Starting phenix.real_space_refine on Tue Sep 15 19:36:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtm_32791/09_2026/7wtm_32791.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 1106 5.49 5 S 49 5.16 5 C 23868 2.51 5 N 8138 2.21 5 O 11461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 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: 44623 Number of models: 1 Model: "" Number of chains: 18 Chain: "C2" Number of atoms: 23575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1106, 23575 Classifications: {'RNAv2': 1106} Modifications used: {'rna2p_pur': 98, 'rna2p_pyr': 86, 'rna3p_pur': 495, 'rna3p_pyr': 427} Link IDs: {'rna2p': 184, 'rna3p': 921} Chain breaks: 6 Chain: "SB" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "SE" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "SG" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "SH" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 171} Chain: "SI" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "SJ" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "SL" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "SN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "SO" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "SW" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "SX" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SY" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Sb" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Se" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 201 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} 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: "JL" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2262 Classifications: {'peptide': 283} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 265} Chain: "Sb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.73, per 1000 atoms: 0.22 Number of scatterers: 44623 At special positions: 0 Unit cell: (153.909, 207.306, 202.071, 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 49 16.00 P 1106 15.00 O 11461 8.00 N 8138 7.00 C 23868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.2 seconds 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4934 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 28 sheets defined 37.9% alpha, 18.7% beta 357 base pairs and 560 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'SB' and resid 58 through 62 removed outlier: 4.157A pdb=" N LYSSB 62 " --> pdb=" O ASPSB 59 " (cutoff:3.500A) Processing helix chain 'SB' and resid 70 through 75 Processing helix chain 'SB' and resid 76 through 80 removed outlier: 3.839A pdb=" N HISSB 79 " --> pdb=" O SERSB 76 " (cutoff:3.500A) Processing helix chain 'SB' and resid 106 through 114 Processing helix chain 'SB' and resid 157 through 178 removed outlier: 3.884A pdb=" N GLYSB 178 " --> pdb=" O LYSSB 174 " (cutoff:3.500A) Processing helix chain 'SB' and resid 180 through 189 Processing helix chain 'SB' and resid 191 through 202 removed outlier: 3.824A pdb=" N LYSSB 195 " --> pdb=" O GLUSB 191 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 232 removed outlier: 3.647A pdb=" N LEUSB 228 " --> pdb=" O ASPSB 224 " (cutoff:3.500A) Processing helix chain 'SE' and resid 15 through 19 removed outlier: 3.686A pdb=" N TRPSE 18 " --> pdb=" O PROSE 15 " (cutoff:3.500A) Processing helix chain 'SE' and resid 44 through 50 Processing helix chain 'SE' and resid 57 through 66 Processing helix chain 'SE' and resid 94 through 96 No H-bonds generated for 'chain 'SE' and resid 94 through 96' 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 25 removed outlier: 3.636A pdb=" N ILESG 24 " --> pdb=" O GLUSG 21 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARGSG 25 " --> pdb=" O HISSG 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'SG' and resid 21 through 25' Processing helix chain 'SG' and resid 39 through 41 No H-bonds generated for 'chain 'SG' and resid 39 through 41' Processing helix chain 'SG' and resid 42 through 46 removed outlier: 3.895A pdb=" N LYSSG 46 " --> pdb=" O ASPSG 43 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 152 through 156 removed outlier: 3.505A pdb=" N ASPSG 155 " --> pdb=" O ASPSG 152 " (cutoff:3.500A) Processing helix chain 'SG' and resid 180 through 217 Processing helix chain 'SH' and resid 14 through 29 Processing helix chain 'SH' and resid 31 through 39 removed outlier: 3.890A pdb=" N ARGSH 39 " --> pdb=" O LYSSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 66 through 74 removed outlier: 3.681A pdb=" N PHESH 70 " --> pdb=" O SERSH 66 " (cutoff:3.500A) Processing helix chain 'SH' and resid 75 through 85 Processing helix chain 'SH' and resid 113 through 116 Processing helix chain 'SH' and resid 117 through 130 removed outlier: 3.586A pdb=" N VALSH 130 " --> pdb=" O LEUSH 126 " (cutoff:3.500A) Processing helix chain 'SH' and resid 158 through 162 removed outlier: 4.410A pdb=" N GLNSH 161 " --> pdb=" O ASPSH 158 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILESH 162 " --> pdb=" O VALSH 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'SH' and resid 158 through 162' Processing helix chain 'SH' and resid 165 through 177 Processing helix chain 'SI' and resid 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 88 through 93 removed outlier: 4.183A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THRSI 93 " --> pdb=" O GLUSI 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 88 through 93' Processing helix chain 'SI' and resid 106 through 117 Processing helix chain 'SI' and resid 136 through 146 removed outlier: 3.905A pdb=" N GLUSI 140 " --> pdb=" O SERSI 136 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 163 removed outlier: 4.445A pdb=" N GLUSI 157 " --> pdb=" O GLUSI 153 " (cutoff:3.500A) Processing helix chain 'SI' and resid 172 through 177 Processing helix chain 'SI' and resid 186 through 200 Processing helix chain 'SJ' and resid 20 through 35 Processing helix chain 'SJ' and resid 39 through 62 removed outlier: 3.679A pdb=" N ARGSJ 62 " --> pdb=" O ASPSJ 58 " (cutoff:3.500A) 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 106 removed outlier: 3.617A pdb=" N PHESJ 104 " --> pdb=" O LYSSJ 100 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 108 through 115 Processing helix chain 'SJ' and resid 121 through 131 removed outlier: 3.505A pdb=" N GLNSJ 131 " --> pdb=" O VALSJ 127 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 152 through 156 removed outlier: 3.754A pdb=" N ILESJ 156 " --> pdb=" O GLUSJ 153 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 162 through 166 Processing helix chain 'SJ' and resid 170 through 183 Processing helix chain 'SL' and resid 45 through 50 removed outlier: 3.760A pdb=" N ILESL 49 " --> pdb=" O PROSL 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLUSL 50 " --> pdb=" O LYSSL 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 45 through 50' Processing helix chain 'SN' and resid 31 through 42 removed outlier: 3.860A pdb=" N GLUSN 35 " --> pdb=" O GLUSN 31 " (cutoff:3.500A) Processing helix chain 'SN' and resid 46 through 58 Processing helix chain 'SN' and resid 62 through 68 removed outlier: 3.705A 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 143 through 151 removed outlier: 3.769A pdb=" N SERSN 147 " --> pdb=" O SERSN 143 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASNSN 151 " --> pdb=" O SERSN 147 " (cutoff:3.500A) Processing helix chain 'SO' and resid 43 through 47 removed outlier: 3.504A pdb=" N METSO 46 " --> pdb=" O THRSO 43 