Starting phenix.real_space_refine on Sat Oct 31 17:27:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sdp_54789/10_2026/9sdp_54789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sdp_54789/10_2026/9sdp_54789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sdp_54789/10_2026/9sdp_54789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sdp_54789/10_2026/9sdp_54789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sdp_54789/10_2026/9sdp_54789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sdp_54789/10_2026/9sdp_54789.map" } resolution = 3.3 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= 0.003 sd= 0.017 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: 8 Type Number sf(0) Gaussians K 3 8.98 5 Zn 1 6.06 5 P 1081 5.49 5 Mg 14 5.21 5 S 90 5.16 5 C 24061 2.51 5 N 8290 2.21 5 O 11262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44802 Number of models: 1 Model: "" Number of chains: 22 Chain: "9" Number of atoms: 23135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 23135 Classifications: {'RNA': 1081} Modifications used: {'rna2p_pur': 104, 'rna2p_pyr': 51, 'rna3p': 13, 'rna3p_pur': 490, 'rna3p_pyr': 418} Link IDs: {'rna2p': 154, 'rna3p': 926} Chain breaks: 15 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 12 Chain: "BA" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1500 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Chain: "BB" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1696 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "BC" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "BE" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2058 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 13, 'TRANS': 241} Chain: "BG" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1579 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain breaks: 3 Chain: "BH" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1439 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 1 Chain: "BI" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1480 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 3, 'TRANS': 179} Chain breaks: 1 Chain: "BJ" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1432 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain: "BL" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 8, 'TRANS': 129} Chain: "BN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1192 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "cS" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "BV" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "BW" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "BX" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1075 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "BY" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 917 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 1 Chain: "BZ" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 783 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "Bb" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "Be" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 292 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Cn" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 211 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "9" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' K': 3, ' MG': 14} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "BZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43022 SG CYSBZ 23 160.483 101.279 100.602 1.00161.53 S ATOM 43042 SG CYSBZ 26 157.538 102.163 103.150 1.00136.35 S ATOM 43427 SG CYSBZ 74 157.380 103.180 99.280 1.00151.55 S ATOM 43446 SG CYSBZ 77 159.601 104.660 101.649 1.00137.98 S Time building chain proxies: 8.64, per 1000 atoms: 0.19 Number of scatterers: 44802 At special positions: 0 Unit cell: (214.2, 176.4, 150.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 K 3 19.00 S 90 16.00 P 1081 15.00 Mg 14 11.99 O 11262 8.00 N 8290 7.00 C 24061 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: 3.75 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNBZ 201 " pdb="ZN ZNBZ 201 " - pdb=" SG CYSBZ 77 " pdb="ZN ZNBZ 201 " - pdb=" SG CYSBZ 26 " pdb="ZN ZNBZ 201 " - pdb=" SG CYSBZ 74 " pdb="ZN ZNBZ 201 " - pdb=" SG CYSBZ 23 " Number of angles added : 6 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4990 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 30 sheets defined 35.1% alpha, 21.2% beta 310 base pairs and 501 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'BA' and resid 16 through 26 removed outlier: 4.078A pdb=" N ILEBA 20 " --> pdb=" O LYSBA 16 " (cutoff:3.500A) Processing helix chain 'BA' and resid 39 through 41 No H-bonds generated for 'chain 'BA' and resid 39 through 41' Processing helix chain 'BA' and resid 55 through 72 Processing helix chain 'BA' and resid 75 through 77 No H-bonds generated for 'chain 'BA' and resid 75 through 77' Processing helix chain 'BA' and resid 85 through 100 removed outlier: 3.848A pdb=" N GLNBA 89 " --> pdb=" O ARGBA 85 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARGBA 90 " --> pdb=" O PROBA 86 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALABA 91 " --> pdb=" O TYRBA 87 " (cutoff:3.500A) Processing helix chain 'BA' and resid 132 through 134 No H-bonds generated for 'chain 'BA' and resid 132 through 134' Processing helix chain 'BA' and resid 135 through 144 removed outlier: 3.711A pdb=" N LEUBA 144 " --> pdb=" O LYSBA 140 " (cutoff:3.500A) Processing helix chain 'BA' and resid 173 through 191 removed outlier: 3.951A pdb=" N GLYBA 177 " --> pdb=" O LYSBA 173 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEUBA 179 " --> pdb=" O SERBA 175 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHEBA 180 " --> pdb=" O ILEBA 176 " (cutoff:3.500A) Processing helix chain 'BA' and resid 203 through 207 Processing helix chain 'BB' and resid 22 through 25 Processing helix chain 'BB' and resid 56 through 62 Processing helix chain 'BB' and resid 70 through 75 Processing helix chain 'BB' and resid 157 through 178 Processing helix chain 'BB' and resid 180 through 189 removed outlier: 3.556A pdb=" N ILEBB 189 " --> pdb=" O VALBB 185 " (cutoff:3.500A) Processing helix chain 'BB' and resid 191 through 202 Processing helix chain 'BB' and resid 224 through 228 removed outlier: 3.712A pdb=" N LYSBB 227 " --> pdb=" O ASPBB 224 " (cutoff:3.500A) Processing helix chain 'BC' and resid 51 through 58 Processing helix chain 'BC' and resid 63 through 70 Processing helix chain 'BC' and resid 76 through 83 Processing helix chain 'BC' and resid 131 through 146 Processing helix chain 'BC' and resid 192 through 201 removed outlier: 3.534A pdb=" N PHEBC 201 " --> pdb=" O LYSBC 197 " (cutoff:3.500A) Processing helix chain 'BC' and resid 220 through 232 Processing helix chain 'BC' and resid 237 through 241 Processing helix chain 'BC' and resid 249 through 254 Processing helix chain 'BC' and resid 254 through 259 Processing helix chain 'BE' and resid 15 through 19 Processing helix chain 'BE' and resid 37 through 41 removed outlier: 4.057A pdb=" N CYSBE 41 " --> pdb=" O SERBE 38 " (cutoff:3.500A) Processing helix chain 'BE' and resid 44 through 50 Processing helix chain 'BE' and resid 57 through 67 removed outlier: 3.641A pdb=" N GLNBE 67 " --> pdb=" O SERBE 63 " (cutoff:3.500A) Processing helix chain 'BE' and resid 116 through 119 Processing helix chain 'BE' and resid 133 through 135 No H-bonds generated for 'chain 'BE' and resid 133 through 135' Processing helix chain 'BE' and resid 247 through 256 Processing helix chain 'BG' and resid 42 through 46 removed outlier: 3.585A pdb=" N LYSBG 46 " --> pdb=" O GLUBG 43 " (cutoff:3.500A) Processing helix chain 'BG' and resid 139 through 148 Processing helix chain 'BG' and resid 158 through 163 Processing helix chain 'BG' and resid 185 through 222 removed outlier: 3.505A pdb=" N LEUBG 189 " --> pdb=" O THRBG 185 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYSBG 199 " --> pdb=" O ARGBG 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYSBG 222 " --> pdb=" O ALABG 218 " (cutoff:3.500A) Processing helix chain 'BH' and resid 17 through 34 Processing helix chain 'BH' and resid 34 through 42 removed outlier: 3.816A pdb=" N SERBH 39 " --> pdb=" O GLNBH 35 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLUBH 40 " --> pdb=" O GLUBH 36 " (cutoff:3.500A) Processing helix chain 'BH' and resid 69 through 76 removed outlier: 3.505A pdb=" N ILEBH 76 " --> pdb=" O ALABH 72 " (cutoff:3.500A) Processing helix chain 'BH' and resid 76 through 88 Processing helix chain 'BH' and resid 118 through 131 removed outlier: 3.544A pdb=" N VALBH 131 " --> pdb=" O LEUBH 127 " (cutoff:3.500A) Processing helix chain 'BH' and resid 159 through 164 Processing helix chain 'BH' and resid 166 through 179 Processing helix chain 'BI' and resid 25 through 29 removed outlier: 3.926A pdb=" N GLUBI 28 " --> pdb=" O ARGBI 25 " (cutoff:3.500A) Processing helix chain 'BI' and resid 50 through 52 No H-bonds generated for 'chain 'BI' and resid 50 through 52' Processing helix chain 'BI' and resid 88 through 95 removed outlier: 4.258A pdb=" N VALBI 92 " --> pdb=" O ASNBI 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARGBI 93 " --> pdb=" O ASNBI 89 " (cutoff:3.500A) Processing helix chain 'BI' and resid 107 through 119 Processing helix chain 'BI' and resid 156 through 166 removed outlier: 3.503A pdb=" N GLUBI 165 " --> pdb=" O ALABI 161 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLYBI 166 " --> pdb=" O SERBI 162 " (cutoff:3.500A) Processing helix chain 'BI' and resid 170 through 180 removed outlier: 3.529A pdb=" N GLUBI 174 " --> pdb=" O ASPBI 170 " (cutoff:3.500A) Processing helix chain 'BI' and resid 189 through 194 Processing helix chain 'BI' and resid 202 through 215 removed outlier: 3.714A pdb=" N LEUBI 206 " --> pdb=" O GLUBI 202 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYSBI 215 " --> pdb=" O LYSBI 211 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 22 through 37 Processing helix chain 'BJ' and resid 40 through 63 removed outlier: 3.913A pdb=" N LEUBJ 44 " --> pdb=" O CYSBJ 40 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VALBJ 47 " --> pdb=" O GLUBJ 43 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 68 through 85 removed outlier: 3.786A pdb=" N TYRBJ 85 " --> pdb=" O ARGBJ 81 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 94 through 100 removed outlier: 3.797A pdb=" N VALBJ 98 " --> pdb=" O LYSBJ 94 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEUBJ 99 " --> pdb=" O LEUBJ 95 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALABJ 100 " --> pdb=" O ASPBJ 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'BJ' and resid 94 through 100' Processing helix chain 'BJ' and resid 102 through 109 removed outlier: 3.771A pdb=" N PHEBJ 106 " --> pdb=" O THRBJ 102 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 110 through 118 Processing helix chain 'BJ' and resid 123 through 133 Processing helix chain 'BJ' and resid 154 through 156 No H-bonds generated for 'chain 'BJ' and resid 154 through 156' Processing helix chain 'BL' and resid 68 through 73 removed outlier: 3.917A pdb=" N ASPBL 73 " --> pdb=" O ARGBL 69 " (cutoff:3.500A) Processing helix chain 'BN' and resid 29 through 44 removed outlier: 3.663A pdb=" N VALBN 33 " --> pdb=" O THRBN 29 " (cutoff:3.500A) Processing helix chain 'BN' and resid 46 through 57 Processing helix chain 'BN' and resid 62 through 68 Processing helix chain 'BN' and resid 70 through 78 Processing helix chain 'BN' and resid 85 through 105 removed outlier: 4.279A pdb=" N ARGBN 104 " --> pdb=" O LYSBN 100 " (cutoff:3.500A) Processing helix chain 'BN' and resid 108 through 133 Processing helix chain 'BN' and resid 143 through 150 removed outlier: 4.251A pdb=" N SERBN 147 " --> pdb=" O THRBN 144 " (cutoff:3.500A) Processing helix chain 'cS' and resid 58 through 60 No H-bonds generated for 'chain 'cS' and resid 58 through 60' Processing helix chain 'cS' and resid 63 through 67 Processing helix chain 'cS' and resid 69 through 87 Processing helix chain 'cS' and resid 109 through 122 removed outlier: 4.381A pdb=" N SERcS 113 " --> pdb=" O PROcS 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLYcS 