Starting phenix.real_space_refine (version: dev) on Thu Dec 22 14:23:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/12_2022/7wtl_32790_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/12_2022/7wtl_32790.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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/12_2022/7wtl_32790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/12_2022/7wtl_32790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/12_2022/7wtl_32790_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/12_2022/7wtl_32790_updated.pdb" } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "SB ASP 59": "OD1" <-> "OD2" Residue "SE ASP 88": "OD1" <-> "OD2" Residue "SE GLU 117": "OE1" <-> "OE2" Residue "SE TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE GLU 199": "OE1" <-> "OE2" Residue "SE GLU 250": "OE1" <-> "OE2" Residue "SG ASP 43": "OD1" <-> "OD2" Residue "SG PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 161": "OE1" <-> "OE2" Residue "SH PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 128": "OD1" <-> "OD2" Residue "SH GLU 134": "OE1" <-> "OE2" Residue "SI GLU 89": "OE1" <-> "OE2" Residue "SI PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI GLU 185": "OE1" <-> "OE2" Residue "SI PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ GLU 20": "OE1" <-> "OE2" Residue "SJ ASP 58": "OD1" <-> "OD2" Residue "SJ GLU 72": "OE1" <-> "OE2" Residue "SJ ASP 157": "OD1" <-> "OD2" Residue "SJ PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN GLU 31": "OE1" <-> "OE2" Residue "SN GLU 35": "OE1" <-> "OE2" Residue "SN GLU 86": "OE1" <-> "OE2" Residue "SN GLU 103": "OE1" <-> "OE2" Residue "SN GLU 142": "OE1" <-> "OE2" Residue "SO GLU 73": "OE1" <-> "OE2" Residue "SO GLU 116": "OE1" <-> "OE2" Residue "SW ASP 9": "OD1" <-> "OD2" Residue "SW GLU 18": "OE1" <-> "OE2" Residue "SW ASP 55": "OD1" <-> "OD2" Residue "SW TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SX GLU 141": "OE1" <-> "OE2" Residue "SY PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Sb ASP 34": "OD1" <-> "OD2" Residue "Sb GLU 57": "OE1" <-> "OE2" Residue "CA TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JL GLU 85": "OE1" <-> "OE2" Residue "JL ASP 219": "OD1" <-> "OD2" Residue "JL PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 49811 Number of models: 1 Model: "" Number of chains: 21 Chain: "C2" Number of atoms: 23488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 23488 Classifications: {'RNA': 1102} Modifications used: {'rna2p_pur': 104, 'rna2p_pyr': 84, 'rna3p_pur': 486, 'rna3p_pyr': 428} Link IDs: {'rna2p': 188, 'rna3p': 913} Chain breaks: 7 Chain: "SB" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "SE" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "SG" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "SH" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 171} Chain: "SI" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "SJ" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "SL" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "SN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "SO" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "SW" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "SX" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 962 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 2 Chain: "SY" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Sb" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "CA" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "CK" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 299 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "CL" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4910 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 38, 'TRANS': 571} Chain breaks: 2 Chain: "UC" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 393 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "JL" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2262 Classifications: {'peptide': 283} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 265} Chain: "Sb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "CL" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.46, per 1000 atoms: 0.59 Number of scatterers: 49811 At special positions: 0 Unit cell: (159.144, 208.353, 221.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 1105 15.00 Mg 1 11.99 O 12374 8.00 N 9055 7.00 C 27202 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 - 3.50 Amino acid : False - 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: 24.82 Conformation dependent library (CDL) restraints added in 4.1 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 31 sheets defined 31.7% alpha, 17.9% beta 360 base pairs and 568 stacking pairs defined. Time for finding SS restraints: 20.97 Creating SS restraints... Processing helix chain 'SB' and resid 23 through 26 No H-bonds generated for 'chain 'SB' and resid 23 through 26' Processing helix chain 'SB' and resid 59 through 61 No H-bonds generated for 'chain 'SB' and resid 59 through 61' Processing helix chain 'SB' and resid 70 through 74 Processing helix chain 'SB' and resid 77 through 79 No H-bonds generated for 