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSSO 47 " --> pdb=" O GLYSO 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'SO' and resid 43 through 47' Processing helix chain 'SO' and resid 56 through 75 Processing helix chain 'SO' and resid 95 through 108 removed outlier: 3.675A pdb=" N GLNSO 99 " --> pdb=" O GLYSO 95 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SERSO 108 " --> pdb=" O ALASO 104 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 21 removed outlier: 3.677A pdb=" N ASPSW 9 " --> pdb=" O SERSW 5 " (cutoff:3.500A) Processing helix chain 'SW' and resid 31 through 44 removed outlier: 3.836A pdb=" N HISSW 44 " --> pdb=" O VALSW 40 " (cutoff:3.500A) Processing helix chain 'SW' and resid 82 through 84 No H-bonds generated for 'chain 'SW' and resid 82 through 84' Processing helix chain 'SW' and resid 85 through 94 Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SX' and resid 11 through 25 removed outlier: 3.955A 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 39 Processing helix chain 'SX' and resid 132 through 137 Processing helix chain 'SY' and resid 36 through 48 removed outlier: 3.761A pdb=" N LEUSY 40 " --> pdb=" O SERSY 36 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.676A pdb=" N ALASY 82 " --> pdb=" O SERSY 78 " (cutoff:3.500A) Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 104 through 116 Processing helix chain 'SY' and resid 122 through 135 removed outlier: 3.804A pdb=" N ASPSY 135 " --> pdb=" O ARGSY 131 " (cutoff:3.500A) Processing helix chain 'Sb' and resid 11 through 18 Processing helix chain 'Se' and resid 32 through 44 Processing helix chain 'CA' and resid 102 through 104 No H-bonds generated for 'chain 'CA' and resid 102 through 104' Processing helix chain 'CA' and resid 105 through 112 Processing helix chain 'CA' and resid 112 through 123 Proline residue: CA 118 - end of helix removed outlier: 3.966A pdb=" N HISCA 123 " --> pdb=" O PROCA 119 " (cutoff:3.500A) Processing helix chain 'CA' and resid 148 through 164 removed outlier: 4.073A pdb=" N LEUCA 152 " --> pdb=" O ASPCA 148 " (cutoff:3.500A) Processing helix chain 'CA' and resid 167 through 177 Processing helix chain 'CA' and resid 187 through 191 Processing helix chain 'CA' and resid 195 through 207 Processing helix chain 'CA' and resid 210 through 220 Processing helix chain 'CA' and resid 236 through 252 Processing helix chain 'CA' and resid 255 through 271 removed outlier: 3.635A pdb=" N VALCA 259 " --> pdb=" O PROCA 255 " (cutoff:3.500A) Processing helix chain 'JL' and resid 41 through 51 removed outlier: 3.764A pdb=" N ALAJL 45 " --> pdb=" O ASNJL 41 " (cutoff:3.500A) Processing helix chain 'JL' and resid 70 through 78 removed outlier: 4.013A pdb=" N ILEJL 74 " --> pdb=" O LEUJL 70 " (cutoff:3.500A) Processing helix chain 'JL' and resid 87 through 97 Processing helix chain 'JL' and resid 103 through 105 No H-bonds generated for 'chain 'JL' and resid 103 through 105' Processing helix chain 'JL' and resid 130 through 132 No H-bonds generated for 'chain 'JL' and resid 130 through 132' Processing helix chain 'JL' and resid 133 through 143 removed outlier: 4.189A pdb=" N VALJL 138 " --> pdb=" O SERJL 134 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHEJL 139 " --> pdb=" O SERJL 135 " (cutoff:3.500A) Processing helix chain 'JL' and resid 157 through 164 removed outlier: 3.650A pdb=" N LEUJL 164 " --> pdb=" O ALAJL 160 " (cutoff:3.500A) Processing helix chain 'JL' and resid 173 through 182 Processing helix chain 'JL' and resid 192 through 196 removed outlier: 3.814A pdb=" N ASNJL 195 " --> pdb=" O GLYJL 192 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEJL 196 " --> pdb=" O LYSJL 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'JL' and resid 192 through 196' Processing helix chain 'JL' and resid 219 through 231 Processing helix chain 'JL' and resid 237 through 242 Processing helix chain 'JL' and resid 245 through 262 Processing helix chain 'JL' and resid 272 through 289 removed outlier: 4.362A pdb=" N VALJL 276 " --> pdb=" O SERJL 272 " (cutoff:3.500A) Processing helix chain 'JL' and resid 299 through 313 removed outlier: 3.580A pdb=" N PHEJL 303 " --> pdb=" O ASPJL 299 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VALJL 313 " --> pdb=" O ALAJL 309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'SB' and resid 44 through 48 removed outlier: 8.332A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SB' and resid 66 through 69 removed outlier: 8.238A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHESB 105 " --> pdb=" O ARGSB 213 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ARGSB 213 " --> pdb=" O PHESB 105 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VALSB 212 " --> pdb=" O ILESB 140 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILESB 140 " --> pdb=" O VALSB 212 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VALSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SE' and resid 9 through 10 removed outlier: 4.668A pdb=" N LEUSE 9 " --> pdb=" O ALASE 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SE' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'SE' and resid 75 through 76 removed outlier: 3.959A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SE' and resid 102 through 104 removed outlier: 4.504A pdb=" N VALSE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'SE' and resid 122 through 126 Processing sheet with id=AA8, first strand: chain 'SE' and resid 128 through 131 Processing sheet with id=AA9, first strand: chain 'SE' and resid 217 through 221 removed outlier: 6.661A pdb=" N LEUSE 207 " --> pdb=" O LYSSE 198 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYSSE 198 " --> pdb=" O LEUSE 207 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HISSE 209 " --> pdb=" O VALSE 196 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLYSE 229 " --> pdb=" O LEUSE 180 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYRSE 182 " --> pdb=" O VALSE 227 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VALSE 227 " --> pdb=" O TYRSE 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SG' and resid 12 through 17 removed outlier: 6.091A pdb=" N LEUSG 106 " --> pdb=" O ASPSG 57 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASPSG 57 " --> pdb=" O LEUSG 106 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VALSG 108 " --> pdb=" O GLYSG 55 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLYSG 55 " --> pdb=" O VALSG 108 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALASG 110 " --> pdb=" O SERSG 53 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VALSG 49 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'SG' and resid 73 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: 5.688A pdb=" N ASNSH 147 " --> pdb=" O TYRSH 142 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYRSH 142 " --> pdb=" O ASNSH 147 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILESH 149 " --> pdb=" O VALSH 140 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VALSH 140 " --> pdb=" O ILESH 149 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYSSH 151 " --> pdb=" O LYSSH 138 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYSSH 138 " --> pdb=" O LYSSH 151 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEUSH 153 " --> pdb=" O VALSH 136 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHESW 50 " --> pdb=" O TYRSH 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 42 through 47 removed outlier: 6.528A pdb=" N HISSI 44 " --> pdb=" O ALASI 