56 (0.24), residues: 488 loop : -1.96 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGSY 8 TYR 0.013 0.001 TYRSG 169 PHE 0.020 0.001 PHESG 144 TRP 0.009 0.001 TRPCA 113 HIS 0.004 0.001 HISSX 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (49814) covalent geometry : angle 1.10213 / 0.45 (73043) hydrogen bonds : bond 0.07815 / 3.98 ( 1809) hydrogen bonds : angle 4.17895 / 1.64 ( 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 480 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 437 time to evaluate : 1.130 Fit side-chains REVERT: SC 181 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7585 (m) REVERT: SI 89 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7462 (mm-30) REVERT: SI 140 GLU cc_start: 0.8534 (mp0) cc_final: 0.8296 (mp0) REVERT: SI 141 ARG cc_start: 0.8915 (ptp-170) cc_final: 0.8330 (ptp-170) REVERT: SL 58 CYS cc_start: 0.8764 (t) cc_final: 0.8082 (m) REVERT: SN 116 ILE cc_start: 0.8898 (mm) cc_final: 0.8688 (mt) REVERT: SN 138 ASN cc_start: 0.7103 (p0) cc_final: 0.6662 (p0) REVERT: SO 46 MET cc_start: 0.8757 (mtp) cc_final: 0.8158 (mpp) REVERT: SX 139 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7501 (mtpt) outliers start: 43 outliers final: 31 residues processed: 456 average time/residue: 0.2945 time to fit residues: 219.0970 Evaluate side-chains 423 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 391 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 193 LEU Chi-restraints excluded: chain SI residue 196 LEU 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 67 THR Chi-restraints excluded: chain SO residue 110 LEU Chi-restraints excluded: chain SO residue 124 ASP 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 SX residue 130 VAL Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Se residue 29 LYS Chi-restraints excluded: chain CA residue 126 LEU Chi-restraints excluded: chain CA residue 177 LEU 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: 2.9990 chunk 161 optimal weight: 50.0000 chunk 185 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 56 ASN SG 197 ASN SG 201 GLN SH 89 HIS SI 20 GLN SI 111 GLN SL 21 ASN SW 12 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 22 GLN CA 153 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091345 restraints weight = 88411.466| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.36 r_work: 0.2920 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 49814 Z= 0.252 Angle : 1.116 16.376 73043 Z= 0.455 Chirality : 0.090 0.891 9192 Planarity : 0.005 0.082 4828 Dihedral : 18.980 177.510 17287 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 2.50 % Allowed : 14.98 % Favored : 82.51 % 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: -1.10 (0.16), residues: 2599 helix: 0.82 (0.18), residues: 870 sheet: -0.69 (0.23), residues: 498 loop : -1.93 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGSC 95 TYR 0.013 0.001 TYRSN 89 PHE 0.016 0.002 PHECA 158 TRP 0.009 0.001 TRPCA 113 HIS 0.005 0.001 HISSX 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 (49814) covalent geometry : angle 1.11621 / 0.46 (73043) hydrogen bonds : bond 0.08100 / 4.13 ( 1809) hydrogen bonds : angle 4.17847 / 1.64 ( 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 474 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 418 time to evaluate : 1.175 Fit side-chains REVERT: SC 181 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7411 (m) REVERT: SE 66 MET cc_start: 0.9162 (tpp) cc_final: 0.8629 (tpp) REVERT: SI 141 ARG cc_start: 0.8984 (ptp-170) cc_final: 0.8457 (ptp-170) REVERT: SL 42 PHE cc_start: 0.7517 (m-10) cc_final: 0.7234 (m-10) REVERT: SN 116 ILE cc_start: 0.8951 (mm) cc_final: 0.8712 (mt) REVERT: SO 46 MET cc_start: 0.8793 (mtp) cc_final: 0.8143 (mpp) REVERT: SO 92 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8157 (ptpp) REVERT: SY 51 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8533 (mp0) REVERT: Se 39 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8294 (mt) outliers start: 56 outliers final: 42 residues processed: 448 average time/residue: 0.2725 time to fit residues: 200.8532 Evaluate side-chains 424 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 380 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 67 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 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 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 SL residue 76 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 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 104 LEU Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 71 CYS 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 Se residue 42 ARG Chi-restraints excluded: chain CA residue 124 