122 " --> pdb=" O LEUcS 118 " (cutoff:3.500A) Processing helix chain 'BV' and resid 55 through 62 Processing helix chain 'BV' and resid 63 through 79 removed outlier: 4.192A pdb=" N VALBV 77 " --> pdb=" O GLNBV 73 " (cutoff:3.500A) Processing helix chain 'BW' and resid 5 through 20 Processing helix chain 'BW' and resid 31 through 44 removed outlier: 3.824A pdb=" N HISBW 44 " --> pdb=" O VALBW 40 " (cutoff:3.500A) Processing helix chain 'BW' and resid 85 through 93 Processing helix chain 'BW' and resid 113 through 120 Processing helix chain 'BX' and resid 9 through 22 removed outlier: 4.150A pdb=" N TRPBX 22 " --> pdb=" O ILEBX 18 " (cutoff:3.500A) Processing helix chain 'BX' and resid 24 through 32 Processing helix chain 'BX' and resid 34 through 38 Processing helix chain 'BX' and resid 129 through 134 Processing helix chain 'BY' and resid 40 through 49 removed outlier: 3.596A pdb=" N LYSBY 44 " --> pdb=" O GLUBY 40 " (cutoff:3.500A) Processing helix chain 'BY' and resid 80 through 87 Processing helix chain 'BY' and resid 89 through 97 Processing helix chain 'BY' and resid 105 through 119 Processing helix chain 'BZ' and resid 49 through 56 removed outlier: 3.543A pdb=" N ALABZ 56 " --> pdb=" O ASPBZ 52 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 74 through 81 Processing helix chain 'Bb' and resid 3 through 7 removed outlier: 3.553A pdb=" N ILEBb 7 " --> pdb=" O GLNBb 4 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 13 through 20 Processing helix chain 'Be' and resid 12 through 17 Processing helix chain 'Be' and resid 33 through 44 Processing helix chain 'Cn' and resid 2 through 21 Processing sheet with id=AA1, first strand: chain 'BA' and resid 43 through 46 removed outlier: 3.535A pdb=" N LYSBA 45 " --> pdb=" O ILEBA 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'BA' and resid 102 through 105 removed outlier: 6.099A pdb=" N ILEBA 79 " --> pdb=" O ASNBA 102 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILEBA 104 " --> pdb=" O ILEBA 79 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VALBA 81 " --> pdb=" O ILEBA 104 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEBA 80 " --> pdb=" O LEUBA 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILEBA 128 " --> pdb=" O ILEBA 80 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEUBA 127 " --> pdb=" O ILEBA 150 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N PHEBA 152 " --> pdb=" O LEUBA 127 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THRBA 149 " --> pdb=" O ILEBA 164 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILEBA 166 " --> pdb=" O THRBA 149 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALABA 151 " --> pdb=" O ILEBA 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'BB' and resid 42 through 49 removed outlier: 3.551A pdb=" N GLYBB 44 " --> pdb=" O VALBB 32 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYSBB 98 " --> pdb=" O LYSBB 33 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VALBB 96 " --> pdb=" O VALBB 91 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VALBB 91 " --> pdb=" O VALBB 96 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N CYSBB 98 " --> pdb=" O GLUBB 89 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLUBB 89 " --> pdb=" O CYSBB 98 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHEBB 100 " --> pdb=" O ARGBB 87 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARGBB 87 " --> pdb=" O PHEBB 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'BB' and resid 42 through 49 removed outlier: 3.551A pdb=" N GLYBB 44 " --> pdb=" O VALBB 32 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYSBB 98 " --> pdb=" O LYSBB 33 " (cutoff:3.500A) removed outlier: 13.313A pdb=" N GLNBB 99 " --> pdb=" O LYSBB 219 " (cutoff:3.500A) removed outlier: 12.891A pdb=" N LYSBB 219 " --> pdb=" O GLNBB 99 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TRPBB 101 " --> pdb=" O ILEBB 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILEBB 217 " --> pdb=" O TRPBB 101 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ARGBB 213 " --> pdb=" O PHEBB 105 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VALBB 210 " --> pdb=" O ILEBB 140 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILEBB 140 " --> pdb=" O VALBB 210 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILEBB 212 " --> pdb=" O PHEBB 138 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHEBB 138 " --> pdb=" O ILEBB 212 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYSBB 214 " --> pdb=" O ARGBB 136 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARGBB 136 " --> pdb=" O LYSBB 214 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYSBB 216 " --> pdb=" O THRBB 134 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THRBB 134 " --> pdb=" O LYSBB 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BC' and resid 88 through 101 removed outlier: 6.815A pdb=" N PHEBC 112 " --> pdb=" O METBC 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILEBC 94 " --> pdb=" O LYSBC 110 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYSBC 110 " --> pdb=" O ILEBC 94 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARGBC 108 " --> pdb=" O PROBC 96 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLNBC 98 " --> pdb=" O ARGBC 106 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARGBC 106 " --> pdb=" O GLNBC 98 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLNBC 100 " --> pdb=" O GLYBC 104 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLYBC 104 " --> pdb=" O GLNBC 100 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VALBC 122 " --> pdb=" O VALBC 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BC' and resid 169 through 173 Processing sheet with id=AA7, first strand: chain 'BE' and resid 42 through 43 Processing sheet with id=AA8, first strand: chain 'BE' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'BE' and resid 99 through 103 Processing sheet with id=AB1, first strand: chain 'BE' and resid 121 through 124 removed outlier: 6.884A pdb=" N LYSBE 161 " --> pdb=" O VALBE 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'BE' and resid 126 through 131 removed outlier: 3.781A pdb=" N SERBE 128 " --> pdb=" O ASNBE 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'BE' and resid 217 through 221 removed outlier: 7.103A pdb=" N THRBE 207 " --> pdb=" O ARGBE 198 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARGBE 198 " --> pdb=" O THRBE 207 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HISBE 209 " --> pdb=" O LYSBE 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'BG' and resid 15 through 17 removed outlier: 6.303A pdb=" N LYSBG 2 " --> pdb=" O LEUBG 111 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEUBG 113 " --> pdb=" O LYSBG 2 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASNBG 4 " --> pdb=" O LEUBG 113 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILEBG 115 " --> pdb=" O ASNBG 4 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALABG 6 " --> pdb=" O ILEBG 115 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LYSBG 117 " --> pdb=" O ALABG 6 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEUBG 108 " --> pdb=" O ASPBG 57 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASPBG 57 " --> pdb=" O LEUBG 108 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VALBG 110 " --> pdb=" O GLYBG 55 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLYBG 55 " --> pdb=" O VALBG 110 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASNBG 112 " --> pdb=" O METBG 53 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VALBG 49 " --> pdb=" O VALBG 116 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLNBG 34 " --> pdb=" O ILEBG 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'BG' and resid 72 through 78 Processing sheet with id=AB6, first strand: chain 'BH' and resid 48 through 53 removed outlier: 3.874A pdb=" N SERBH 48 " --> pdb=" O ASNBH 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'BH' and resid 182 through 185 removed outlier: 8.509A pdb=" N VALBH 183 " --> pdb=" O LYSBH 149 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N METBH 151 " --> pdb=" O VALBH 183 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLUBH 185 " --> pdb=" O METBH 151 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VALBH 153 " --> pdb=" O GLUBH 185 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYBH 138 " --> pdb=" O PHEBH 154 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHEBW 50 " --> pdb=" O TYRBH 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'BI' and resid 37 through 38 removed outlier: 6.252A pdb=" N THRBI 43 " --> pdb=" O LEUBI 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'BI' and resid 63 through 68 removed outlier: 7.205A pdb=" N LEUBI 80 " --> pdb=" O ASPBI 106 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASPBI 106 " --> pdb=" O LEUBI 80 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VALBI 82 " --> pdb=" O GLNBI 104 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLNBI 104 " --> pdb=" O VALBI 82 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLYBI 198 " --> pdb=" O THRBI 63 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASNBI 65 " --> pdb=" O GLYBI 198 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILEBI 200 " --> pdb=" O ASNBI 65 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SERBI 67 " --> pdb=" O ILEBI 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'BJ' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'BL' and resid 89 through 98 removed outlier: 27.853A pdb=" N GLYBL 91 " --> pdb=" O PHEBL 116 " (cutoff:3.500A) removed outlier: 24.300A pdb=" N PHEBL 116 " --> pdb=" O GLYBL 91 " (cutoff:3.500A) removed outlier: 17.486A pdb=" N ILEBL 93 " --> pdb=" O LEUBL 114 " (cutoff:3.500A) removed outlier: 14.979A pdb=" N LEUBL 114 " --> pdb=" O ILEBL 93 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N ALABL 95 " --> pdb=" O ASPBL 112 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASPBL 112 " --> pdb=" O ALABL 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARGBL 122 " --> pdb=" O VALBL 117 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N VALBL 158 " --> pdb=" O ASNBL 129 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHEBL 160 " --> pdb=" O PROBL 131 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VALBL 158 " --> pdb=" O LEUBL 154 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHEBL 160 " --> pdb=" O ARGBL 152 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ARGBL 152 " --> pdb=" O PHEBL 160 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VALBL 162 " --> pdb=" O GLNBL 150 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N GLNBL 150 " --> pdb=" O VALBL 162 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYSBL 164 " --> pdb=" O ILEBL 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILEBL 148 " --> pdb=" O LYSBL 164 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILEBL 166 " --> pdb=" O ILEBL 146 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILEBL 146 " --> pdb=" O ILEBL 166 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARGBL 92 " --> pdb=" O GLNBL 150 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARGBL 152 " --> pdb=" O ARGBL 90 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ARGBL 90 " --> pdb=" O ARGBL 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'cS' and resid 51 through 56 removed outlier: 3.609A pdb=" N VALcS 53 " --> pdb=" O VALcS 43 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLYcS 28 " --> pdb=" O HIScS 93 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LYScS 95 " --> pdb=" O GLYcS 28 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VALcS 30 " --> pdb=" O LYScS 95 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARGcS 97 " --> pdb=" O VALcS 30 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VALcS 32 " --> pdb=" O ARGcS 97 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILEcS 92 " --> pdb=" O ILEcS 125 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARGcS 127 " --> pdb=" O ILEcS 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'BV' and resid 32 through 39 removed outlier: 5.561A pdb=" N GLNBV 48 " --> pdb=" O HISBV 