57 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALASI 57 " --> pdb=" O HISSI 44 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VALSI 46 " --> pdb=" O TYRSI 55 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYRSI 55 " --> pdb=" O VALSI 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SI' and resid 72 through 75 removed outlier: 6.935A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 181 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILESI 183 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SERSI 66 " --> pdb=" O ILESI 183 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLNSI 103 " --> pdb=" O VALSI 81 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VALSI 81 " --> pdb=" O GLNSI 103 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASPSI 105 " --> pdb=" O ALASI 79 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALASI 79 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SJ' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain 'SL' and resid 70 through 80 removed outlier: 18.500A pdb=" N ILESL 70 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 15.311A pdb=" N LEUSL 91 " --> pdb=" O ILESL 70 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N THRSL 72 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALASL 89 " --> pdb=" O THRSL 72 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VALSL 85 " --> pdb=" O VALSL 76 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N THRSL 78 " --> pdb=" O THRSL 83 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THRSL 83 " --> pdb=" O THRSL 78 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N VALSL 135 " --> pdb=" O ASNSL 106 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHESL 137 " --> pdb=" O PROSL 108 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VALSL 135 " --> pdb=" O PROSL 130 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N PHESL 137 " --> pdb=" O CYSSL 128 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N CYSSL 128 " --> pdb=" O PHESL 137 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VALSL 139 " --> pdb=" O GLYSL 126 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLYSL 126 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASPSL 121 " --> pdb=" O VALSL 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SO' and resid 40 through 42 removed outlier: 6.622A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SO' and resid 40 through 42 removed outlier: 6.622A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLUSO 116 " --> pdb=" O VALSO 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SW' and resid 71 through 74 removed outlier: 5.446A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SX' and resid 49 through 57 removed outlier: 5.868A pdb=" N VALSX 53 " --> pdb=" O GLNSX 75 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLNSX 75 " --> pdb=" O VALSX 53 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VALSX 72 " --> pdb=" O ALASX 85 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N PHESX 122 " --> pdb=" O LYSSX 82 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THRSX 84 " --> pdb=" O PHESX 122 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VALSX 124 " --> pdb=" O THRSX 84 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHESX 86 " --> pdb=" O VALSX 124 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LYSSX 126 " --> pdb=" O PHESX 86 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEUSX 103 " --> pdb=" O VALSX 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'SY' and resid 6 through 15 removed outlier: 4.247A pdb=" N VALSY 12 " --> pdb=" O GLNSY 22 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLNSY 22 " --> pdb=" O VALSY 12 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N SERSY 14 " --> pdb=" O ARGSY 20 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARGSY 20 " --> pdb=" O SERSY 14 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VALSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHESY 60 " --> pdb=" O VALSY 70 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHESY 72 " --> pdb=" O PHESY 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Sb' and resid 44 through 47 Processing sheet with id=AC7, first strand: chain 'Sb' and resid 64 through 65 Processing sheet with id=AC8, first strand: chain 'CA' and resid 95 through 100 Processing sheet with id=AC9, first strand: chain 'CA' and resid 181 through 186 Processing sheet with id=AD1, first strand: chain 'JL' and resid 107 through 111 removed outlier: 6.564A pdb=" N VALJL 81 " --> pdb=" O GLUJL 108 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N METJL 110 " --> pdb=" O VALJL 81 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALAJL 83 " --> pdb=" O METJL 110 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VALJL 60 " --> pdb=" O VALJL 82 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VALJL 84 " --> pdb=" O VALJL 60 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLUJL 62 " --> pdb=" O VALJL 84 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VALJL 59 " --> pdb=" O ILEJL 124 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILEJL 126 " --> pdb=" O VALJL 59 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEUJL 61 " --> pdb=" O ILEJL 126 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N METJL 189 " --> pdb=" O VALJL 206 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARGJL 208 " --> pdb=" O HISJL 187 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HISJL 187 " --> pdb=" O ARGJL 208 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLUJL 210 " --> pdb=" O VALJL 185 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VALJL 185 " --> pdb=" O GLUJL 210 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 854 hydrogen bonds 1328 hydrogen bond angles 0 basepair planarities 357 basepair parallelities 560 stacking parallelities Total time for adding SS restraints: 16.81 Time building geometry restraints manager: 5.33 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: 7775 1.33 - 1.45: 17787 1.45 - 1.58: 19935 1.58 - 1.70: 2202 1.70 - 1.82: 79 Bond restraints: 47778 Sorted by residual: bond pdb=" C SERJL 135 " pdb=" N PROJL 136 " ideal model delta sigma weight residual 1.336 1.375 -0.039 1.20e-02 6.94e+03 1.06e+01 bond pdb=" C GLNSX 63 " pdb=" N PROSX 64 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.08e-02 8.57e+03 8.07e+00 bond pdb=" C LEUSN 45 " pdb=" N THRSN 46 " ideal model delta sigma weight residual 1.329 1.290 0.038 1.60e-02 3.91e+03 5.75e+00 bond pdb=" CB VALSE 126 " pdb=" CG1 VALSE 126 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.38e+00 bond pdb=" CB VALSL 109 " pdb=" CG1 VALSL 109 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 ... (remaining 47773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 68771 3.87 - 7.74: 1030 7.74 - 11.60: 28 11.60 - 15.47: 5 15.47 - 19.34: 1 Bond angle restraints: 69835 Sorted by residual: angle pdb=" C3' UC2 272 " pdb=" O3' UC2 272 " pdb=" P GC2 273 " ideal model delta sigma weight residual 119.70 127.34 -7.64 1.20e+00 6.94e-01 4.06e+01 angle pdb=" C SERSH 30 " pdb=" N SERSH 31 " pdb=" CA SERSH 31 " ideal model delta sigma weight residual 121.70 132.35 -10.65 1.80e+00 3.09e-01 3.50e+01 angle pdb=" CA LEUSG 69 " pdb=" CB LEUSG 69 " pdb=" CG LEUSG 69 " ideal model delta sigma weight residual 116.30 135.64 -19.34 3.50e+00 8.16e-02 3.05e+01 angle pdb=" C3' UC21097 " pdb=" O3' UC21097 " pdb=" P UC21098 " ideal model delta sigma weight residual 119.70 126.31 -6.61 1.20e+00 