LEU Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 302 optimal weight: 0.9990 chunk 331 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 GLN SE 130 GLN SE 157 ASN SH 89 HIS SI 20 GLN SI 111 GLN ** SI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 21 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 127 GLN CA 218 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087303 restraints weight = 88333.947| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.57 r_work: 0.2795 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 49814 Z= 0.377 Angle : 1.223 18.386 73043 Z= 0.500 Chirality : 0.098 1.071 9192 Planarity : 0.006 0.106 4828 Dihedral : 19.098 178.661 17287 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.89 % Favored : 91.04 % Rotamer: Outliers : 3.18 % Allowed : 16.23 % Favored : 80.59 % 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: -1.28 (0.16), residues: 2599 helix: 0.74 (0.18), residues: 866 sheet: -0.87 (0.23), residues: 507 loop : -2.05 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGSX 20 TYR 0.020 0.002 TYRSJ 114 PHE 0.020 0.002 PHESI 21 TRP 0.010 0.002 TRPCA 113 HIS 0.006 0.001 HISSX 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.38 (49814) covalent geometry : angle 1.22284 / 0.50 (73043) hydrogen bonds : bond 0.09137 / 4.67 ( 1809) hydrogen bonds : angle 4.32330 / 1.70 ( 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 459 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 388 time to evaluate : 1.185 Fit side-chains REVERT: SC 116 LYS cc_start: 0.7689 (tppp) cc_final: 0.7206 (tptt) REVERT: SC 137 ILE cc_start: 0.8884 (tp) cc_final: 0.8624 (mp) REVERT: SC 181 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7496 (m) REVERT: SE 66 MET cc_start: 0.9082 (tpp) cc_final: 0.8606 (tpp) REVERT: SH 142 TYR cc_start: 0.8840 (m-80) cc_final: 0.8487 (m-80) REVERT: SI 29 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7777 (pt) REVERT: SI 141 ARG cc_start: 0.9007 (ptp-170) cc_final: 0.8482 (ptp-170) REVERT: SO 46 MET cc_start: 0.8767 (mtp) cc_final: 0.8165 (mpp) REVERT: SO 92 LYS cc_start: 0.8417 (ptpp) cc_final: 0.8185 (ptpp) REVERT: SO 99 GLN cc_start: 0.8540 (mp10) cc_final: 0.8330 (mp10) REVERT: SX 139 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7280 (mtmm) REVERT: CA 157 ASP cc_start: 0.8610 (m-30) cc_final: 0.8377 (m-30) REVERT: CA 167 ASP cc_start: 0.7512 (t0) cc_final: 0.7245 (t0) outliers start: 71 outliers final: 53 residues processed: 429 average time/residue: 0.2860 time to fit residues: 201.6191 Evaluate side-chains 438 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 382 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 157 ASN Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SG residue 67 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 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 113 VAL Chi-restraints excluded: chain SJ residue 130 THR 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 46 THR Chi-restraints excluded: chain SN residue 67 THR Chi-restraints excluded: chain SN residue 103 GLU 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 SX residue 132 LEU Chi-restraints excluded: chain SX residue 139 LYS Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Sb residue 9 HIS 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 124 LEU Chi-restraints excluded: chain CA residue 126 LEU Chi-restraints excluded: chain CA residue 177 LEU Chi-restraints excluded: chain CA residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 326 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 260 optimal weight: 0.0020 chunk 249 optimal weight: 0.9990 chunk 371 optimal weight: 7.9990 chunk 335 optimal weight: 3.9990 chunk 138 optimal weight: 0.0370 chunk 163 optimal weight: 2.9990 overall best weight: 0.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 177 GLN SE 130 GLN SE 157 ASN SH 89 HIS SI 20 GLN SL 21 ASN ** SO 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 64 GLN CA 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.132986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094749 restraints weight = 88429.963| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.37 r_work: 0.2967 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 49814 Z= 0.156 Angle : 1.017 15.861 73043 Z= 0.415 Chirality : 0.081 0.786 9192 Planarity : 0.005 0.106 4828 Dihedral : 19.049 179.053 17287 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 2.59 % Allowed : 17.98 % Favored : 79.43 % 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: -0.92 (0.17), residues: 2599 helix: 1.13 (0.18), residues: 854 sheet: -0.78 (0.23), residues: 500 loop : -1.83 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGSC 140 TYR 0.022 0.001 