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'BW' and resid 71 through 74 Processing sheet with id=AC6, first strand: chain 'BW' and resid 71 through 74 removed outlier: 5.493A pdb=" N VALBW 125 " --> pdb=" O THRBW 105 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N THRBW 105 " --> pdb=" O VALBW 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLYBW 127 " --> pdb=" O VALBW 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'BX' and resid 127 through 128 removed outlier: 4.981A pdb=" N VALBX 121 " --> pdb=" O ALABX 102 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALABX 102 " --> pdb=" O VALBX 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYSBX 123 " --> pdb=" O LEUBX 100 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VALBX 50 " --> pdb=" O GLNBX 72 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLNBX 72 " --> pdb=" O VALBX 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHEBX 119 " --> pdb=" O ALABX 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VALBX 121 " --> pdb=" O PHEBX 83 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'BY' and resid 7 through 9 removed outlier: 6.473A pdb=" N SERBY 72 " --> pdb=" O PHEBY 62 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHEBY 62 " --> pdb=" O SERBY 72 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'BZ' and resid 20 through 22 Processing sheet with id=AD1, first strand: chain 'BZ' and resid 36 through 43 Processing sheet with id=AD2, first strand: chain 'Bb' and resid 45 through 49 Processing sheet with id=AD3, first strand: chain 'Bb' and resid 56 through 57 removed outlier: 7.495A pdb=" N VALBb 56 " --> pdb=" O LEUBb 65 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 754 hydrogen bonds 1180 hydrogen bond angles 0 basepair planarities 310 basepair parallelities 501 stacking parallelities Total time for adding SS restraints: 16.04 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4695 1.31 - 1.43: 19350 1.43 - 1.56: 21576 1.56 - 1.69: 2151 1.69 - 1.82: 137 Bond restraints: 47909 Sorted by residual: bond pdb=" O4' A2M 9 468 " pdb=" C1' A2M 9 468 " ideal model delta sigma weight residual 1.396 1.617 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" O4' A2M 9 978 " pdb=" C1' A2M 9 978 " ideal model delta sigma weight residual 1.396 1.615 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C2' A2M 9 978 " pdb=" C1' A2M 9 978 " ideal model delta sigma weight residual 1.526 1.307 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C2' A2M 91758 " pdb=" C1' A2M 91758 " ideal model delta sigma weight residual 1.526 1.307 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" O4' A2M 9 28 " pdb=" C1' A2M 9 28 " ideal model delta sigma weight residual 1.396 1.615 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 47904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.09: 69709 8.09 - 16.18: 62 16.18 - 24.26: 22 24.26 - 32.35: 6 32.35 - 40.44: 8 Bond angle restraints: 69807 Sorted by residual: angle pdb=" OP1 A2M 9 28 " pdb=" P A2M 9 28 " pdb=" OP2 A2M 9 28 " ideal model delta sigma weight residual 115.21 74.77 40.44 3.00e+00 1.11e-01 1.82e+02 angle pdb=" OP1 A2M 9 468 " pdb=" P A2M 9 468 " pdb=" O5' A2M 9 468 " ideal model delta sigma weight residual 99.72 139.04 -39.32 3.00e+00 1.11e-01 1.72e+02 angle pdb=" OP1 A2M 9 28 " pdb=" P A2M 9 28 " pdb=" O5' A2M 9 28 " ideal model delta sigma weight residual 99.72 138.98 -39.26 3.00e+00 1.11e-01 1.71e+02 angle pdb=" OP1 A2M 91758 " pdb=" P A2M 91758 " pdb=" OP2 A2M 91758 " ideal model delta sigma weight residual 115.21 76.58 38.63 3.00e+00 1.11e-01 1.66e+02 angle pdb=" OP1 A2M 9 468 " pdb=" P A2M 9 468 " pdb=" OP2 A2M 9 468 " ideal model delta sigma weight residual 115.21 76.75 38.46 3.00e+00 1.11e-01 1.64e+02 ... (remaining 69802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 27428 35.90 - 71.79: 2519 71.79 - 107.69: 299 107.69 - 143.59: 7 143.59 - 179.49: 17 Dihedral angle restraints: 30270 sinusoidal: 22533 harmonic: 7737 Sorted by residual: dihedral pdb=" O4' U 9 21 " pdb=" C1' U 9 21 " pdb=" N1 U 9 21 " pdb=" C2 U 9 21 " ideal model delta sinusoidal sigma weight residual -160.00 18.37 -178.37 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 9 573 " pdb=" C1' C 9 573 " pdb=" N1 C 9 573 " pdb=" C2 C 9 573 " ideal model delta sinusoidal sigma weight residual -160.00 7.64 -167.64 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' C 9 593 " pdb=" C1' C 9 593 " pdb=" N1 C 9 593 " pdb=" C2 C 9 593 " ideal model delta sinusoidal sigma weight residual 200.00 44.97 155.03 1 1.50e+01 4.44e-03 8.13e+01 ... (remaining 30267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6501 0.053 - 0.106: 1188 0.106 - 0.159: 907 0.159 - 0.211: 17 0.211 - 0.264: 5 Chirality restraints: 8618 Sorted by residual: chirality pdb=" P U 9 939 " pdb=" OP1 U 9 939 " pdb=" OP2 U 9 939 " pdb=" O5' U 9 939 " both_signs ideal model delta sigma weight residual True 2.41 -2.67 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3' U 91769 " pdb=" C4' U 91769 " pdb=" O3' U 91769 " pdb=" C2' U 91769 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" P G 9 211 " pdb=" OP1 G 9 211 " pdb=" OP2 G 9 211 " pdb=" O5' G 9 211 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 8615 not shown) Planarity restraints: 4832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 91081 " -0.017 2.00e-02 2.50e+03 2.27e-02 1.16e+01 pdb=" N1 C 91081 " 0.012 2.00e-02 2.50e+03 pdb=" C2 C 91081 " 0.054 2.00e-02 2.50e+03 pdb=" O2 C 91081 " -0.027 2.00e-02 2.50e+03 pdb=" N3 C 91081 " -0.010 2.00e-02 2.50e+03 pdb=" C4 C 91081 " 0.013 2.00e-02 2.50e+03 pdb=" N4 C 91081 " -0.015 2.00e-02 2.50e+03 pdb=" C5 C 91081 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C 91081 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 91046 " -0.029 2.00e-02 2.50e+03 1.80e-02 9.75e+00 pdb=" N9 G 91046 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G 91046 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 91046 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G 91046 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 91046 " -0.012 2.00e-02 2.50e+03 pdb=" O6 G 91046 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G 91046 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G 91046 " -0.034 2.00e-02 2.50e+03 pdb=" N2 G 91046 " 0.028 2.00e-02 2.50e+03 pdb=" N3 G 91046 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G 91046 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 9 193 " -0.022 2.00e-02 2.50e+03 1.74e-02 9.04e+00 pdb=" N9 G 9 193 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G 9 193 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G 9 193 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 9 193 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 9 193 " -0.021 2.00e-02 2.50e+03 pdb=" O6 G 9 193 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G 9 193 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 9 193 " -0.033 2.00e-02 2.50e+03 pdb=" N2 G 9 193 " 0.028 2.00e-02 2.50e+03 pdb=" N3 G 9 193 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 9 193 " 0.001 2.00e-02 2.50e+03 ... (remaining 4829 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.42: 207 2.42 - 3.10: 32051 3.10 - 3.78: 92026 3.78 - 4.46: 136713 4.46 - 5.14: 192881 Nonbonded interactions: 453878 Sorted by model distance: nonbonded pdb=" OP2 A 9 405 " pdb="MG MG 91906 " model vdw 1.737 2.170 nonbonded pdb=" O3' U 9 972 " pdb="MG MG 91913 " model vdw 1.770 2.170 nonbonded pdb=" OP2 C 9 428 " pdb="MG MG 91909 " model vdw 1.772 2.170 nonbonded pdb=" OP2 A 9 981 " pdb="MG MG 91911 " model vdw 1.778 2.170 nonbonded pdb=" N7 G 9 359 " pdb="MG MG 91914 " model vdw 1.785 2.250 ... (remaining 453873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.130 Process input model: 54.520 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.221 47913 Z= 0.458 Angle : 1.018 40.439 69813 Z= 0.646 Chirality : 0.053 0.264 8618 Planarity : 0.004 0.061 4832 Dihedral : 21.861 179.486 25280 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.18 % Rotamer: Outliers : 1.20 % Allowed : 11.06 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.62 (0.17), residues: 2645 helix: 1.36 (0.18), residues: 819 sheet: 0.33 (0.23), residues: 528 loop : -0.08 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGBX 11 TYR 0.012 0.001 TYRBZ 68 PHE 0.012 0.001 PHEBW 50 TRP 0.007 0.001 TRPBX 36 HIS 0.004 0.001 HISBN 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.46 (47909) covalent geometry : angle 1.01560 / 0.65 (69807) hydrogen bonds : bond 0.12593 / 13.34 ( 1567) hydrogen bonds : angle 5.38048 / 6.45 ( 3505) metal coordination : bond 0.00833 / 0.51 ( 4) metal coordination : angle 7.81160 / 14.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 465 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 118 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: BB 104 ASP cc_start: 0.8714 (t0) cc_final: 0.8457 (t0) REVERT: BB 142 PHE cc_start: 0.8128 (m-80) cc_final: 0.7821 (m-10) REVERT: BB 191 GLU cc_start: 0.9129 (pm20) cc_final: 0.8850 (pm20) REVERT: BE 201 HIS cc_start: 0.5918 (t70) cc_final: 0.5383 (t70) REVERT: BG 153 ASP cc_start: 0.6401 (t0) cc_final: 0.6039 (t0) REVERT: BH 61 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7625 (tp) REVERT: BH 170 PHE cc_start: 0.9047 (m-10) cc_final: 0.8332 (m-80) REVERT: BI 35 ASN cc_start: 0.9021 (m-40) cc_final: 0.8785 (m110) REVERT: BJ 48 GLN cc_start: 0.9245 (mp10) cc_final: 0.8836 (mp10) REVERT: BJ 68 ASN cc_start: 0.8945 (t0) cc_final: 0.8668 (t0) REVERT: BN 31 GLN cc_start: 0.9521 (mp10) cc_final: 0.9301 (mp10) REVERT: BN 110 ASP cc_start: 0.9302 (t70) cc_final: 0.8834 (t0) REVERT: cS 25 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7340 (mm-40) REVERT: BV 12 TYR cc_start: 0.8769 (p90) cc_final: 0.8555 (p90) REVERT: BW 80 ASP cc_start: 0.9218 (p0) cc_final: 0.8965 (p0) REVERT: BW 85 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8781 (mt-10) REVERT: BW 111 MET cc_start: 0.8555 (mtm) cc_final: 0.8194 (ptm) REVERT: BW 114 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8654 (tm-30) REVERT: BW 115 GLU cc_start: 0.9380 (tp30) cc_final: 0.9111 (tp30) REVERT: BX 57 GLU cc_start: 0.9011 (pm20) cc_final: 0.8780 (pm20) REVERT: BX 97 ASP cc_start: 0.7527 (t0) cc_final: 0.7237 (t0) REVERT: BY 74 PHE cc_start: 0.9059 (t80) cc_final: 0.8481 (t80) REVERT: Bb 17 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8242 (tm-30) outliers start: 28 outliers final: 16 residues processed: 482 average time/residue: 0.2665 time to fit residues: 211.9465 Evaluate side-chains 424 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 406 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 118 GLN Chi-restraints excluded: chain BB residue 131 ASP Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 205 ASP Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 98 ASN Chi-restraints excluded: chain BE residue 134 LYS Chi-restraints excluded: chain BE residue 230 LYS Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BI residue 90 GLU Chi-restraints excluded: chain BJ residue 67 LYS Chi-restraints excluded: chain BL residue 112 ASP Chi-restraints excluded: chain BN residue 117 LEU Chi-restraints excluded: chain cS residue 96 LEU Chi-restraints excluded: chain cS residue 137 ASP Chi-restraints excluded: chain BX residue 101 ILE Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 76 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 130 GLN BG 87 HIS BJ 125 HIS BL 129 ASN BY 30 HIS BZ 72 GLN Be 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.051270 restraints weight = 232802.713| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.79 r_work: 0.2842 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 47913 Z= 0.181 Angle : 0.574 12.505 69813 Z= 0.313 Chirality : 0.039 0.443 8618 Planarity : 0.005 0.086 4832 Dihedral : 23.061 179.331 19727 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.49 % Allowed : 13.81 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.48 (0.17), residues: 2645 helix: 1.25 (0.18), residues: 847 sheet: 0.17 (0.23), residues: 526 loop : -0.15 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGBN 3 TYR 0.018 0.001 TYRBZ 73 PHE 0.023 0.002 PHEBW 50 TRP 0.024 0.001 TRPBC 45 HIS 0.006 0.001 HISBC 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (47909) covalent geometry : angle 0.57158 / 0.31 (69807) hydrogen bonds : bond 0.06786 / 7.03 ( 1567) hydrogen bonds : angle 4.33680 / 5.33 ( 3505) metal coordination : bond 0.01003 / 0.55 ( 4) metal coordination : angle 5.44475 / 9.