6.94e-01 3.03e+01 angle pdb=" C3' AC2 417 " pdb=" O3' AC2 417 " pdb=" P GC2 418 " ideal model delta sigma weight residual 119.70 126.19 -6.49 1.20e+00 6.94e-01 2.93e+01 ... (remaining 69830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 24094 35.77 - 71.53: 2281 71.53 - 107.30: 119 107.30 - 143.07: 4 143.07 - 178.83: 6 Dihedral angle restraints: 26504 sinusoidal: 18869 harmonic: 7635 Sorted by residual: dihedral pdb=" C4' AC2 93 " pdb=" C3' AC2 93 " pdb=" C2' AC2 93 " pdb=" C1' AC2 93 " ideal model delta sinusoidal sigma weight residual 36.34 -41.25 77.60 1 3.10e+00 1.04e-01 7.84e+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 -41.10 77.44 1 3.10e+00 1.04e-01 7.82e+02 dihedral pdb=" C4' AC2 103 " pdb=" C3' AC2 103 " pdb=" C2' AC2 103 " pdb=" C1' AC2 103 " ideal model delta sinusoidal sigma weight residual 36.34 -39.31 75.66 1 3.10e+00 1.04e-01 7.52e+02 ... (remaining 26501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 6844 0.101 - 0.201: 693 0.201 - 0.302: 1172 0.302 - 0.402: 37 0.402 - 0.503: 4 Chirality restraints: 8750 Sorted by residual: chirality pdb=" CB ILESX 117 " pdb=" CA ILESX 117 " pdb=" CG1 ILESX 117 " pdb=" CG2 ILESX 117 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" P UC2 794 " pdb=" OP1 UC2 794 " pdb=" OP2 UC2 794 " pdb=" O5' UC2 794 " both_signs ideal model delta sigma weight residual True 2.17 -2.63 -0.46 2.00e-01 2.50e+01 5.23e+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 4.13e+00 ... (remaining 8747 not shown) Planarity restraints: 4782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CC2 962 " 0.029 2.00e-02 2.50e+03 4.21e-02 3.99e+01 pdb=" N1 CC2 962 " -0.028 2.00e-02 2.50e+03 pdb=" C2 CC2 962 " -0.099 2.00e-02 2.50e+03 pdb=" O2 CC2 962 " 0.057 2.00e-02 2.50e+03 pdb=" N3 CC2 962 " 0.012 2.00e-02 2.50e+03 pdb=" C4 CC2 962 " -0.018 2.00e-02 2.50e+03 pdb=" N4 CC2 962 " 0.025 2.00e-02 2.50e+03 pdb=" C5 CC2 962 " 0.009 2.00e-02 2.50e+03 pdb=" C6 CC2 962 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CC2 224 " 0.005 2.00e-02 2.50e+03 3.13e-02 2.21e+01 pdb=" N1 CC2 224 " 0.004 2.00e-02 2.50e+03 pdb=" C2 CC2 224 " -0.077 2.00e-02 2.50e+03 pdb=" O2 CC2 224 " 0.047 2.00e-02 2.50e+03 pdb=" N3 CC2 224 " 0.004 2.00e-02 2.50e+03 pdb=" C4 CC2 224 " -0.015 2.00e-02 2.50e+03 pdb=" N4 CC2 224 " 0.013 2.00e-02 2.50e+03 pdb=" C5 CC2 224 " 0.016 2.00e-02 2.50e+03 pdb=" C6 CC2 224 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC2 430 " 0.011 2.00e-02 2.50e+03 2.67e-02 2.13e+01 pdb=" N9 GC2 430 " -0.004 2.00e-02 2.50e+03 pdb=" C8 GC2 430 " -0.002 2.00e-02 2.50e+03 pdb=" N7 GC2 430 " 0.003 2.00e-02 2.50e+03 pdb=" C5 GC2 430 " 0.003 2.00e-02 2.50e+03 pdb=" C6 GC2 430 " -0.010 2.00e-02 2.50e+03 pdb=" O6 GC2 430 " 0.019 2.00e-02 2.50e+03 pdb=" N1 GC2 430 " -0.001 2.00e-02 2.50e+03 pdb=" C2 GC2 430 " -0.074 2.00e-02 2.50e+03 pdb=" N2 GC2 430 " 0.049 2.00e-02 2.50e+03 pdb=" N3 GC2 430 " 0.001 2.00e-02 2.50e+03 pdb=" C4 GC2 430 " 0.005 2.00e-02 2.50e+03 ... (remaining 4779 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 2111 2.67 - 3.23: 37421 3.23 - 3.78: 82429 3.78 - 4.34: 108607 4.34 - 4.90: 152947 Nonbonded interactions: 383515 Sorted by model distance: nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.110 3.040 nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.114 3.040 nonbonded pdb=" OG1 THRSb 55 " pdb="ZN ZNSb 101 " model vdw 2.128 2.230 nonbonded pdb=" O ILESb 62 " pdb="ZN ZNSb 101 " model vdw 2.141 2.230 nonbonded pdb=" O2 UC2 231 " pdb=" O6 GC2 234 " model vdw 2.199 3.040 ... (remaining 383510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.130 Process input model: 52.050 Find NCS groups from input model: 0.240 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.006 0.077 47778 Z= 0.300 Angle : 1.121 19.338 69835 Z= 0.489 Chirality : 0.107 0.503 8750 Planarity : 0.007 0.080 4782 Dihedral : 20.831 178.834 21570 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.57 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 1.77 % Twisted General : 0.20 % 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: -1.86 (0.16), residues: 2617 helix: -0.69 (0.16), residues: 864 sheet: -0.99 (0.24), residues: 494 loop : -1.67 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGSI 164 TYR 0.039 0.003 TYRSJ 43 PHE 0.036 0.003 PHESJ 104 TRP 0.041 0.002 TRPSX 136 HIS 0.018 0.002 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.30 (47778) covalent geometry : angle 1.12082 / 0.49 (69835) hydrogen bonds : bond 0.12114 / 6.21 ( 1714) hydrogen bonds : angle 5.91799 / 2.31 ( 3758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 30 PHE cc_start: 0.7711 (m-80) cc_final: 0.7437 (m-80) REVERT: SH 174 ASN cc_start: 0.7843 (t0) cc_final: 0.7483 (t0) REVERT: SL 77 SER cc_start: 0.8238 (t) cc_final: 0.7924 (t) REVERT: SO 36 LYS cc_start: 0.8950 (tttp) cc_final: 0.8713 (ttmm) REVERT: SY 13 ILE cc_start: 0.7974 (tt) cc_final: 0.7737 (tt) REVERT: CA 183 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6729 (mm-30) REVERT: JL 179 VAL cc_start: 0.7070 (m) cc_final: 0.6783 (t) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.2704 time to fit residues: 172.0113 Evaluate side-chains 285 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 112 GLN SN 36 GLN SX 18 HIS CA 239 HIS ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.128367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108323 restraints weight = 98082.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103467 restraints weight = 133395.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099580 restraints weight = 112449.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099930 restraints weight = 113533.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099578 restraints weight = 77715.260| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47778 Z= 0.210 Angle : 1.322 19.772 69835 Z= 0.529 Chirality : 0.109 1.672 8750 Planarity : 0.005 0.066 4782 Dihedral : 19.178 176.419 16186 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.93 % Rotamer: Outliers : 1.01 % Allowed : 9.47 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.88 % Twisted General : 0.12 % 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: -1.18 (0.16), residues: 2617 helix: 0.34 (0.18), residues: 865 sheet: -0.91 (0.24), residues: 485 loop : -1.51 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGSE 256 TYR 0.032 0.001 TYRCA 117 PHE 0.031 0.002 PHESH 24 TRP 0.012 0.001 TRPSX 136 HIS 0.005 0.001 HISSX 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (47778) covalent geometry : angle 1.32204 / 0.53 (69835) hydrogen bonds : bond 0.07451 / 3.86 ( 1714) hydrogen bonds : angle 4.64499 / 1.81 ( 3758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 325 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 30 PHE cc_start: 0.7879 (m-80) cc_final: 0.7511 (m-80) REVERT: SG 1 MET cc_start: 0.5373 (tpt) cc_final: 0.4781 (tpt) REVERT: SH 174 ASN cc_start: 0.8095 (t0) cc_final: 0.7636 (t0) REVERT: SL 77 SER cc_start: 0.8675 (t) cc_final: 0.8343 (t) REVERT: SN 104 ARG cc_start: 0.7242 (mtm-85) cc_final: 0.6892 (ptm-80) outliers start: 23 outliers final: 12 residues processed: 338 average time/residue: 0.2753 time to fit residues: 154.4887 Evaluate side-chains 301 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 289 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SI residue 179 CYS Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SY residue 7 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 163 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 307 optimal weight: 0.9990 chunk 264 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 ASN SH 110 GLN ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 103 GLN SI 159 GLN SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 155 HIS SN 36 GLN CA 239 HIS JL 77 GLN ** JL 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.126015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.106225 restraints weight = 96893.