TYRSJ 114 PHE 0.014 0.001 PHECA 158 TRP 0.012 0.001 TRPCA 113 HIS 0.003 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (49814) covalent geometry : angle 1.01680 / 0.42 (73043) hydrogen bonds : bond 0.07506 / 3.83 ( 1809) hydrogen bonds : angle 4.04663 / 1.60 ( 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 481 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 423 time to evaluate : 0.866 Fit side-chains REVERT: SC 116 LYS cc_start: 0.7751 (tppp) cc_final: 0.7327 (tptt) REVERT: SC 137 ILE cc_start: 0.8852 (tp) cc_final: 0.8606 (mp) REVERT: SC 181 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7436 (m) REVERT: SE 66 MET cc_start: 0.9011 (tpp) cc_final: 0.8576 (tpp) REVERT: SG 149 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7635 (mmtp) REVERT: SH 142 TYR cc_start: 0.8792 (m-80) cc_final: 0.8518 (m-80) REVERT: SI 29 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7647 (pt) REVERT: SI 141 ARG cc_start: 0.9012 (ptp-170) cc_final: 0.8577 (ptp-170) REVERT: SO 46 MET cc_start: 0.8676 (mtp) cc_final: 0.8118 (mpp) REVERT: SO 92 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7930 (ptpp) REVERT: Se 39 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8159 (mt) REVERT: CA 157 ASP cc_start: 0.8457 (m-30) cc_final: 0.8233 (m-30) REVERT: CA 167 ASP cc_start: 0.7419 (t0) cc_final: 0.7080 (t0) REVERT: CA 263 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8381 (mp) REVERT: CB 243 LYS cc_start: 0.7887 (tttt) cc_final: 0.7596 (ttmt) REVERT: CB 248 ARG cc_start: 0.7892 (tmm-80) cc_final: 0.7486 (tmm-80) REVERT: CB 249 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7588 (mmtt) outliers start: 58 outliers final: 34 residues processed: 452 average time/residue: 0.2556 time to fit residues: 188.1703 Evaluate side-chains 433 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 395 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 157 ASN 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 129 VAL 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 SH residue 136 VAL Chi-restraints excluded: chain SI residue 29 LEU Chi-restraints excluded: chain SI residue 36 THR 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 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 SW residue 104 LEU Chi-restraints excluded: chain SW residue 107 SER Chi-restraints excluded: chain SX residue 71 CYS 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 39 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 344 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 348 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN SG 197 ASN SH 89 HIS SI 20 GLN SI 111 GLN ** SI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 21 ASN ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.128495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.089675 restraints weight = 88114.464| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.45 r_work: 0.2818 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 49814 Z= 0.310 Angle : 1.136 16.479 73043 Z= 0.465 Chirality : 0.090 0.947 9192 Planarity : 0.006 0.109 4828 Dihedral : 18.961 178.279 17287 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.50 % Favored : 91.42 % Rotamer: Outliers : 2.77 % Allowed : 18.38 % Favored : 78.85 % 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: -1.04 (0.17), residues: 2599 helix: 1.04 (0.18), residues: 859 sheet: -0.89 (0.23), residues: 515 loop : -1.91 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGSC 95 TYR 0.015 0.002 TYRSJ 114 PHE 0.018 0.002 PHESI 21 TRP 0.010 0.001 TRPCA 113 HIS 0.005 0.001 HISSX 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.31 (49814) covalent geometry : angle 1.13647 / 0.46 (73043) hydrogen bonds : bond 0.08534 / 4.35 ( 1809) hydrogen bonds : angle 4.15988 / 1.64 ( 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 464 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 402 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SC 116 LYS cc_start: 0.7780 (tppp) cc_final: 0.7348 (tptt) REVERT: SC 137 ILE cc_start: 0.8857 (tp) cc_final: 0.8611 (mp) REVERT: SC 143 TYR cc_start: 0.8628 (m-80) cc_final: 0.8390 (m-80) REVERT: SC 181 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7433 (m) REVERT: SE 66 MET cc_start: 0.9057 (tpp) cc_final: 0.8629 (tpp) REVERT: SH 133 THR cc_start: 0.8053 (p) cc_final: 0.7829 (t) REVERT: SH 142 TYR cc_start: 0.8880 (m-80) cc_final: 0.8537 (m-80) REVERT: SI 29 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7894 (pt) REVERT: SO 24 ASN cc_start: 0.8109 (t0) cc_final: 0.7828 (t0) REVERT: SO 46 MET cc_start: 0.8759 (mtp) cc_final: 0.8113 (mpp) REVERT: SO 92 LYS cc_start: 0.8330 (ptpp) cc_final: 0.8083 (ptpp) REVERT: Se 39 