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 444 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 23 MET cc_start: 0.9655 (OUTLIER) cc_final: 0.9261 (mpp) REVERT: BA 82 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7979 (mm-40) REVERT: BB 104 ASP cc_start: 0.8838 (t0) cc_final: 0.8596 (t0) REVERT: BB 105 PHE cc_start: 0.8930 (m-10) cc_final: 0.8684 (m-80) REVERT: BC 212 ARG cc_start: 0.9488 (mmm-85) cc_final: 0.8951 (mmm-85) REVERT: BE 134 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8829 (ptpp) REVERT: BE 201 HIS cc_start: 0.6053 (t70) cc_final: 0.5444 (t70) REVERT: BG 153 ASP cc_start: 0.6355 (t0) cc_final: 0.6104 (t0) REVERT: BH 131 VAL cc_start: 0.9311 (t) cc_final: 0.9061 (t) REVERT: BH 170 PHE cc_start: 0.9047 (m-10) cc_final: 0.8168 (m-80) REVERT: BJ 12 LYS cc_start: 0.9238 (mtmt) cc_final: 0.8944 (mtpp) REVERT: BJ 60 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8762 (pp20) REVERT: BJ 68 ASN cc_start: 0.8863 (t0) cc_final: 0.8387 (t0) REVERT: BJ 142 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6861 (pt) REVERT: BL 124 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8247 (mm-30) REVERT: BN 31 GLN cc_start: 0.9546 (mp10) cc_final: 0.9289 (mp10) REVERT: BN 103 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9052 (mt-10) REVERT: BN 142 GLU cc_start: 0.9067 (tp30) cc_final: 0.8569 (tp30) REVERT: cS 25 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7699 (mm-40) REVERT: cS 82 GLN cc_start: 0.9323 (tp40) cc_final: 0.8411 (tp40) REVERT: BW 49 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8549 (mt-10) REVERT: BW 64 GLU cc_start: 0.8588 (pt0) cc_final: 0.8254 (mt-10) REVERT: BW 80 ASP cc_start: 0.9276 (p0) cc_final: 0.8994 (p0) REVERT: BW 85 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8932 (mp0) REVERT: BW 114 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8866 (tm-30) REVERT: BY 74 PHE cc_start: 0.9094 (t80) cc_final: 0.8514 (t80) REVERT: BZ 54 GLN cc_start: 0.9180 (mt0) cc_final: 0.8948 (pt0) REVERT: Cn 17 ARG cc_start: 0.8012 (ptp-170) cc_final: 0.7696 (ptp-170) outliers start: 58 outliers final: 31 residues processed: 473 average time/residue: 0.2502 time to fit residues: 196.7582 Evaluate side-chains 430 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 397 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BE residue 45 VAL Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BJ residue 142 LEU Chi-restraints excluded: chain BL residue 32 LEU Chi-restraints excluded: chain BL residue 147 ILE Chi-restraints excluded: chain BN residue 117 LEU Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 125 ILE Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 53 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 96 ASN Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BY residue 10 THR Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BZ residue 58 VAL Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Bb residue 77 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [257, 173, 158, 362, 57, 258, 10, 86, 164, 236, 77] chunk 257 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 362 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 258 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 86 optimal weight: 40.0000 chunk 164 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 157 HIS cS 42 HIS BV 29 HIS Bb 44 ASN ** Be 17 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 = 0.3415 r_free = 0.3415 target = 0.065329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049733 restraints weight = 234720.490| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.75 r_work: 0.2800 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 47913 Z= 0.200 Angle : 0.574 11.769 69813 Z= 0.314 Chirality : 0.040 0.493 8618 Planarity : 0.005 0.064 4832 Dihedral : 23.001 179.933 19693 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.82 % Allowed : 14.37 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.32 (0.17), residues: 2645 helix: 1.21 (0.18), residues: 851 sheet: 0.03 (0.22), residues: 530 loop : -0.32 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGBe 10 TYR 0.027 0.002 TYRBI 84 PHE 0.027 0.002 PHEBW 99 TRP 0.010 0.001 TRPBW 89 HIS 0.005 0.001 HISBe 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (47909) covalent geometry : angle 0.57391 / 0.31 (69807) hydrogen bonds : bond 0.06978 / 7.26 ( 1567) hydrogen bonds : angle 4.22043 / 5.24 ( 3505) metal coordination : bond 0.01011 / 0.65 ( 4) metal coordination : angle 2.13482 / 3.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 408 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 82 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7971 (mm-40) REVERT: BC 106 ARG cc_start: 0.7663 (ptt-90) cc_final: 0.7412 (ptt90) REVERT: BC 212 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.8906 (mmm-85) REVERT: BC 221 PHE cc_start: 0.9556 (OUTLIER) cc_final: 0.9345 (t80) REVERT: BE 19 MET cc_start: 0.9184 (mtt) cc_final: 0.8348 (mtt) REVERT: BE 133 GLN cc_start: 0.9631 (pp30) cc_final: 0.9361 (pp30) REVERT: BE 134 LYS cc_start: 0.9216 (ptpp) cc_final: 0.8945 (ptpp) REVERT: BE 201 HIS cc_start: 0.6402 (t70) cc_final: 0.5829 (t70) REVERT: BG 153 ASP cc_start: 0.6340 (t0) cc_final: 0.6051 (t0) REVERT: BH 45 TYR cc_start: 0.7548 (p90) cc_final: 0.7083 (p90) REVERT: BH 73 TYR cc_start: 0.9057 (m-80) cc_final: 0.8696 (m-80) REVERT: BH 131 VAL cc_start: 0.9498 (t) cc_final: 0.9264 (t) REVERT: BH 146 ASP cc_start: 0.9489 (p0) cc_final: 0.9250 (p0) REVERT: BH 170 PHE cc_start: 0.9097 (m-10) cc_final: 0.8470 (m-80) REVERT: BI 27 TYR cc_start: 0.9307 (p90) cc_final: 0.8741 (p90) REVERT: BJ 12 LYS cc_start: 0.9394 (mtmt) cc_final: 0.9151 (mtpt) REVERT: BJ 68 ASN cc_start: 0.8795 (t0) cc_final: 0.8530 (t0) REVERT: BJ 96 ASP cc_start: 0.9361 (m-30) cc_final: 0.9158 (m-30) REVERT: BJ 149 MET cc_start: 0.8634 (tpp) cc_final: 0.8282 (tmm) REVERT: BL 124 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8272 (mm-30) REVERT: BN 31 GLN cc_start: 0.9552 (mp10) cc_final: 0.9236 (mp10) REVERT: BN 103 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9089 (mt-10) REVERT: BN 110 ASP cc_start: 0.9241 (t70) cc_final: 0.8725 (t0) REVERT: BN 142 GLU cc_start: 0.9092 (tp30) cc_final: 0.8571 (tp30) REVERT: cS 25 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7776 (mm-40) REVERT: cS 86 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8406 (mt-10) REVERT: BW 69 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9312 (tt) REVERT: BW 85 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9095 (mt-10) REVERT: BW 99 PHE cc_start: 0.8467 (m-80) cc_final: 0.8249 (m-10) REVERT: BW 114 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8810 (pp20) REVERT: BX 97 ASP cc_start: 0.8025 (t0) cc_final: 0.7527 (t0) REVERT: BY 74 PHE cc_start: 0.9070 (t80) cc_final: 0.8226 (t80) REVERT: BZ 54 GLN cc_start: 0.9265 (mt0) cc_final: 0.8894 (pt0) REVERT: BZ 63 THR cc_start: 0.9035 (m) cc_final: 0.8624 (p) REVERT: BZ 64 LEU cc_start: 0.9384 (mm) cc_final: 0.9148 (mm) REVERT: Bb 8 ASP cc_start: 0.8953 (t0) cc_final: 0.8533 (p0) REVERT: Bb 82 ARG cc_start: 0.9154 (mmm-85) cc_final: 0.8954 (mmp80) REVERT: Cn 2 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6876 (ttt-90) outliers start: 89 outliers final: 51 residues processed: 462 average time/residue: 0.2583 time to fit residues: 198.4639 Evaluate side-chains 439 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 385 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BA residue 183 LEU Chi-restraints excluded: chain BB residue 91 VAL Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 221 PHE Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 90 VAL Chi-restraints excluded: chain BE residue 160 ILE Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BL residue 32 LEU Chi-restraints excluded: chain BL residue 112 ASP Chi-restraints excluded: chain BL residue 134 VAL Chi-restraints excluded: chain BN residue 65 SER Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 96 LEU Chi-restraints excluded: chain cS residue 125 ILE Chi-restraints excluded: chain cS residue 137 ASP Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BW residue 7 LEU Chi-restraints excluded: chain BW residue 25 VAL Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 54 ILE Chi-restraints excluded: chain BX residue 68 CYS Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BZ residue 24 SER Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 58 VAL Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Bb residue 56 VAL Chi-restraints excluded: chain Cn residue 2 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [204, 37, 10, 211, 41, 33, 86, 238, 249, 309, 246] chunk 204 optimal weight: 40.0000 chunk 37 optimal weight: 40.0000 chunk 10 optimal weight: 30.0000 chunk 211 optimal weight: 30.0000 chunk 41 optimal weight: 50.0000 chunk 33 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 238 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 309 optimal weight: 0.0370 chunk 246 optimal weight: 0.1980 overall best weight: 9.8466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... BB 63 HIS ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 179 ASN BG 112 ASN BI 155 HIS ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 42 ASN ** BV 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Be 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.046850 restraints weight = 239820.850| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.67 r_work: 0.2721 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 47913 Z= 0.325 Angle : 0.730 12.677 69813 Z= 0.388 Chirality : 0.049 0.541 8618 Planarity : 0.006 0.081 4832 Dihedral : 23.155 178.837 19691 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.85 % Allowed : 15.87 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.31 (0.16), residues: 2645 helix: 0.74 (0.17), residues: 863 sheet: -0.48 (0.22), residues: 548 loop : -0.67 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGBE 221 TYR 0.018 0.002 TYRBL 120 PHE 0.034 0.002 PHEBH 27 TRP 0.023 0.002 TRPBV 72 HIS 0.008 0.002 HISBN 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.32 (47909) covalent geometry : angle 0.72717 / 0.39 (69807) hydrogen bonds : bond 0.08718 / 8.99 ( 1567) hydrogen bonds : angle 4.59082 / 5.64 ( 3505) metal coordination : bond 0.01647 / 1.03 ( 4) metal coordination : angle 7.07711 / 13.