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099210 restraints weight = 132165.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096084 restraints weight = 163464.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096845 restraints weight = 135674.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096789 restraints weight = 90239.947| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 47778 Z= 0.275 Angle : 1.177 17.802 69835 Z= 0.481 Chirality : 0.095 1.221 8750 Planarity : 0.005 0.067 4782 Dihedral : 19.254 176.806 16186 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.60 % Favored : 92.32 % Rotamer: Outliers : 1.76 % Allowed : 13.39 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.05 (0.16), residues: 2617 helix: 0.64 (0.18), residues: 862 sheet: -0.98 (0.24), residues: 489 loop : -1.53 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGSb 17 TYR 0.029 0.002 TYRCA 117 PHE 0.037 0.002 PHESH 24 TRP 0.012 0.001 TRPSX 24 HIS 0.005 0.001 HISCA 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.28 (47778) covalent geometry : angle 1.17718 / 0.48 (69835) hydrogen bonds : bond 0.07883 / 4.07 ( 1714) hydrogen bonds : angle 4.48533 / 1.75 ( 3758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 30 PHE cc_start: 0.7907 (m-80) cc_final: 0.7695 (m-80) REVERT: SG 1 MET cc_start: 0.5523 (tpt) cc_final: 0.4991 (tpt) REVERT: SH 174 ASN cc_start: 0.8269 (t0) cc_final: 0.7805 (t0) REVERT: SL 77 SER cc_start: 0.8861 (t) cc_final: 0.8595 (t) REVERT: SY 49 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7326 (mmtt) REVERT: Sb 82 LYS cc_start: 0.7046 (ptpt) cc_final: 0.6781 (ptpp) REVERT: CA 259 VAL cc_start: 0.8502 (m) cc_final: 0.8296 (t) outliers start: 40 outliers final: 29 residues processed: 335 average time/residue: 0.2642 time to fit residues: 149.2763 Evaluate side-chains 305 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 207 LEU 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 SG residue 20 ASP Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 93 THR Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SX residue 130 VAL Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 7 ILE Chi-restraints excluded: chain Sb residue 24 LEU Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Se residue 38 LEU Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain CA residue 246 SER Chi-restraints excluded: chain JL residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 210 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 288 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... SB 74 GLN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 67 GLN ** SE 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 5 GLN ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 159 GLN SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 110 HIS SN 58 HIS SO 29 HIS Sb 19 HIS ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JL 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103612 restraints weight = 97381.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100150 restraints weight = 138937.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097839 restraints weight = 88205.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097126 restraints weight = 110182.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097018 restraints weight = 86115.993| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 47778 Z= 0.327 Angle : 1.212 17.871 69835 Z= 0.493 Chirality : 0.097 1.229 8750 Planarity : 0.006 0.069 4782 Dihedral : 19.283 174.860 16186 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.76 % Favored : 92.17 % Rotamer: Outliers : 2.73 % Allowed : 15.28 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % 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: -1.12 (0.16), residues: 2617 helix: 0.58 (0.18), residues: 879 sheet: -1.09 (0.24), residues: 498 loop : -1.54 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGSb 17 TYR 0.030 0.002 TYRCA 117 PHE 0.025 0.002 PHEJL 159 TRP 0.014 0.002 TRPCA 113 HIS 0.026 0.002 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.33 (47778) covalent geometry : angle 1.21161 / 0.49 (69835) hydrogen bonds : bond 0.08158 / 4.21 ( 1714) hydrogen bonds : angle 4.47450 / 1.75 ( 3758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SE 66 MET cc_start: 0.8097 (mmm) cc_final: 0.7769 (mmm) REVERT: SH 174 ASN cc_start: 0.8201 (t0) cc_final: 0.7801 (t0) REVERT: SL 77 SER cc_start: 0.8938 (t) cc_final: 0.8727 (t) REVERT: Sb 26 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7294 (pp30) REVERT: Sb 82 LYS cc_start: 0.6951 (ptpt) cc_final: 0.6733 (ptpp) outliers start: 62 outliers final: 41 residues processed: 345 average time/residue: 0.2668 time to fit residues: 154.4512 Evaluate side-chains 316 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 101 HIS Chi-restraints excluded: chain SB residue 171 ILE 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 162 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SG residue 89 ASP Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 151 LYS Chi-restraints excluded: chain SJ residue 49 LEU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SN residue 134 VAL Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 122 PHE Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 5 VAL Chi-restraints excluded: chain SY residue 7 ILE Chi-restraints excluded: chain Sb residue 24 LEU Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Se residue 38 LEU Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 152 LEU Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain CA residue 246 SER Chi-restraints excluded: chain JL residue 86 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 330 optimal weight: 2.9990 chunk 183 optimal weight: 0.0040 chunk 323 optimal weight: 9.9990 chunk 367 optimal weight: 8.9990 chunk 357 optimal weight: 0.5980 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 5 GLN ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 159 GLN SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JL 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107954 restraints weight = 97243.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.100940 restraints weight = 128839.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097607 restraints weight = 159317.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098347 restraints weight = 132017.