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8204 (mt) REVERT: CA 157 ASP cc_start: 0.8550 (m-30) cc_final: 0.8311 (m-30) REVERT: CB 243 LYS cc_start: 0.7905 (tttt) cc_final: 0.7615 (ttmt) outliers start: 62 outliers final: 49 residues processed: 434 average time/residue: 0.2403 time to fit residues: 173.2544 Evaluate side-chains 434 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 382 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 32 ILE 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 181 SER 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 SE residue 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SG residue 67 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 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 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 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 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 Sb residue 9 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 116 optimal weight: 30.0000 chunk 175 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 302 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 312 optimal weight: 0.6980 chunk 279 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 177 GLN SE 157 ASN SH 89 HIS ** SI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 21 ASN ** SO 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 24 GLN 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 = 0.3796 r_free = 0.3796 target = 0.130709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.092310 restraints weight = 88355.012| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.57 r_work: 0.2885 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 49814 Z= 0.202 Angle : 1.052 16.671 73043 Z= 0.431 Chirality : 0.084 0.880 9192 Planarity : 0.005 0.113 4828 Dihedral : 18.966 179.322 17287 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 2.91 % Allowed : 18.38 % Favored : 78.71 % 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: 1.13 (0.18), residues: 857 sheet: -0.86 (0.23), residues: 509 loop : -1.86 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGSC 95 TYR 0.017 0.001 TYRSJ 114 PHE 0.016 0.001 PHESH 70 TRP 0.012 0.001 TRPCA 113 HIS 0.004 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (49814) covalent geometry : angle 1.05207 / 0.43 (73043) hydrogen bonds : bond 0.07809 / 3.98 ( 1809) hydrogen bonds : angle 4.09521 / 1.61 ( 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 474 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 409 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: SC 116 LYS cc_start: 0.7739 (tppp) cc_final: 0.7306 (tptt) REVERT: SC 137 ILE cc_start: 0.8830 (tp) cc_final: 0.8583 (mp) REVERT: SC 181 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7332 (m) REVERT: SE 66 MET cc_start: 0.9051 (tpp) cc_final: 0.8684 (tpp) REVERT: SG 97 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8986 (m) REVERT: SG 149 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7851 (mmtp) REVERT: SH 49 ILE cc_start: 0.8653 (tp) cc_final: 0.8442 (tp) REVERT: SH 142 TYR cc_start: 0.8837 (m-80) cc_final: 0.8501 (m-80) REVERT: SH 162 ILE cc_start: 0.9084 (mm) cc_final: 0.8719 (mt) REVERT: SI 29 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7793 (pt) REVERT: SI 61 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7753 (pp20) REVERT: SL 58 CYS cc_start: 0.8833 (t) cc_final: 0.8438 (m) REVERT: SO 24 ASN cc_start: 0.8064 (t0) cc_final: 0.7789 (t0) REVERT: SO 46 MET cc_start: 0.8675 (mtp) cc_final: 0.8077 (mpp) REVERT: SO 92 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7877 (ptpp) REVERT: Se 39 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8231 (mt) REVERT: CA 157 ASP cc_start: 0.8559 (m-30) cc_final: 0.8292 (m-30) REVERT: CA 263 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8392 (mp) REVERT: CB 248 ARG cc_start: 0.7991 (tmm-80) cc_final: 0.7756 (tmm-80) outliers start: 65 outliers final: 50 residues processed: 443 average time/residue: 0.2133 time to fit residues: 155.5086 Evaluate side-chains 455 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 399 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 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 67 VAL Chi-restraints excluded: chain SG residue 69 LEU 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 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 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 110 LEU 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 71 CYS 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 Sb residue 9 HIS 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 226 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CA residue 263 LEU 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: 3.9990 chunk 374 optimal weight: 0.9980 chunk 338 optimal weight: 0.8980 chunk 328 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 148 optimal weight: 30.