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 380 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 75 GLU cc_start: 0.9165 (mp0) cc_final: 0.8895 (mp0) REVERT: BC 89 ASP cc_start: 0.9252 (p0) cc_final: 0.8774 (p0) REVERT: BC 206 ASP cc_start: 0.8528 (m-30) cc_final: 0.8159 (m-30) REVERT: BC 212 ARG cc_start: 0.9502 (mmm-85) cc_final: 0.8925 (mmm-85) REVERT: BC 221 PHE cc_start: 0.9610 (OUTLIER) cc_final: 0.9358 (t80) REVERT: BE 19 MET cc_start: 0.9217 (mtt) cc_final: 0.8960 (mtt) REVERT: BE 133 GLN cc_start: 0.9531 (pp30) cc_final: 0.9305 (pp30) REVERT: BE 146 THR cc_start: 0.9547 (m) cc_final: 0.9326 (t) REVERT: BE 201 HIS cc_start: 0.6754 (t70) cc_final: 0.6178 (t70) REVERT: BE 240 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7805 (mtpt) REVERT: BG 153 ASP cc_start: 0.6437 (t0) cc_final: 0.6157 (t0) REVERT: BH 45 TYR cc_start: 0.7846 (p90) cc_final: 0.7412 (p90) REVERT: BH 73 TYR cc_start: 0.9083 (m-80) cc_final: 0.8688 (m-80) REVERT: BH 170 PHE cc_start: 0.9324 (m-10) cc_final: 0.8684 (m-80) REVERT: BI 160 ILE cc_start: 0.9310 (mm) cc_final: 0.9073 (pt) REVERT: BJ 60 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8764 (pp20) REVERT: BJ 68 ASN cc_start: 0.8878 (t0) cc_final: 0.8622 (t0) REVERT: BL 124 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8195 (mm-30) REVERT: BN 31 GLN cc_start: 0.9555 (mp10) cc_final: 0.9208 (mp10) REVERT: BN 103 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9046 (mt-10) REVERT: BN 110 ASP cc_start: 0.9246 (t70) cc_final: 0.8682 (t0) REVERT: BN 142 GLU cc_start: 0.9045 (tp30) cc_final: 0.8482 (tp30) REVERT: cS 113 SER cc_start: 0.9284 (m) cc_final: 0.8988 (p) REVERT: BV 78 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8869 (tm-30) REVERT: BW 69 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9230 (tt) REVERT: BW 85 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9158 (mt-10) REVERT: BX 97 ASP cc_start: 0.7968 (t0) cc_final: 0.7500 (t0) REVERT: BY 74 PHE cc_start: 0.9061 (t80) cc_final: 0.8217 (t80) REVERT: BY 93 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9229 (mm) REVERT: BZ 14 ASN cc_start: 0.8604 (t0) cc_final: 0.8359 (t0) REVERT: BZ 54 GLN cc_start: 0.9333 (mt0) cc_final: 0.8946 (pt0) REVERT: BZ 63 THR cc_start: 0.9302 (m) cc_final: 0.8994 (p) REVERT: BZ 64 LEU cc_start: 0.9447 (mm) cc_final: 0.9208 (mm) REVERT: BZ 72 GLN cc_start: 0.8802 (mt0) cc_final: 0.8597 (mt0) REVERT: Bb 8 ASP cc_start: 0.8911 (t0) cc_final: 0.8505 (p0) REVERT: Cn 2 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7358 (ttt-90) outliers start: 113 outliers final: 79 residues processed: 453 average time/residue: 0.2560 time to fit residues: 192.1999 Evaluate side-chains 441 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 357 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 19 ASP Chi-restraints excluded: chain BA residue 63 LEU Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 139 ILE Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BA residue 183 LEU Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 80 ASP Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 165 VAL Chi-restraints excluded: chain BC residue 221 PHE Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 45 VAL Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 64 ILE Chi-restraints excluded: chain BE residue 90 VAL Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 160 ILE Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BE residue 240 LYS Chi-restraints excluded: chain BG residue 27 PHE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 81 THR Chi-restraints excluded: chain BG residue 180 ILE Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 94 ILE Chi-restraints excluded: chain BH residue 101 ILE Chi-restraints excluded: chain BI residue 43 THR Chi-restraints excluded: chain BJ residue 3 ASN Chi-restraints excluded: chain BJ residue 9 ASN Chi-restraints excluded: chain BJ residue 48 GLN Chi-restraints excluded: chain BJ residue 64 LEU Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BL residue 73 ASP Chi-restraints excluded: chain BL residue 112 ASP Chi-restraints excluded: chain BL residue 146 ILE Chi-restraints excluded: chain BN residue 116 ILE Chi-restraints excluded: chain cS residue 30 VAL Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 125 ILE Chi-restraints excluded: chain cS residue 150 LEU Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BV residue 36 ILE Chi-restraints excluded: chain BV residue 77 VAL Chi-restraints excluded: chain BW residue 7 LEU Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 39 ILE Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BW residue 105 THR Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 54 ILE Chi-restraints excluded: chain BX residue 68 CYS Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BX residue 132 LEU Chi-restraints excluded: chain BY residue 10 THR Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BY residue 93 LEU Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 50 ILE Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 58 VAL Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Bb residue 56 VAL Chi-restraints excluded: chain Bb residue 64 ILE Chi-restraints excluded: chain Be residue 17 GLN Chi-restraints excluded: chain Cn residue 2 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [237, 246, 80, 1, 0, 221, 349, 65, 257, 38, 328] chunk 237 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 80 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 349 optimal weight: 7.9990 chunk 65 optimal weight: 50.0000 chunk 257 optimal weight: 0.8980 chunk 38 optimal weight: 40.0000 chunk 328 optimal weight: 7.9990 overall best weight: 7.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 179 ASN ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 8 ASN ** BX 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 17 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 = 0.3362 r_free = 0.3362 target = 0.062844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047118 restraints weight = 235063.784| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.66 r_work: 0.2731 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 47913 Z= 0.236 Angle : 0.600 8.466 69813 Z= 0.329 Chirality : 0.043 0.510 8618 Planarity : 0.005 0.050 4832 Dihedral : 23.136 179.210 19691 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.95 % Allowed : 18.65 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.23 (0.16), residues: 2645 helix: 0.98 (0.18), residues: 855 sheet: -0.55 (0.22), residues: 542 loop : -0.70 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGBI 93 TYR 0.028 0.002 TYRBC 67 PHE 0.022 0.002 PHEBW 99 TRP 0.012 0.001 TRPBV 72 HIS 0.009 0.001 HISBL 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.24 (47909) covalent geometry : angle 0.59953 / 0.33 (69807) hydrogen bonds : bond 0.07548 / 7.80 ( 1567) hydrogen bonds : angle 4.38728 / 5.41 ( 3505) metal coordination : bond 0.01292 / 0.84 ( 4) metal coordination : angle 3.06033 / 5.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 382 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BB 104 ASP cc_start: 0.8995 (t0) cc_final: 0.8778 (t0) REVERT: BC 67 TYR cc_start: 0.9221 (m-10) cc_final: 0.8923 (m-10) REVERT: BC 89 ASP cc_start: 0.9184 (p0) cc_final: 0.8769 (p0) REVERT: BC 206 ASP cc_start: 0.8557 (m-30) cc_final: 0.8194 (m-30) REVERT: BC 212 ARG cc_start: 0.9475 (mmm-85) cc_final: 0.8848 (mmm-85) REVERT: BE 19 MET cc_start: 0.9244 (mtt) cc_final: 0.9031 (mtt) REVERT: BE 146 THR cc_start: 0.9526 (m) cc_final: 0.9302 (t) REVERT: BE 201 HIS cc_start: 0.6827 (t70) cc_final: 0.6258 (t70) REVERT: BE 240 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7749 (mtpt) REVERT: BG 153 ASP cc_start: 0.6458 (t0) cc_final: 0.6197 (t0) REVERT: BH 45 TYR cc_start: 0.7780 (p90) cc_final: 0.7311 (p90) REVERT: BH 73 TYR cc_start: 0.9080 (m-80) cc_final: 0.8710 (m-80) REVERT: BH 131 VAL cc_start: 0.9641 (OUTLIER) cc_final: 0.9405 (t) REVERT: BH 170 PHE cc_start: 0.9276 (m-10) cc_final: 0.8667 (m-80) REVERT: BI 27 TYR cc_start: 0.9534 (p90) cc_final: 0.8992 (p90) REVERT: BI 160 ILE cc_start: 0.9314 (mm) cc_final: 0.9080 (pt) REVERT: BJ 48 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.8954 (mp10) REVERT: BJ 68 ASN cc_start: 0.8911 (t0) cc_final: 0.8671 (t0) REVERT: BJ 170 ARG cc_start: 0.3370 (OUTLIER) cc_final: 0.1923 (ttt180) REVERT: BL 124 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8161 (mm-30) REVERT: BN 31 GLN cc_start: 0.9564 (mp10) cc_final: 0.9239 (mp10) REVERT: BN 103 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9077 (mt-10) REVERT: BN 110 ASP cc_start: 0.9179 (t70) cc_final: 0.8553 (t0) REVERT: BN 142 GLU cc_start: 0.9046 (tp30) cc_final: 0.8487 (tp30) REVERT: cS 25 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8015 (mm-40) REVERT: cS 113 SER cc_start: 0.9263 (m) cc_final: 0.8955 (p) REVERT: BV 23 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8585 (mpp) REVERT: BW 69 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9238 (tt) REVERT: BW 85 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9098 (mt-10) REVERT: BX 97 ASP cc_start: 0.7935 (t0) cc_final: 0.7531 (t0) REVERT: BY 74 PHE cc_start: 0.9006 (t80) cc_final: 0.8145 (t80) REVERT: BZ 14 ASN cc_start: 0.8570 (t0) cc_final: 0.8255 (t0) REVERT: BZ 54 GLN cc_start: 0.9317 (mt0) cc_final: 0.8926 (pt0) REVERT: BZ 63 THR cc_start: 0.9288 (m) cc_final: 0.8997 (p) REVERT: BZ 64 LEU cc_start: 0.9450 (mm) cc_final: 0.9192 (mm) REVERT: Bb 8 ASP cc_start: 0.8881 (t0) cc_final: 0.8488 (p0) REVERT: Bb 43 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8476 (t80) outliers start: 92 outliers final: 63 residues processed: 440 average time/residue: 0.2599 time to fit residues: 188.6329 Evaluate side-chains 436 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 366 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 119 THR Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 165 VAL Chi-restraints excluded: chain BE residue 23 LEU Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 45 VAL Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 64 ILE Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BE residue 240 LYS Chi-restraints excluded: chain BG residue 27 PHE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 94 ILE Chi-restraints excluded: chain BH residue 131 VAL Chi-restraints excluded: chain BJ residue 3 ASN Chi-restraints excluded: chain BJ residue 48 GLN Chi-restraints excluded: chain BJ residue 64 LEU Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BJ residue 170 ARG Chi-restraints excluded: chain BL residue 32 LEU Chi-restraints excluded: chain BL residue 146 ILE Chi-restraints excluded: chain BN residue 116 ILE Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 118 LEU Chi-restraints excluded: chain cS residue 125 ILE Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BV residue 23 MET Chi-restraints excluded: chain BV residue 36 ILE Chi-restraints excluded: chain BW residue 7 LEU Chi-restraints excluded: chain BW residue 14 MET Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BW residue 105 THR Chi-restraints excluded: chain BW residue 115 GLU Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 68 CYS Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BX residue 132 LEU Chi-restraints excluded: chain BY residue 10 THR Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BZ residue 19 LYS Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 58 VAL Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 43 PHE Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Bb residue 54 THR Chi-restraints excluded: chain Bb residue 64 ILE Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Cn residue 7 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [226, 50, 300, 287, 62, 72, 234, 154, 129, 213, 285] chunk 226 optimal weight: 9.9990 chunk 50 optimal weight: 40.0000 chunk 300 optimal weight: 4.9990 chunk 287 optimal weight: 2.9990 chunk 62 optimal weight: 40.0000 chunk 72 optimal weight: 30.0000 chunk 234 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.063487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.047780 restraints weight = 232186.066| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.69 r_work: 0.2753 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47913 Z= 0.162 Angle : 0.538 9.782 69813 Z= 0.300 Chirality : 0.039 0.469 8618 Planarity : 0.004 0.050 4832 Dihedral : 23.070 179.909 19689 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.33 % Allowed : 18.70 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.05 (0.16), residues: 2645 helix: 1.21 (0.18), residues: 851 sheet: -0.54 (0.22), residues: 544 loop : -0.59 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGBX 70 TYR 0.018 0.001 TYRBC 67 PHE 0.025 0.002 PHEBB 188 TRP 0.012 0.001 TRPBV 72 HIS 0.007 0.001 HISBE 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (47909) covalent geometry : angle 0.53770 / 0.30 (69807) hydrogen bonds : bond 0.06683 / 6.97 ( 1567) hydrogen bonds : angle 4.15052 / 5.10 ( 3505) metal coordination : bond 0.00898 / 0.58 ( 4) metal coordination : angle 3.04367 / 5.