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098366 restraints weight = 89381.079| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 47778 Z= 0.193 Angle : 1.054 17.725 69835 Z= 0.429 Chirality : 0.085 1.132 8750 Planarity : 0.005 0.065 4782 Dihedral : 19.241 176.787 16186 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 2.55 % Allowed : 17.31 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.88 % 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: -0.88 (0.17), residues: 2617 helix: 0.81 (0.18), residues: 880 sheet: -0.98 (0.24), residues: 494 loop : -1.42 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSb 17 TYR 0.029 0.002 TYRCA 117 PHE 0.039 0.002 PHESH 24 TRP 0.011 0.001 TRPCA 113 HIS 0.014 0.001 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (47778) covalent geometry : angle 1.05417 / 0.43 (69835) hydrogen bonds : bond 0.07331 / 3.78 ( 1714) hydrogen bonds : angle 4.26665 / 1.67 ( 3758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 318 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 229 MET cc_start: 0.6398 (mmm) cc_final: 0.6117 (mmm) REVERT: SE 66 MET cc_start: 0.8013 (mmm) cc_final: 0.7794 (mmm) REVERT: SH 174 ASN cc_start: 0.8167 (t0) cc_final: 0.7724 (t0) REVERT: SI 121 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6146 (pp) REVERT: SI 151 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6907 (ptpp) REVERT: SL 77 SER cc_start: 0.8892 (t) cc_final: 0.8683 (t) REVERT: Se 44 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6396 (p90) outliers start: 58 outliers final: 34 residues processed: 357 average time/residue: 0.2641 time to fit residues: 156.5169 Evaluate side-chains 324 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 207 LEU Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 162 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 220 THR Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 60 ILE Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SI residue 151 LYS Chi-restraints excluded: chain SJ residue 49 LEU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SO residue 48 VAL Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 93 THR Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SY residue 7 ILE Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Se residue 38 LEU Chi-restraints excluded: chain Se residue 44 PHE Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 152 LEU Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain JL residue 86 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 347 optimal weight: 50.0000 chunk 351 optimal weight: 0.5980 chunk 245 optimal weight: 0.4980 chunk 292 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 260 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 69 HIS ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 5 GLN ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS ** JL 77 GLN ** 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 = 0.3904 r_free = 0.3904 target = 0.128778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107536 restraints weight = 97983.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103721 restraints weight = 140176.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100313 restraints weight = 116882.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100492 restraints weight = 109082.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100421 restraints weight = 80361.207| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47778 Z= 0.164 Angle : 1.012 17.809 69835 Z= 0.412 Chirality : 0.081 1.088 8750 Planarity : 0.005 0.067 4782 Dihedral : 19.143 177.737 16186 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.20 % Rotamer: Outliers : 2.77 % Allowed : 17.31 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % 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: -0.70 (0.17), residues: 2617 helix: 1.04 (0.18), residues: 876 sheet: -0.93 (0.24), residues: 496 loop : -1.36 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGSb 17 TYR 0.020 0.002 TYRCA 117 PHE 0.030 0.001 PHESX 95 TRP 0.013 0.001 TRPCA 113 HIS 0.014 0.001 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (47778) covalent geometry : angle 1.01235 / 0.41 (69835) hydrogen bonds : bond 0.07056 / 3.63 ( 1714) hydrogen bonds : angle 4.14496 / 1.62 ( 3758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 299 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SE 66 MET cc_start: 0.8049 (mmm) cc_final: 0.7800 (mmm) REVERT: SH 5 GLN cc_start: 0.5662 (mm110) cc_final: 0.5284 (mm-40) REVERT: SH 174 ASN cc_start: 0.8166 (t0) cc_final: 0.7642 (t0) REVERT: SI 121 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6175 (pp) REVERT: SI 151 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6906 (ptpp) REVERT: SL 77 SER cc_start: 0.8931 (t) cc_final: 0.8685 (t) REVERT: Sb 26 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7207 (pp30) REVERT: Se 44 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6319 (p90) outliers start: 63 outliers final: 42 residues processed: 346 average time/residue: 0.2663 time to fit residues: 154.1450 Evaluate side-chains 328 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 113 MET Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 207 LEU 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 159 THR Chi-restraints excluded: chain SE residue 162 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 220 THR Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 60 ILE Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SI residue 151 LYS Chi-restraints excluded: chain SJ residue 49 LEU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SN residue 134 VAL Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 48 VAL Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 93 THR Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 75 GLN Chi-restraints excluded: chain SX residue 122 PHE Chi-restraints excluded: chain SY residue 5 VAL Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Se residue 44 PHE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 152 LEU Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain CA residue 239 HIS Chi-restraints excluded: chain JL residue 176 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 138 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 317 optimal weight: 7.9990 chunk 212 optimal weight: 0.3980 chunk 342 optimal weight: 0.6980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 159 GLN SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106358 restraints weight = 96496.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101397 restraints weight = 133644.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098122 restraints weight = 120194.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098457 restraints weight = 129028.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098507 restraints weight = 84242.055| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 47778 Z= 0.213 Angle : 1.054 17.526 69835 Z= 0.430 Chirality : 0.083 1.054 8750 Planarity : 0.005 0.068 4782 Dihedral : 19.132 178.090 16186 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.88 % Favored : 93.08 % Rotamer: Outliers : 2.73 % Allowed : 18.36 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.73 (0.17), residues: 2617 helix: 1.02 (0.18), residues: 875 sheet: -1.00 (0.24), residues: 503 loop : -1.34 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGSN 20 TYR 0.026 0.002 TYRCA 117 PHE 0.063 0.002 PHESH 24 TRP 0.017 0.001 TRPCA 113 HIS 0.026 0.001 HISCA 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (47778) covalent geometry : angle 1.05357 / 0.43 (69835) hydrogen bonds : bond 0.07338 / 3.78 ( 1714) hydrogen bonds : angle 4.18138 / 1.64 ( 3758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SE 66 MET cc_start: 0.8074 (mmm) cc_final: 0.7768 (mmm) REVERT: SH 5 GLN cc_start: 0.5987 (mm110) cc_final: 0.5768 (mm-40) REVERT: SH 174 ASN cc_start: 0.8203 (t0) cc_final: 0.7698 (t0) REVERT: SI 121 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6196 (pp) REVERT: SL 77 SER cc_start: 0.8935 (t) cc_final: 0.8694 (t) REVERT: Sb 26 