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN SG 197 ASN SH 89 HIS ** SI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 21 ASN ** SO 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093885 restraints weight = 87838.483| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.35 r_work: 0.2943 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 49814 Z= 0.171 Angle : 1.025 16.188 73043 Z= 0.420 Chirality : 0.081 0.820 9192 Planarity : 0.005 0.115 4828 Dihedral : 18.933 179.876 17287 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 2.95 % Allowed : 18.78 % Favored : 78.26 % 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: -0.91 (0.17), residues: 2599 helix: 1.18 (0.18), residues: 857 sheet: -0.89 (0.23), residues: 494 loop : -1.80 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGSC 95 TYR 0.029 0.001 TYRSC 143 PHE 0.015 0.001 PHESH 70 TRP 0.013 0.001 TRPCA 113 HIS 0.004 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (49814) covalent geometry : angle 1.02522 / 0.42 (73043) hydrogen bonds : bond 0.07607 / 3.87 ( 1809) hydrogen bonds : angle 4.05302 / 1.59 ( 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 479 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 413 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: SC 115 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7627 (mm) REVERT: SC 116 LYS cc_start: 0.7706 (tppp) cc_final: 0.7341 (tptt) REVERT: SC 137 ILE cc_start: 0.8842 (tp) cc_final: 0.8597 (mp) REVERT: SC 181 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7420 (m) REVERT: SE 66 MET cc_start: 0.8974 (tpp) cc_final: 0.8570 (tpp) REVERT: SG 149 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7698 (mmtp) REVERT: SH 49 ILE cc_start: 0.8646 (tp) cc_final: 0.8423 (tp) REVERT: SH 142 TYR cc_start: 0.8796 (m-80) cc_final: 0.8501 (m-80) REVERT: SH 162 ILE cc_start: 0.9018 (mm) cc_final: 0.8618 (mt) REVERT: SI 29 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7737 (pt) REVERT: SI 61 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7533 (pp20) REVERT: SI 142 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9165 (tttt) REVERT: SJ 19 TYR cc_start: 0.9102 (m-80) cc_final: 0.8847 (m-80) REVERT: SL 58 CYS cc_start: 0.8730 (t) cc_final: 0.8395 (m) REVERT: SO 46 MET cc_start: 0.8655 (mtp) cc_final: 0.8072 (mpp) REVERT: SO 92 LYS cc_start: 0.8199 (ptpp) cc_final: 0.7966 (ptpp) REVERT: SW 107 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.7999 (t) REVERT: Se 39 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8150 (mt) REVERT: CA 157 ASP cc_start: 0.8530 (m-30) cc_final: 0.8260 (m-30) REVERT: CB 247 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8989 (mm) REVERT: CB 251 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7953 (pm20) outliers start: 66 outliers final: 45 residues processed: 448 average time/residue: 0.2249 time to fit residues: 165.7121 Evaluate side-chains 452 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 398 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 115 ILE 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 181 VAL Chi-restraints excluded: chain SE residue 227 VAL Chi-restraints excluded: chain SE residue 248 ILE Chi-restraints excluded: chain SG residue 12 SER Chi-restraints excluded: chain SG residue 67 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 153 VAL Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 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 142 LYS 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 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 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 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 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 226 LEU Chi-restraints excluded: chain CA residue 259 VAL Chi-restraints excluded: chain CB residue 247 LEU 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 11 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 229 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN SG 197 ASN SH 89 HIS SI 20 GLN ** SI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 21 ASN ** SO 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 64 GLN ** 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 = 0.3795 r_free = 0.3795 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092375 restraints weight = 88301.557| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.34 r_work: 0.2896 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2736 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= 