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 406 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BB 104 ASP cc_start: 0.8984 (t0) cc_final: 0.8725 (t0) REVERT: BC 67 TYR cc_start: 0.9286 (m-10) cc_final: 0.8997 (m-80) REVERT: BC 75 GLU cc_start: 0.9056 (mp0) cc_final: 0.8716 (mp0) REVERT: BC 89 ASP cc_start: 0.9191 (p0) cc_final: 0.8815 (p0) REVERT: BC 206 ASP cc_start: 0.8591 (m-30) cc_final: 0.8228 (m-30) REVERT: BC 212 ARG cc_start: 0.9493 (mmm-85) cc_final: 0.8836 (mmm-85) REVERT: BC 243 GLU cc_start: 0.8629 (tp30) cc_final: 0.7418 (tp30) REVERT: BC 246 PHE cc_start: 0.8995 (m-10) cc_final: 0.7771 (m-10) REVERT: BE 146 THR cc_start: 0.9517 (m) cc_final: 0.9280 (t) REVERT: BE 201 HIS cc_start: 0.6798 (t70) cc_final: 0.6212 (t70) REVERT: BG 153 ASP cc_start: 0.6508 (t0) cc_final: 0.6223 (t0) REVERT: BH 45 TYR cc_start: 0.7808 (p90) cc_final: 0.7318 (p90) REVERT: BH 73 TYR cc_start: 0.9083 (m-80) cc_final: 0.8714 (m-80) REVERT: BH 131 VAL cc_start: 0.9614 (OUTLIER) cc_final: 0.9369 (t) REVERT: BH 170 PHE cc_start: 0.9223 (m-10) cc_final: 0.8659 (m-80) REVERT: BI 27 TYR cc_start: 0.9542 (p90) cc_final: 0.9011 (p90) REVERT: BI 93 ARG cc_start: 0.9514 (mtm110) cc_final: 0.9274 (mtm-85) REVERT: BI 160 ILE cc_start: 0.9320 (mm) cc_final: 0.9088 (pt) REVERT: BJ 68 ASN cc_start: 0.8916 (t0) cc_final: 0.8674 (t0) REVERT: BJ 82 MET cc_start: 0.9410 (tpp) cc_final: 0.9101 (tpp) REVERT: BJ 170 ARG cc_start: 0.3476 (OUTLIER) cc_final: 0.2097 (ttt180) REVERT: BL 124 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8384 (mt-10) REVERT: BN 31 GLN cc_start: 0.9562 (mp10) cc_final: 0.9226 (mp10) REVERT: BN 103 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9099 (mt-10) REVERT: BN 142 GLU cc_start: 0.9028 (tp30) cc_final: 0.8476 (tp30) REVERT: cS 74 MET cc_start: 0.8487 (ttt) cc_final: 0.7696 (tmm) REVERT: cS 113 SER cc_start: 0.9280 (m) cc_final: 0.8957 (p) REVERT: BV 23 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8796 (mpp) REVERT: BW 26 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8843 (ttp) REVERT: BW 69 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9229 (tt) REVERT: BW 85 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9091 (mt-10) REVERT: BX 5 ARG cc_start: 0.9472 (OUTLIER) cc_final: 0.8759 (ttp-170) REVERT: BX 97 ASP cc_start: 0.7973 (t0) cc_final: 0.7455 (t0) REVERT: BY 74 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8233 (t80) REVERT: BZ 14 ASN cc_start: 0.8547 (t0) cc_final: 0.8277 (t0) REVERT: BZ 54 GLN cc_start: 0.9333 (mt0) cc_final: 0.8905 (pt0) REVERT: BZ 63 THR cc_start: 0.9282 (m) cc_final: 0.8995 (p) REVERT: BZ 64 LEU cc_start: 0.9417 (mm) cc_final: 0.9170 (mm) REVERT: Bb 8 ASP cc_start: 0.8843 (t0) cc_final: 0.8642 (p0) REVERT: Bb 43 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8452 (t80) REVERT: Cn 2 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7303 (ttt-90) outliers start: 101 outliers final: 68 residues processed: 467 average time/residue: 0.2601 time to fit residues: 200.6674 Evaluate side-chains 464 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 387 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BB residue 119 THR Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 90 GLU Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 165 VAL Chi-restraints excluded: chain BE residue 23 LEU Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 45 VAL Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 64 ILE Chi-restraints excluded: chain BE residue 92 ILE Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BG residue 27 PHE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 94 ILE Chi-restraints excluded: chain BH residue 101 ILE Chi-restraints excluded: chain BH residue 131 VAL Chi-restraints excluded: chain BJ residue 48 GLN Chi-restraints excluded: chain BJ residue 64 LEU Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BJ residue 170 ARG Chi-restraints excluded: chain BL residue 32 LEU Chi-restraints excluded: chain BL residue 73 ASP Chi-restraints excluded: chain BL residue 146 ILE Chi-restraints excluded: chain BN residue 46 THR Chi-restraints excluded: chain BN residue 50 ILE Chi-restraints excluded: chain cS residue 30 VAL Chi-restraints excluded: chain cS residue 36 PHE Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 115 LEU Chi-restraints excluded: chain cS residue 118 LEU Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BV residue 23 MET Chi-restraints excluded: chain BV residue 32 VAL Chi-restraints excluded: chain BV residue 36 ILE Chi-restraints excluded: chain BW residue 7 LEU Chi-restraints excluded: chain BW residue 14 MET Chi-restraints excluded: chain BW residue 26 MET Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 5 ARG Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 74 PHE Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BZ residue 19 LYS Chi-restraints excluded: chain BZ residue 24 SER Chi-restraints excluded: chain BZ residue 44 ILE Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 58 VAL Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 43 PHE Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Bb residue 56 VAL Chi-restraints excluded: chain Be residue 18 THR Chi-restraints excluded: chain Cn residue 2 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [276, 354, 65, 77, 118, 345, 326, 314, 166, 259, 180] chunk 276 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 chunk 65 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 345 optimal weight: 0.9980 chunk 326 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 162 ASN ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.063544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047841 restraints weight = 232842.673| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.69 r_work: 0.2756 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47913 Z= 0.166 Angle : 0.540 9.488 69813 Z= 0.300 Chirality : 0.039 0.468 8618 Planarity : 0.004 0.044 4832 Dihedral : 23.025 179.971 19689 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.67 % Allowed : 19.13 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.01 (0.16), residues: 2645 helix: 1.26 (0.18), residues: 850 sheet: -0.48 (0.22), residues: 538 loop : -0.58 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGBX 70 TYR 0.015 0.001 TYRBC 67 PHE 0.022 0.001 PHEBB 188 TRP 0.011 0.001 TRPBV 72 HIS 0.007 0.001 HISBE 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (47909) covalent geometry : angle 0.53985 / 0.30 (69807) hydrogen bonds : bond 0.06542 / 6.84 ( 1567) hydrogen bonds : angle 4.10787 / 5.05 ( 3505) metal coordination : bond 0.00822 / 0.54 ( 4) metal coordination : angle 2.74336 / 5.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 402 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 87 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: BB 104 ASP cc_start: 0.8998 (t0) cc_final: 0.8775 (t0) REVERT: BC 67 TYR cc_start: 0.9286 (m-10) cc_final: 0.9056 (m-80) REVERT: BC 75 GLU cc_start: 0.9009 (mp0) cc_final: 0.8661 (mp0) REVERT: BC 89 ASP cc_start: 0.9174 (p0) cc_final: 0.8819 (p0) REVERT: BC 131 GLU cc_start: 0.8461 (mp0) cc_final: 0.8116 (mp0) REVERT: BC 206 ASP cc_start: 0.8594 (m-30) cc_final: 0.8233 (m-30) REVERT: BC 212 ARG cc_start: 0.9491 (mmm-85) cc_final: 0.8819 (mmm-85) REVERT: BC 245 ARG cc_start: 0.8536 (mmp80) cc_final: 0.8320 (mmp80) REVERT: BC 253 GLU cc_start: 0.9436 (tp30) cc_final: 0.9177 (tp30) REVERT: BE 19 MET cc_start: 0.9107 (mtt) cc_final: 0.8819 (mtt) REVERT: BE 133 GLN cc_start: 0.9516 (pp30) cc_final: 0.9301 (pp30) REVERT: BE 146 THR cc_start: 0.9515 (m) cc_final: 0.9265 (t) REVERT: BE 201 HIS cc_start: 0.6830 (t70) cc_final: 0.6229 (t70) REVERT: BG 153 ASP cc_start: 0.6491 (t0) cc_final: 0.6160 (t0) REVERT: BH 45 TYR cc_start: 0.7872 (p90) cc_final: 0.7383 (p90) REVERT: BH 54 ILE cc_start: 0.8236 (mt) cc_final: 0.8018 (mp) REVERT: BH 73 TYR cc_start: 0.9105 (m-80) cc_final: 0.8741 (m-80) REVERT: BH 131 VAL cc_start: 0.9614 (OUTLIER) cc_final: 0.9363 (t) REVERT: BH 170 PHE cc_start: 0.9217 (m-10) cc_final: 0.8656 (m-80) REVERT: BI 27 TYR cc_start: 0.9567 (p90) cc_final: 0.9146 (p90) REVERT: BI 160 ILE cc_start: 0.9315 (mm) cc_final: 0.9083 (pt) REVERT: BJ 68 ASN cc_start: 0.8922 (t0) cc_final: 0.8677 (t0) REVERT: BJ 170 ARG cc_start: 0.3466 (OUTLIER) cc_final: 0.2063 (ttt180) REVERT: BL 124 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8264 (mm-30) REVERT: BN 31 GLN cc_start: 0.9568 (mp10) cc_final: 0.9200 (mp10) REVERT: BN 103 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9101 (mt-10) REVERT: BN 142 GLU cc_start: 0.9023 (tp30) cc_final: 0.8470 (tp30) REVERT: cS 74 MET cc_start: 0.8477 (ttt) cc_final: 0.7658 (tmm) REVERT: cS 113 SER cc_start: 0.9273 (m) cc_final: 0.8953 (p) REVERT: BV 23 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8856 (mpp) REVERT: BW 26 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8815 (ttp) REVERT: BW 69 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9233 (tt) REVERT: BW 85 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9099 (mt-10) REVERT: BX 5 ARG cc_start: 0.9467 (OUTLIER) cc_final: 0.8755 (ttp-170) REVERT: BX 97 ASP cc_start: 0.8058 (t0) cc_final: 0.7538 (t0) REVERT: BY 74 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8192 (t80) REVERT: BZ 4 LYS cc_start: 0.8792 (tttt) cc_final: 0.8401 (tttt) REVERT: BZ 14 ASN cc_start: 0.8553 (t0) cc_final: 0.8290 (t0) REVERT: BZ 54 GLN cc_start: 0.9334 (mt0) cc_final: 0.8916 (pt0) REVERT: BZ 63 THR cc_start: 0.9284 (m) cc_final: 0.8995 (p) REVERT: BZ 64 LEU cc_start: 0.9426 (mm) cc_final: 0.9181 (mm) REVERT: Bb 43 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8435 (t80) REVERT: Be 43 ARG cc_start: 0.8375 (ttt180) cc_final: 0.8139 (ttm170) REVERT: Cn 2 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7287 (ttt-90) outliers start: 109 outliers final: 80 residues processed: 468 average time/residue: 0.2659 time to fit residues: 204.8646 Evaluate side-chains 477 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 387 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 87 TYR Chi-restraints excluded: chain BA residue 119 THR Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BB residue 119 THR Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 80 ASP Chi-restraints excluded: chain BC residue 90 GLU Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 150 ILE Chi-restraints excluded: chain BC residue 165 VAL Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 45 VAL Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 64 ILE Chi-restraints excluded: chain BE residue 92 ILE Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BG residue 27 PHE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 94 ILE Chi-restraints excluded: chain BH residue 131 VAL Chi-restraints excluded: chain BI residue 22 ARG Chi-restraints excluded: chain BJ residue 3 ASN Chi-restraints excluded: chain BJ residue 48 GLN Chi-restraints excluded: chain BJ residue 64 LEU Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BJ residue 170 ARG Chi-restraints excluded: chain BL residue 32 LEU Chi-restraints excluded: chain BL residue 146 ILE Chi-restraints excluded: chain BN residue 46 THR Chi-restraints excluded: chain BN residue 50 ILE Chi-restraints excluded: chain cS residue 30 VAL Chi-restraints excluded: chain cS residue 36 PHE Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 115 LEU Chi-restraints excluded: chain cS residue 118 LEU Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BV residue 23 MET Chi-restraints excluded: chain BV residue 36 ILE Chi-restraints excluded: chain BW residue 7 LEU Chi-restraints excluded: chain BW residue 26 MET Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BW residue 105 THR Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 5 ARG Chi-restraints excluded: chain BX residue 29 LYS Chi-restraints excluded: chain BX residue 32 LEU Chi-restraints excluded: chain BX residue 68 CYS Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BX residue 132 LEU Chi-restraints excluded: chain BY residue 10 THR Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 45 LEU Chi-restraints excluded: chain BY residue 57 ILE Chi-restraints excluded: chain BY residue 74 PHE Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BY residue 87 PHE Chi-restraints excluded: chain BZ residue 19 LYS Chi-restraints excluded: chain BZ residue 24 SER Chi-restraints excluded: chain BZ residue 26 CYS Chi-restraints excluded: chain BZ residue 44 ILE Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 58 VAL Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 43 PHE Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Bb residue 56 VAL Chi-restraints excluded: chain Be residue 18 THR Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Cn residue 2 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [233, 183, 244, 271, 76, 108, 10, 4, 24, 358, 0] chunk 233 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 4 optimal weight: 40.0000 chunk 24 optimal weight: 30.0000 chunk 358 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 11 ASN ** Be 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.046304 restraints weight = 237342.632| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.70 r_work: 0.2709 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 47913 Z= 0.315 Angle : 0.694 11.351 69813 Z= 0.366 Chirality : 0.048 0.538 8618 Planarity : 0.005 0.043 4832 Dihedral : 23.077 179.583 19689 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.59 % Allowed : 19.55 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.36 (0.16), residues: 2645 helix: 0.95 (0.18), residues: 849 sheet: -0.69 (0.21), residues: 543 loop : -0.79 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGBJ 140 TYR 0.023 0.002 TYRBC 67 PHE 0.028 0.002 PHEBW 99 TRP 0.012 0.002 TRPBV 72 HIS 0.006 0.001 HISBC 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.32 (47909) covalent geometry : angle 0.69268 / 0.37 (69807) hydrogen bonds : bond 0.07972 / 8.24 ( 1567) hydrogen bonds : angle 4.47293 / 5.50 ( 3505) metal coordination : bond 0.01614 / 1.08 ( 4) metal coordination : angle 4.87349 / 8.