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7263 (pp30) REVERT: Se 44 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6385 (p90) outliers start: 62 outliers final: 43 residues processed: 343 average time/residue: 0.2689 time to fit residues: 155.7202 Evaluate side-chains 323 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 113 MET Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 207 LEU 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 159 THR Chi-restraints excluded: chain SE residue 162 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 220 THR Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SG residue 71 THR Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 60 ILE Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SI residue 151 LYS Chi-restraints excluded: chain SJ residue 49 LEU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SN residue 134 VAL Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 48 VAL Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SW residue 121 VAL Chi-restraints excluded: chain SX residue 75 GLN Chi-restraints excluded: chain SY residue 5 VAL Chi-restraints excluded: chain Sb residue 3 LEU Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Se residue 44 PHE Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 152 LEU Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain JL residue 312 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 44 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 188 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 112 GLN ** SN 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.127793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107664 restraints weight = 97876.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.102981 restraints weight = 137636.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100053 restraints weight = 110789.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100026 restraints weight = 100383.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099892 restraints weight = 78574.946| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 47778 Z= 0.195 Angle : 1.039 17.510 69835 Z= 0.424 Chirality : 0.082 1.021 8750 Planarity : 0.005 0.065 4782 Dihedral : 19.133 178.252 16186 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.88 % Favored : 93.05 % Rotamer: Outliers : 2.69 % Allowed : 18.41 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.69 (0.17), residues: 2617 helix: 1.04 (0.18), residues: 881 sheet: -0.91 (0.24), residues: 497 loop : -1.36 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGSE 11 TYR 0.026 0.002 TYRCA 117 PHE 0.031 0.002 PHESX 86 TRP 0.017 0.001 TRPCA 113 HIS 0.013 0.001 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (47778) covalent geometry : angle 1.03934 / 0.42 (69835) hydrogen bonds : bond 0.07229 / 3.73 ( 1714) hydrogen bonds : angle 4.14411 / 1.63 ( 3758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 293 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 229 MET cc_start: 0.6317 (mmm) cc_final: 0.6039 (mmm) REVERT: SE 66 MET cc_start: 0.8080 (mmm) cc_final: 0.7776 (mmm) REVERT: SH 174 ASN cc_start: 0.8176 (t0) cc_final: 0.7665 (t0) REVERT: SI 121 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6202 (pp) REVERT: SL 77 SER cc_start: 0.8928 (t) cc_final: 0.8687 (t) REVERT: Sb 26 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7243 (pp30) REVERT: Se 44 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6325 (p90) REVERT: JL 261 MET cc_start: 0.6741 (ppp) cc_final: 0.6407 (ppp) outliers start: 61 outliers final: 50 residues processed: 339 average time/residue: 0.2547 time to fit residues: 144.7197 Evaluate side-chains 332 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 101 HIS Chi-restraints excluded: chain SB residue 113 MET Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 207 LEU 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 159 THR Chi-restraints excluded: chain SE residue 162 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 220 THR Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 60 ILE Chi-restraints excluded: chain SI residue 77 ARG Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SI residue 151 LYS Chi-restraints excluded: chain SJ residue 49 LEU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 157 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SL residue 101 GLU Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SN residue 134 VAL Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 48 VAL Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SW residue 121 VAL Chi-restraints excluded: chain SX residue 75 GLN Chi-restraints excluded: chain SX residue 122 PHE Chi-restraints excluded: chain SY residue 5 VAL Chi-restraints excluded: chain SY residue 7 ILE Chi-restraints excluded: chain Sb residue 3 LEU Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Se residue 44 PHE Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 152 LEU Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain JL residue 312 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 94 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 159 GLN SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JL 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.125739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105305 restraints weight = 97453.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.099564 restraints weight = 139194.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096526 restraints weight = 124939.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096813 restraints weight = 121456.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096702 restraints weight = 85713.166| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 47778 Z= 0.281 Angle : 1.127 20.089 69835 Z= 0.461 Chirality : 0.088 0.979 8750 Planarity : 0.005 0.064 4782 Dihedral : 19.170 178.810 16186 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.64 % Favored : 92.28 % Rotamer: Outliers : 2.55 % Allowed : 18.93 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2617 helix: 0.89 (0.18), residues: 890 sheet: -1.07 (0.24), residues: 501 loop : -1.41 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGSH 79 TYR 0.026 0.002 TYRCA 117 PHE 0.048 0.002 PHESH 24 TRP 0.016 0.002 TRPCA 113 HIS 0.013 0.001 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.28 (47778) covalent geometry : angle 1.12713 / 0.46 (69835) hydrogen bonds : bond 0.07789 / 4.02 ( 1714) hydrogen bonds : angle 4.26463 / 1.67 ( 3758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SB 229 MET cc_start: 0.6509 (mmm) cc_final: 0.6229 (mmm) REVERT: SE 66 MET cc_start: 0.8115 (mmm) cc_final: 0.7769 (mmm) REVERT: SH 174 ASN cc_start: 0.8261 (t0) cc_final: 0.7856 (t0) REVERT: SI 121 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6302 (pp) REVERT: SL 77 SER cc_start: 0.8922 (t) cc_final: 0.8696 (t) REVERT: Sb 26 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7202 (pp30) REVERT: Sb 82 LYS cc_start: 0.7211 (pttm) cc_final: 0.6972 (ptpp) REVERT: Se 44 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.6865 (p90) outliers start: 58 outliers final: 50 residues processed: 329 average time/residue: 0.2590 time to fit residues: 143.0548 Evaluate side-chains 327 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 101 HIS Chi-restraints excluded: chain SB residue 113 MET Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 207 LEU 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 159 THR Chi-restraints