0.214 Angle : 1.051 16.036 73043 Z= 0.431 Chirality : 0.083 0.838 9192 Planarity : 0.005 0.114 4828 Dihedral : 18.890 179.489 17287 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 2.64 % Allowed : 19.19 % Favored : 78.18 % 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: -0.92 (0.17), residues: 2599 helix: 1.17 (0.18), residues: 859 sheet: -0.90 (0.23), residues: 494 loop : -1.81 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARGSC 95 TYR 0.024 0.001 TYRSC 143 PHE 0.021 0.001 PHESb 79 TRP 0.014 0.001 TRPCA 113 HIS 0.004 0.001 HISSC 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (49814) covalent geometry : angle 1.05134 / 0.43 (73043) hydrogen bonds : bond 0.07873 / 4.01 ( 1809) hydrogen bonds : angle 4.07466 / 1.60 ( 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 455 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 396 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: SC 116 LYS cc_start: 0.7645 (tppp) cc_final: 0.7391 (tptt) REVERT: SC 137 ILE cc_start: 0.8934 (tp) cc_final: 0.8683 (mp) REVERT: SC 181 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7420 (m) REVERT: SE 66 MET cc_start: 0.9033 (tpp) cc_final: 0.8601 (tpp) REVERT: SG 149 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7704 (mmtp) REVERT: SH 47 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8700 (tpp80) REVERT: SH 142 TYR cc_start: 0.8811 (m-80) cc_final: 0.8527 (m-80) REVERT: SI 29 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7768 (pt) REVERT: SI 61 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7638 (pp20) REVERT: SI 142 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9159 (tttt) REVERT: SJ 19 TYR cc_start: 0.9106 (m-80) cc_final: 0.8838 (m-80) REVERT: SL 58 CYS cc_start: 0.8770 (t) cc_final: 0.8326 (m) REVERT: SO 24 ASN cc_start: 0.8067 (t0) cc_final: 0.7803 (t0) REVERT: SO 46 MET cc_start: 0.8685 (mtp) cc_final: 0.8092 (mpp) REVERT: SO 92 LYS cc_start: 0.8249 (ptpp) cc_final: 0.8001 (ptpp) REVERT: Sb 79 PHE cc_start: 0.8848 (p90) cc_final: 0.8501 (p90) REVERT: Se 39 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8157 (mt) REVERT: CA 117 TYR cc_start: 0.8578 (p90) cc_final: 0.8354 (p90) REVERT: CA 157 ASP cc_start: 0.8531 (m-30) cc_final: 0.8263 (m-30) REVERT: CB 251 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7972 (pm20) outliers start: 59 outliers final: 51 residues processed: 426 average time/residue: 0.1891 time to fit residues: 132.0891 Evaluate side-chains 450 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 393 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 67 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 9 LEU Chi-restraints excluded: chain SH residue 73 VAL Chi-restraints excluded: chain SH residue 106 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 142 LYS 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 110 LEU 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 48 TYR Chi-restraints excluded: chain SY residue 74 LEU Chi-restraints excluded: chain SY residue 104 SER Chi-restraints excluded: chain Sb residue 9 HIS 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 226 LEU Chi-restraints excluded: chain CA residue 259 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: 5.9990 chunk 214 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 222 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 335 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 130 GLN SG 197 ASN SH 89 HIS ** SI 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 21 ASN ** SO 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.091644 restraints weight = 88170.998| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.46 r_work: 0.2865 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 49814 Z= 0.260 Angle : 1.077 17.329 73043 Z= 0.443 Chirality : 0.085 0.865 9192 Planarity : 0.006 0.115 4828 Dihedral : 18.882 179.470 17287 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.23 % Favored : 91.69 % Rotamer: Outliers : 2.77 % Allowed : 19.10 % Favored : 78.13 % Cbeta Deviations : 0.04 % 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: -0.95 (0.17), residues: 2599 helix: 1.15 (0.18), residues: 858 sheet: -0.92 (0.23), residues: 494 loop : -1.82 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGSC 95 TYR 0.025 0.002 TYRSC 143 PHE 0.023 0.002 PHESb 79 TRP 0.012 0.001 TRPCA 113 HIS 0.004 0.001 HISCA 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (49814) covalent geometry : angle 1.07749 / 0.44 (73043) hydrogen bonds : bond 0.08058 / 4.11 ( 1809) hydrogen bonds : angle 4.09282 / 1.61 ( 3936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9503.40 seconds wall clock time: 163 minutes 45.33 seconds (9825.33 seconds total)