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 379 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 87 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8624 (m-80) REVERT: BC 89 ASP cc_start: 0.9192 (p0) cc_final: 0.8828 (p0) REVERT: BC 90 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: BC 206 ASP cc_start: 0.8576 (m-30) cc_final: 0.8208 (m-30) REVERT: BC 212 ARG cc_start: 0.9496 (mmm-85) cc_final: 0.8819 (mmm-85) REVERT: BC 233 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8392 (t80) REVERT: BE 19 MET cc_start: 0.9210 (mtt) cc_final: 0.8949 (mtt) REVERT: BE 146 THR cc_start: 0.9536 (m) cc_final: 0.9308 (t) REVERT: BE 201 HIS cc_start: 0.6967 (t70) cc_final: 0.6384 (t70) REVERT: BG 153 ASP cc_start: 0.6595 (t0) cc_final: 0.6282 (t0) REVERT: BH 45 TYR cc_start: 0.7927 (p90) cc_final: 0.6973 (p90) REVERT: BH 73 TYR cc_start: 0.9128 (m-80) cc_final: 0.8777 (m-80) REVERT: BH 131 VAL cc_start: 0.9676 (OUTLIER) cc_final: 0.9408 (t) REVERT: BH 170 PHE cc_start: 0.9316 (m-10) cc_final: 0.8743 (m-80) REVERT: BI 22 ARG cc_start: 0.9504 (OUTLIER) cc_final: 0.9238 (mtm110) REVERT: BI 27 TYR cc_start: 0.9576 (p90) cc_final: 0.9323 (p90) REVERT: BI 160 ILE cc_start: 0.9305 (mm) cc_final: 0.9077 (pt) REVERT: BJ 48 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.8954 (mp10) REVERT: BJ 68 ASN cc_start: 0.8971 (t0) cc_final: 0.8720 (t0) REVERT: BJ 170 ARG cc_start: 0.3196 (OUTLIER) cc_final: 0.1670 (ttt180) REVERT: BN 31 GLN cc_start: 0.9568 (mp10) cc_final: 0.9234 (mp10) REVERT: BN 103 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9077 (mt-10) REVERT: BN 142 GLU cc_start: 0.9029 (tp30) cc_final: 0.8468 (tp30) REVERT: cS 113 SER cc_start: 0.9318 (m) cc_final: 0.9009 (p) REVERT: BV 23 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8918 (mpp) REVERT: BW 26 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8888 (ttp) REVERT: BW 69 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9240 (tt) REVERT: BW 85 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9136 (mt-10) REVERT: BX 97 ASP cc_start: 0.8062 (t0) cc_final: 0.7757 (t0) REVERT: BY 74 PHE cc_start: 0.8981 (t80) cc_final: 0.8128 (t80) REVERT: BZ 14 ASN cc_start: 0.8533 (t0) cc_final: 0.8172 (t0) REVERT: BZ 54 GLN cc_start: 0.9336 (mt0) cc_final: 0.8944 (pt0) REVERT: BZ 63 THR cc_start: 0.9335 (m) cc_final: 0.9051 (p) REVERT: BZ 64 LEU cc_start: 0.9464 (mm) cc_final: 0.9210 (mm) REVERT: Bb 43 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8460 (t80) REVERT: Bb 82 ARG cc_start: 0.9002 (mmp80) cc_final: 0.8791 (mmp80) REVERT: Cn 2 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7332 (ttt-90) outliers start: 107 outliers final: 85 residues processed: 444 average time/residue: 0.2648 time to fit residues: 192.5986 Evaluate side-chains 468 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 371 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 87 TYR Chi-restraints excluded: chain BA residue 119 THR Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BA residue 183 LEU Chi-restraints excluded: chain BB residue 96 VAL Chi-restraints excluded: chain BB residue 119 THR Chi-restraints excluded: chain BB residue 127 VAL Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 90 GLU Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 165 VAL Chi-restraints excluded: chain BC residue 173 CYS Chi-restraints excluded: chain BC residue 233 TYR Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 45 VAL Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 64 ILE Chi-restraints excluded: chain BE residue 92 ILE Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BG residue 18 ILE Chi-restraints excluded: chain BG residue 27 PHE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 123 LEU Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 61 ILE Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 94 ILE Chi-restraints excluded: chain BH residue 101 ILE Chi-restraints excluded: chain BH residue 131 VAL Chi-restraints excluded: chain BI residue 22 ARG Chi-restraints excluded: chain BI residue 28 GLU Chi-restraints excluded: chain BJ residue 3 ASN Chi-restraints excluded: chain BJ residue 48 GLN Chi-restraints excluded: chain BJ residue 64 LEU Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BJ residue 170 ARG Chi-restraints excluded: chain BL residue 146 ILE Chi-restraints excluded: chain BN residue 46 THR Chi-restraints excluded: chain BN residue 50 ILE Chi-restraints excluded: chain BN residue 116 ILE Chi-restraints excluded: chain cS residue 30 VAL Chi-restraints excluded: chain cS residue 36 PHE Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 115 LEU Chi-restraints excluded: chain cS residue 118 LEU Chi-restraints excluded: chain cS residue 142 LYS Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BV residue 23 MET Chi-restraints excluded: chain BV residue 36 ILE Chi-restraints excluded: chain BV residue 77 VAL Chi-restraints excluded: chain BW residue 7 LEU Chi-restraints excluded: chain BW residue 26 MET Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 39 ILE Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BW residue 105 THR Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 29 LYS Chi-restraints excluded: chain BX residue 32 LEU Chi-restraints excluded: chain BX residue 54 ILE Chi-restraints excluded: chain BX residue 68 CYS Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BX residue 132 LEU Chi-restraints excluded: chain BY residue 10 THR Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 45 LEU Chi-restraints excluded: chain BY residue 57 ILE Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BY residue 87 PHE Chi-restraints excluded: chain BZ residue 24 SER Chi-restraints excluded: chain BZ residue 26 CYS Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 58 VAL Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 3 LEU Chi-restraints excluded: chain Bb residue 43 PHE Chi-restraints excluded: chain Bb residue 46 THR Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Bb residue 56 VAL Chi-restraints excluded: chain Bb residue 64 ILE Chi-restraints excluded: chain Be residue 18 THR Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Cn residue 2 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [33, 307, 105, 245, 337, 231, 275, 55, 71, 244, 38] chunk 33 optimal weight: 30.0000 chunk 307 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 337 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 71 optimal weight: 40.0000 chunk 244 optimal weight: 6.9990 chunk 38 optimal weight: 40.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... BC 230 GLN ** BE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.063738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.047973 restraints weight = 231560.921| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.71 r_work: 0.2763 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 47913 Z= 0.134 Angle : 0.540 9.857 69813 Z= 0.301 Chirality : 0.038 0.445 8618 Planarity : 0.004 0.048 4832 Dihedral : 23.069 179.388 19689 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.56 % Allowed : 21.14 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2645 helix: 1.22 (0.18), residues: 849 sheet: -0.63 (0.21), residues: 551 loop : -0.57 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGBI 93 TYR 0.010 0.001 TYRBW 130 PHE 0.022 0.001 PHEBW 99 TRP 0.014 0.001 TRPBC 45 HIS 0.008 0.001 HISBE 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (47909) covalent geometry : angle 0.53926 / 0.30 (69807) hydrogen bonds : bond 0.06330 / 6.61 ( 1567) hydrogen bonds : angle 4.07415 / 5.00 ( 3505) metal coordination : bond 0.00739 / 0.50 ( 4) metal coordination : angle 3.17312 / 5.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 404 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 189 GLN cc_start: 0.9641 (tp40) cc_final: 0.9338 (mt0) REVERT: BA 209 TYR cc_start: 0.7626 (t80) cc_final: 0.7360 (t80) REVERT: BC 67 TYR cc_start: 0.9249 (m-10) cc_final: 0.8938 (m-10) REVERT: BC 89 ASP cc_start: 0.9198 (p0) cc_final: 0.8854 (p0) REVERT: BC 90 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: BC 206 ASP cc_start: 0.8579 (m-30) cc_final: 0.8231 (m-30) REVERT: BC 243 GLU cc_start: 0.8407 (tp30) cc_final: 0.8192 (tp30) REVERT: BC 245 ARG cc_start: 0.8557 (mmp80) cc_final: 0.8270 (mmp80) REVERT: BE 19 MET cc_start: 0.9133 (mtt) cc_final: 0.8745 (mtt) REVERT: BE 146 THR cc_start: 0.9485 (m) cc_final: 0.9219 (t) REVERT: BE 201 HIS cc_start: 0.6932 (t70) cc_final: 0.6307 (t70) REVERT: BG 153 ASP cc_start: 0.6587 (t0) cc_final: 0.6275 (t0) REVERT: BH 73 TYR cc_start: 0.9107 (m-80) cc_final: 0.8737 (m-80) REVERT: BH 131 VAL cc_start: 0.9617 (OUTLIER) cc_final: 0.9346 (t) REVERT: BH 170 PHE cc_start: 0.9201 (m-10) cc_final: 0.8638 (m-80) REVERT: BI 22 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.9123 (mtm110) REVERT: BI 27 TYR cc_start: 0.9547 (p90) cc_final: 0.9291 (p90) REVERT: BI 84 TYR cc_start: 0.8808 (t80) cc_final: 0.8429 (t80) REVERT: BI 93 ARG cc_start: 0.9439 (mtm110) cc_final: 0.9218 (mtm-85) REVERT: BI 160 ILE cc_start: 0.9314 (mm) cc_final: 0.9078 (pt) REVERT: BJ 68 ASN cc_start: 0.8940 (t0) cc_final: 0.8706 (t0) REVERT: BJ 170 ARG cc_start: 0.3525 (OUTLIER) cc_final: 0.2106 (ttt180) REVERT: BN 31 GLN cc_start: 0.9593 (mp10) cc_final: 0.9246 (mp10) REVERT: BN 103 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9109 (mt-10) REVERT: BN 142 GLU cc_start: 0.9005 (tp30) cc_final: 0.8457 (tp30) REVERT: cS 74 MET cc_start: 0.8421 (ttt) cc_final: 0.7598 (tmm) REVERT: cS 113 SER cc_start: 0.9292 (m) cc_final: 0.8980 (p) REVERT: BW 26 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8822 (ttp) REVERT: BW 69 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9182 (tt) REVERT: BX 5 ARG cc_start: 0.9440 (OUTLIER) cc_final: 0.8654 (ttp-170) REVERT: BX 97 ASP cc_start: 0.8169 (t0) cc_final: 0.7841 (t0) REVERT: BY 74 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8211 (t80) REVERT: BZ 14 ASN cc_start: 0.8514 (t0) cc_final: 0.8265 (t0) REVERT: BZ 54 GLN cc_start: 0.9293 (mt0) cc_final: 0.8888 (pt0) REVERT: BZ 63 THR cc_start: 0.9296 (m) cc_final: 0.9016 (p) REVERT: BZ 64 LEU cc_start: 0.9424 (mm) cc_final: 0.9191 (mm) REVERT: Bb 43 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8463 (t80) REVERT: Cn 2 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7223 (ttt-90) outliers start: 83 outliers final: 62 residues processed: 451 average time/residue: 0.2573 time to fit residues: 189.0475 Evaluate side-chains 462 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 390 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 119 THR Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 90 GLU Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 