excluded: chain SE residue 162 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 220 THR Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SG residue 89 ASP Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 60 ILE Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SI residue 151 LYS Chi-restraints excluded: chain SJ residue 49 LEU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 157 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SL residue 101 GLU Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SN residue 134 VAL Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 48 VAL Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SW residue 121 VAL Chi-restraints excluded: chain SX residue 75 GLN Chi-restraints excluded: chain SY residue 5 VAL Chi-restraints excluded: chain SY residue 7 ILE Chi-restraints excluded: chain Sb residue 3 LEU Chi-restraints excluded: chain Sb residue 25 VAL Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Se residue 44 PHE Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 152 LEU Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain JL residue 312 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 236 optimal weight: 0.0870 chunk 174 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 272 optimal weight: 0.1980 chunk 268 optimal weight: 6.9990 chunk 341 optimal weight: 6.9990 chunk 326 optimal weight: 10.0000 overall best weight: 3.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.104686 restraints weight = 97830.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099025 restraints weight = 133998.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095304 restraints weight = 124361.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095702 restraints weight = 124414.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095554 restraints weight = 84026.262| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 47778 Z= 0.298 Angle : 1.154 20.132 69835 Z= 0.473 Chirality : 0.090 0.982 8750 Planarity : 0.005 0.065 4782 Dihedral : 19.241 179.583 16186 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.55 % Rotamer: Outliers : 2.82 % Allowed : 18.80 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.17), residues: 2617 helix: 0.78 (0.18), residues: 889 sheet: -1.09 (0.24), residues: 495 loop : -1.45 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGSb 17 TYR 0.025 0.002 TYRCA 117 PHE 0.031 0.002 PHESG 144 TRP 0.015 0.002 TRPCA 113 HIS 0.011 0.001 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.30 (47778) covalent geometry : angle 1.15433 / 0.47 (69835) hydrogen bonds : bond 0.07973 / 4.12 ( 1714) hydrogen bonds : angle 4.34593 / 1.71 ( 3758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 268 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 229 MET cc_start: 0.6508 (mmm) cc_final: 0.6223 (mmm) REVERT: SE 66 MET cc_start: 0.8104 (mmm) cc_final: 0.7751 (mmm) REVERT: SH 174 ASN cc_start: 0.8277 (t0) cc_final: 0.7927 (t0) REVERT: SI 121 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6322 (pp) REVERT: Sb 26 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7231 (pp30) REVERT: Se 44 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7180 (p90) outliers start: 64 outliers final: 55 residues processed: 316 average time/residue: 0.2648 time to fit residues: 139.9294 Evaluate side-chains 322 residues out of total 2271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 101 HIS Chi-restraints excluded: chain SB residue 113 MET Chi-restraints excluded: chain SB residue 171 ILE Chi-restraints excluded: chain SB residue 207 LEU 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 159 THR Chi-restraints excluded: chain SE residue 162 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 220 THR Chi-restraints excluded: chain SG residue 20 ASP Chi-restraints excluded: chain SG residue 71 THR Chi-restraints excluded: chain SG residue 89 ASP Chi-restraints excluded: chain SG residue 97 VAL Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 91 ILE Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 77 ARG Chi-restraints excluded: chain SI residue 81 VAL Chi-restraints excluded: chain SI residue 114 GLU Chi-restraints excluded: chain SI residue 121 LEU Chi-restraints excluded: chain SI residue 151 LYS Chi-restraints excluded: chain SJ residue 49 LEU Chi-restraints excluded: chain SJ residue 96 VAL Chi-restraints excluded: chain SJ residue 157 ASP Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 9 SER Chi-restraints excluded: chain SL residue 101 GLU Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 138 ASN Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 131 THR Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SN residue 134 VAL Chi-restraints excluded: chain SO residue 33 LEU Chi-restraints excluded: chain SO residue 48 VAL Chi-restraints excluded: chain SO residue 55 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 76 SER Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SW residue 121 VAL Chi-restraints excluded: chain SX residue 57 LEU Chi-restraints excluded: chain SX residue 75 GLN Chi-restraints excluded: chain SX residue 135 LEU Chi-restraints excluded: chain SY residue 5 VAL Chi-restraints excluded: chain SY residue 7 ILE Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 33 LEU Chi-restraints excluded: chain Se residue 44 PHE Chi-restraints excluded: chain CA residue 99 ILE Chi-restraints excluded: chain CA residue 127 GLN Chi-restraints excluded: chain CA residue 152 LEU Chi-restraints excluded: chain CA residue 214 PHE Chi-restraints excluded: chain CA residue 246 SER Chi-restraints excluded: chain JL residue 312 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 205 optimal weight: 6.9990 chunk 316 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 327 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 112 GLN ** SJ 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SN 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 239 HIS ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105470 restraints weight = 97618.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099113 restraints weight = 134953.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095397 restraints weight = 136787.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095955 restraints weight = 127106.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095848 restraints weight = 84377.047| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 47778 Z= 0.278 Angle : 1.135 21.395 69835 Z= 0.465 Chirality : 0.089 0.987 8750 Planarity : 0.005 0.063 4782 Dihedral : 19.230 179.584 16186 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.68 % Favored : 92.24 % Rotamer: Outliers : 2.64 % Allowed : 19.51 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.54 % Cis-general : 0.08 % Twisted Proline : 0.88 % Twisted General : 0.12 % 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: 2617 helix: 0.80 (0.18), residues: 887 sheet: -1.06 (0.24), residues: 487 loop : -1.46 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGSH 79 TYR 0.031 0.002 TYRSL 93 PHE 0.022 0.002 PHESX 95 TRP 0.036 0.002 TRPCA 113 HIS 0.011 0.001 HISSW 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.28 (47778) covalent geometry : angle 1.13498 / 0.47 (69835) hydrogen bonds : bond 0.07834 / 4.05 ( 1714) hydrogen bonds : angle 4.33604 / 1.71 ( 3758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6755.36 seconds wall clock time: 118 minutes 31.21 seconds (7111.21 seconds total)