150 ILE Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 92 ILE Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BG residue 18 ILE Chi-restraints excluded: chain BG residue 27 PHE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 123 LEU Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 94 ILE Chi-restraints excluded: chain BH residue 101 ILE Chi-restraints excluded: chain BH residue 131 VAL Chi-restraints excluded: chain BI residue 22 ARG Chi-restraints excluded: chain BJ residue 3 ASN Chi-restraints excluded: chain BJ residue 48 GLN Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BJ residue 170 ARG Chi-restraints excluded: chain BL residue 106 THR Chi-restraints excluded: chain BN residue 46 THR Chi-restraints excluded: chain BN residue 50 ILE Chi-restraints excluded: chain cS residue 30 VAL Chi-restraints excluded: chain cS residue 36 PHE Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 115 LEU Chi-restraints excluded: chain cS residue 118 LEU Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BV residue 32 VAL Chi-restraints excluded: chain BV residue 36 ILE Chi-restraints excluded: chain BW residue 26 MET Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BW residue 105 THR Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 5 ARG Chi-restraints excluded: chain BX residue 29 LYS Chi-restraints excluded: chain BX residue 32 LEU Chi-restraints excluded: chain BX residue 68 CYS Chi-restraints excluded: chain BX residue 71 VAL Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BY residue 45 LEU Chi-restraints excluded: chain BY residue 57 ILE Chi-restraints excluded: chain BY residue 74 PHE Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BY residue 87 PHE Chi-restraints excluded: chain BZ residue 24 SER Chi-restraints excluded: chain BZ residue 26 CYS Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 43 PHE Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Cn residue 2 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [225, 127, 26, 295, 35, 16, 262, 308, 265, 130, 67] chunk 225 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 35 optimal weight: 40.0000 chunk 16 optimal weight: 50.0000 chunk 262 optimal weight: 40.0000 chunk 308 optimal weight: 3.9990 chunk 265 optimal weight: 0.0570 chunk 130 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** BE 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 60 GLN Bb 44 ASN ** Be 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.063238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.047550 restraints weight = 233420.588| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.67 r_work: 0.2749 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 47913 Z= 0.185 Angle : 0.580 9.675 69813 Z= 0.316 Chirality : 0.040 0.474 8618 Planarity : 0.004 0.048 4832 Dihedral : 23.000 179.724 19687 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.39 % Allowed : 21.05 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2645 helix: 1.16 (0.18), residues: 852 sheet: -0.57 (0.22), residues: 529 loop : -0.62 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGBI 93 TYR 0.016 0.001 TYRBH 45 PHE 0.031 0.001 PHEBW 99 TRP 0.089 0.002 TRPBC 45 HIS 0.006 0.001 HISBE 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (47909) covalent geometry : angle 0.57942 / 0.32 (69807) hydrogen bonds : bond 0.06539 / 6.82 ( 1567) hydrogen bonds : angle 4.15105 / 5.09 ( 3505) metal coordination : bond 0.00958 / 0.63 ( 4) metal coordination : angle 3.15129 / 5.87 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5290 Ramachandran restraints generated. 2645 Oldfield, 0 Emsley, 2645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 399 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 87 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: BA 186 MET cc_start: 0.9139 (mtp) cc_final: 0.8886 (ptm) REVERT: BA 189 GLN cc_start: 0.9629 (tp40) cc_final: 0.9330 (mt0) REVERT: BA 209 TYR cc_start: 0.7643 (t80) cc_final: 0.7439 (t80) REVERT: BC 67 TYR cc_start: 0.9287 (m-10) cc_final: 0.8985 (m-80) REVERT: BC 89 ASP cc_start: 0.9193 (p0) cc_final: 0.8862 (p0) REVERT: BC 90 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: BC 206 ASP cc_start: 0.8603 (m-30) cc_final: 0.8234 (m-30) REVERT: BC 212 ARG cc_start: 0.9448 (mmm-85) cc_final: 0.8906 (mmm-85) REVERT: BC 233 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.7928 (t80) REVERT: BC 243 GLU cc_start: 0.8416 (tp30) cc_final: 0.8214 (tp30) REVERT: BC 245 ARG cc_start: 0.8536 (mmp80) cc_final: 0.8316 (mmp80) REVERT: BE 19 MET cc_start: 0.9177 (mtt) cc_final: 0.8834 (mtt) REVERT: BE 146 THR cc_start: 0.9511 (m) cc_final: 0.9246 (t) REVERT: BE 201 HIS cc_start: 0.6900 (t70) cc_final: 0.6287 (t70) REVERT: BG 153 ASP cc_start: 0.6667 (t0) cc_final: 0.6361 (t0) REVERT: BH 45 TYR cc_start: 0.7844 (p90) cc_final: 0.7424 (p90) REVERT: BH 73 TYR cc_start: 0.9110 (m-80) cc_final: 0.8748 (m-80) REVERT: BH 131 VAL cc_start: 0.9623 (OUTLIER) cc_final: 0.9356 (t) REVERT: BH 170 PHE cc_start: 0.9240 (m-10) cc_final: 0.8710 (m-80) REVERT: BI 22 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.9152 (mtm110) REVERT: BI 27 TYR cc_start: 0.9572 (p90) cc_final: 0.9304 (p90) REVERT: BI 160 ILE cc_start: 0.9325 (mm) cc_final: 0.9092 (pt) REVERT: BJ 68 ASN cc_start: 0.8943 (t0) cc_final: 0.8703 (t0) REVERT: BJ 170 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.2182 (ttt180) REVERT: BN 31 GLN cc_start: 0.9581 (mp10) cc_final: 0.9193 (mp10) REVERT: BN 103 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9102 (mt-10) REVERT: BN 142 GLU cc_start: 0.9014 (tp30) cc_final: 0.8458 (tp30) REVERT: cS 74 MET cc_start: 0.8438 (ttt) cc_final: 0.7589 (tmm) REVERT: cS 113 SER cc_start: 0.9299 (m) cc_final: 0.8975 (p) REVERT: BV 23 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8615 (mtm) REVERT: BW 26 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8819 (ttp) REVERT: BW 69 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9235 (tt) REVERT: BW 85 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8973 (mp0) REVERT: BX 97 ASP cc_start: 0.8163 (t0) cc_final: 0.7831 (t0) REVERT: BY 74 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8114 (t80) REVERT: BZ 14 ASN cc_start: 0.8549 (t0) cc_final: 0.8258 (t0) REVERT: BZ 54 GLN cc_start: 0.9324 (mt0) cc_final: 0.8904 (pt0) REVERT: BZ 63 THR cc_start: 0.9310 (m) cc_final: 0.9022 (p) REVERT: BZ 64 LEU cc_start: 0.9416 (mm) cc_final: 0.9190 (mm) REVERT: Bb 43 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8424 (t80) REVERT: Cn 2 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7216 (ttt-90) outliers start: 79 outliers final: 65 residues processed: 444 average time/residue: 0.2509 time to fit residues: 183.0059 Evaluate side-chains 466 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 389 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 23 MET Chi-restraints excluded: chain BA residue 87 TYR Chi-restraints excluded: chain BA residue 119 THR Chi-restraints excluded: chain BA residue 122 SER Chi-restraints excluded: chain BA residue 153 CYS Chi-restraints excluded: chain BB residue 148 ASN Chi-restraints excluded: chain BC residue 90 GLU Chi-restraints excluded: chain BC residue 145 LEU Chi-restraints excluded: chain BC residue 173 CYS Chi-restraints excluded: chain BC residue 233 TYR Chi-restraints excluded: chain BE residue 44 LEU Chi-restraints excluded: chain BE residue 47 ILE Chi-restraints excluded: chain BE residue 64 ILE Chi-restraints excluded: chain BE residue 92 ILE Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 228 ILE Chi-restraints excluded: chain BG residue 18 ILE Chi-restraints excluded: chain BG residue 27 PHE Chi-restraints excluded: chain BG residue 67 VAL Chi-restraints excluded: chain BG residue 68 LEU Chi-restraints excluded: chain BG residue 123 LEU Chi-restraints excluded: chain BH residue 22 GLN Chi-restraints excluded: chain BH residue 78 VAL Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 94 ILE Chi-restraints excluded: chain BH residue 101 ILE Chi-restraints excluded: chain BH residue 131 VAL Chi-restraints excluded: chain BI residue 22 ARG Chi-restraints excluded: chain BJ residue 3 ASN Chi-restraints excluded: chain BJ residue 48 GLN Chi-restraints excluded: chain BJ residue 89 ASP Chi-restraints excluded: chain BJ residue 91 THR Chi-restraints excluded: chain BJ residue 170 ARG Chi-restraints excluded: chain BN residue 46 THR Chi-restraints excluded: chain BN residue 50 ILE Chi-restraints excluded: chain cS residue 30 VAL Chi-restraints excluded: chain cS residue 36 PHE Chi-restraints excluded: chain cS residue 61 VAL Chi-restraints excluded: chain cS residue 84 CYS Chi-restraints excluded: chain cS residue 115 LEU Chi-restraints excluded: chain cS residue 118 LEU Chi-restraints excluded: chain BV residue 11 LEU Chi-restraints excluded: chain BV residue 23 MET Chi-restraints excluded: chain BV residue 32 VAL Chi-restraints excluded: chain BV residue 36 ILE Chi-restraints excluded: chain BW residue 26 MET Chi-restraints excluded: chain BW residue 33 VAL Chi-restraints excluded: chain BW residue 69 LEU Chi-restraints excluded: chain BW residue 74 VAL Chi-restraints excluded: chain BW residue 104 LEU Chi-restraints excluded: chain BW residue 105 THR Chi-restraints excluded: chain BX residue 4 THR Chi-restraints excluded: chain BX residue 29 LYS Chi-restraints excluded: chain BX residue 32 LEU Chi-restraints excluded: chain BX residue 60 GLN Chi-restraints excluded: chain BX residue 68 CYS Chi-restraints excluded: chain BX residue 74 ILE Chi-restraints excluded: chain BX residue 76 ASN Chi-restraints excluded: chain BX residue 104 PHE Chi-restraints excluded: chain BX residue 117 VAL Chi-restraints excluded: chain BX residue 122 VAL Chi-restraints excluded: chain BY residue 18 LEU Chi-restraints excluded: chain BY residue 45 LEU Chi-restraints excluded: chain BY residue 57 ILE Chi-restraints excluded: chain BY residue 74 PHE Chi-restraints excluded: chain BY residue 76 LEU Chi-restraints excluded: chain BY residue 87 PHE Chi-restraints excluded: chain BZ residue 19 LYS Chi-restraints excluded: chain BZ residue 24 SER Chi-restraints excluded: chain BZ residue 26 CYS Chi-restraints excluded: chain BZ residue 45 VAL Chi-restraints excluded: chain BZ residue 57 SER Chi-restraints excluded: chain BZ residue 90 THR Chi-restraints excluded: chain Bb residue 43 PHE Chi-restraints excluded: chain Bb residue 48 VAL Chi-restraints excluded: chain Be residue 21 VAL Chi-restraints excluded: chain Cn residue 2 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: [224, 251, 118, 299, 89, 116, 342, 283, 86, 290, 190] chunk 224 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 118 optimal weight: 0.0070 chunk 299 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 342 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 290 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 overall best weight: 2.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... BC 230 GLN ** BE 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.048428 restraints weight = 233095.033| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.68 r_work: 0.2776 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47913 Z= 0.128 Angle : 0.538 10.012 69813 Z= 0.299 Chirality : 0.037 0.442 8618 Planarity : 0.004 0.048 4832 Dihedral : 22.996 179.284 19687 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.17 % Allowed : 21.14 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.16), residues: 2645 helix: 1.21 (0.18), residues: 852 sheet: -0.54 (0.22), residues: 529 loop : -0.53 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGBX 70 TYR 0.014 0.001 TYRBH 45 PHE 0.044 0.001 PHEBW 99 TRP 0.053 0.001 TRPBC 45 HIS 0.008 0.001 HISBE 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (47909) covalent geometry : angle 0.53704 / 0.30 (69807) hydrogen bonds : bond 0.06104 / 6.40 ( 1567) hydrogen bonds : angle 4.01580 / 4.92 ( 3505) metal coordination : bond 0.00665 / 0.44 ( 4) metal coordination : angle 2.74701 / 5.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10309.69 seconds wall clock time: 177 minutes 33.17 seconds (10653.17 seconds total)