'chain 'SB' and resid 77 through 79' Processing helix chain 'SB' and resid 107 through 113 Processing helix chain 'SB' and resid 158 through 177 Processing helix chain 'SB' and resid 181 through 188 Processing helix chain 'SB' and resid 192 through 200 Processing helix chain 'SB' and resid 225 through 231 Processing helix chain 'SE' and resid 16 through 18 No H-bonds generated for 'chain 'SE' and resid 16 through 18' Processing helix chain 'SE' and resid 44 through 49 Processing helix chain 'SE' and resid 58 through 67 removed outlier: 3.512A pdb=" N GLNSE 67 " --> pdb=" O ALASE 63 " (cutoff:3.500A) Processing helix chain 'SE' and resid 133 through 135 No H-bonds generated for 'chain 'SE' and resid 133 through 135' Processing helix chain 'SE' and resid 222 through 224 No H-bonds generated for 'chain 'SE' and resid 222 through 224' Processing helix chain 'SE' and resid 248 through 258 Processing helix chain 'SG' and resid 23 through 27 removed outlier: 4.484A pdb=" N VALSG 26 " --> pdb=" O ARGSG 23 " (cutoff:3.500A) Processing helix chain 'SG' and resid 138 through 145 Processing helix chain 'SG' and resid 153 through 155 No H-bonds generated for 'chain 'SG' and resid 153 through 155' Processing helix chain 'SG' and resid 181 through 217 removed outlier: 3.514A pdb=" N SERSG 217 " --> pdb=" O ALASG 213 " (cutoff:3.500A) Processing helix chain 'SH' and resid 15 through 28 Processing helix chain 'SH' and resid 32 through 38 Processing helix chain 'SH' and resid 67 through 73 Processing helix chain 'SH' and resid 76 through 84 Processing helix chain 'SH' and resid 114 through 116 No H-bonds generated for 'chain 'SH' and resid 114 through 116' Processing helix chain 'SH' and resid 118 through 129 Processing helix chain 'SH' and resid 166 through 177 Processing helix chain 'SI' and resid 26 through 28 No H-bonds generated for 'chain 'SI' and resid 26 through 28' Processing helix chain 'SI' and resid 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 89 through 92 No H-bonds generated for 'chain 'SI' and resid 89 through 92' Processing helix chain 'SI' and resid 107 through 116 Processing helix chain 'SI' and resid 137 through 145 Processing helix chain 'SI' and resid 154 through 162 Processing helix chain 'SI' and resid 173 through 176 No H-bonds generated for 'chain 'SI' and resid 173 through 176' Processing helix chain 'SI' and resid 187 through 199 Processing helix chain 'SJ' and resid 21 through 33 Processing helix chain 'SJ' and resid 40 through 61 Processing helix chain 'SJ' and resid 67 through 83 Processing helix chain 'SJ' and resid 93 through 96 No H-bonds generated for 'chain 'SJ' and resid 93 through 96' Processing helix chain 'SJ' and resid 101 through 106 Processing helix chain 'SJ' and resid 109 through 114 Processing helix chain 'SJ' and resid 122 through 130 Processing helix chain 'SJ' and resid 153 through 155 No H-bonds generated for 'chain 'SJ' and resid 153 through 155' Processing helix chain 'SJ' and resid 163 through 165 No H-bonds generated for 'chain 'SJ' and resid 163 through 165' Processing helix chain 'SJ' and resid 171 through 182 Processing helix chain 'SL' and resid 46 through 49 No H-bonds generated for 'chain 'SL' and resid 46 through 49' Processing helix chain 'SN' and resid 32 through 42 Processing helix chain 'SN' and resid 47 through 57 Processing helix chain 'SN' and resid 63 through 66 No H-bonds generated for 'chain 'SN' and resid 63 through 66' Processing helix chain 'SN' and resid 71 through 77 Processing helix chain 'SN' and resid 86 through 104 Processing helix chain 'SN' and resid 109 through 132 Processing helix chain 'SN' and resid 143 through 150 removed outlier: 3.987A pdb=" N ALASN 148 " --> pdb=" O ALASN 144 " (cutoff:3.500A) Processing helix chain 'SO' and resid 44 through 46 No H-bonds generated for 'chain 'SO' and resid 44 through 46' Processing helix chain 'SO' and resid 57 through 74 Processing helix chain 'SO' and resid 96 through 107 Processing helix chain 'SW' and resid 6 through 20 Processing helix chain 'SW' and resid 32 through 43 Processing helix chain 'SW' and resid 86 through 93 Processing helix chain 'SW' and resid 113 through 119 Processing helix chain 'SX' and resid 12 through 25 removed outlier: 4.344A pdb=" N TRPSX 24 " --> pdb=" O ARGSX 20 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALASX 25 " --> pdb=" O ASNSX 21 " (cutoff:3.500A) Processing helix chain 'SX' and resid 27 through 33 Processing helix chain 'SX' and resid 90 through 94 Processing helix chain 'SX' and resid 132 through 136 Processing helix chain 'SY' and resid 37 through 47 Processing helix chain 'SY' and resid 52 through 54 No H-bonds generated for 'chain 'SY' and resid 52 through 54' Processing helix chain 'SY' and resid 80 through 85 Processing helix chain 'SY' and resid 88 through 93 Processing helix chain 'SY' and resid 105 through 117 removed outlier: 3.783A pdb=" N LYSSY 117 " --> pdb=" O ASNSY 113 " (cutoff:3.500A) Processing helix chain 'SY' and resid 123 through 134 Processing helix chain 'Sb' and resid 12 through 17 Processing helix chain 'CA' and resid 103 through 122 removed outlier: 4.665A pdb=" N THRCA 107 " --> pdb=" O HISCA 104 " (cutoff:3.500A) Proline residue: CA 108 - end of helix removed outlier: 5.404A pdb=" N THRCA 114 " --> pdb=" O ASNCA 111 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYRCA 117 " --> pdb=" O THRCA 114 " (cutoff:3.500A) Proline residue: CA 118 - end of helix Processing helix chain 'CA' and resid 149 through 163 Processing helix chain 'CA' and resid 168 through 176 Processing helix chain 'CA' and resid 196 through 206 Processing helix chain 'CA' and resid 208 through 219 removed outlier: 6.206A pdb=" N THRCA 212 " --> pdb=" O ASPCA 209 " (cutoff:3.500A) Processing helix chain 'CA' and resid 237 through 251 Processing helix chain 'CA' and resid 256 through 270 Processing helix chain 'CK' and resid 299 through 319 Processing helix chain 'CK' and resid 324 through 326 No H-bonds generated for 'chain 'CK' and resid 324 through 326' Processing helix chain 'CL' and resid 36 through 52 Processing helix chain 'CL' and resid 78 through 80 No H-bonds generated for 'chain 'CL' and resid 78 through 80' Processing helix chain 'CL' and resid 82 through 94 Processing helix chain 'CL' and resid 126 through 134 Processing helix chain 'CL' and resid 150 through 162 Processing helix chain 'CL' and resid 180 through 197 Processing helix chain 'CL' and resid 217 through 227 Processing helix chain 'CL' and resid 237 through 239 No H-bonds generated for 'chain 'CL' and resid 237 through 239' Processing helix chain 'CL' and resid 255 through 260 Processing helix chain 'CL' and resid 311 through 321 Processing helix chain 'CL' and resid 750 through 770 Processing helix chain 'CL' and resid 774 through 781 Processing helix chain 'CL' and resid 817 through 819 No H-bonds generated for 'chain 'CL' and resid 817 through 819' Processing helix chain 'CL' and resid 955 through 960 Processing helix chain 'CL' and resid 1020 through 1022 No H-bonds generated for 'chain 'CL' and resid 1020 through 1022' Processing helix chain 'CL' and resid 1035 through 1042 Processing helix chain 'UC' and resid 542 through 545 No H-bonds generated for 'chain 'UC' and resid 542 through 545' Processing helix chain 'UC' and resid 556 through 558 No H-bonds generated for 'chain 'UC' and resid 556 through 558' Processing helix chain 'UC' and resid 561 through 579 Processing helix chain 'JL' and resid 44 through 52 Processing helix chain 'JL' and resid 71 through 77 Processing helix chain 'JL' and resid 88 through 97 Processing helix chain 'JL' and resid 104 through 106 No H-bonds generated for 'chain 'JL' and resid 104 through 106' Processing helix chain 'JL' and resid 131 through 142 removed outlier: 4.839A pdb=" N SERJL 135 " --> pdb=" O GLNJL 132 " (cutoff:3.500A) Proline residue: JL 136 - end of helix Processing helix chain 'JL' and resid 157 through 163 Processing helix chain 'JL' and resid 174 through 182 Processing helix chain 'JL' and resid 193 through 195 No H-bonds generated for 'chain 'JL' and resid 193 through 195' Processing helix chain 'JL' and resid 220 through 231 Processing helix chain 'JL' and resid 238 through 241 No H-bonds generated for 'chain 'JL' and resid 238 through 241' Processing helix chain 'JL' and resid 245 through 262 Processing helix chain 'JL' and resid 273 through 286 Processing helix chain 'JL' and resid 295 through 297 No H-bonds generated for 'chain 'JL' and resid 295 through 297' Processing helix chain 'JL' and resid 300 through 312 Processing sheet with id= A, first strand: chain 'SB' and resid 66 through 69 removed outlier: 8.681A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEUSB 217 " --> pdb=" O HISSB 101 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYSSB 214 " --> pdb=" O PHESB 138 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VALSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'SB' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'SB' and resid 28 through 33 Processing sheet with id= D, first strand: chain 'SE' and resid 102 through 104 removed outlier: 4.365A pdb=" N VALSE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARGSE 108 " --> pdb=" O ASPSE 104 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'SE' and resid 158 through 162 removed outlier: 6.844A pdb=" N VALSE 140 " --> pdb=" O LYSSE 127 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VALSE 129 " --> pdb=" O TYRSE 138 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYRSE 138 " --> pdb=" O VALSE 129 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'SE' and resid 225 through 230 removed outlier: 6.496A pdb=" N LEUSE 180 " --> pdb=" O ILESE 228 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYSSE 179 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HISSE 209 " --> pdb=" O VALSE 196 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYSSE 198 " --> pdb=" O LEUSE 207 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEUSE 207 " --> pdb=" O LYSSE 198 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'SG' and resid 12 through 17 removed outlier: 6.620A pdb=" N VALSG 49 " --> pdb=" O VALSG 114 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'SG' and resid 72 through 77 Processing sheet with id= I, first strand: chain 'SG' and resid 160 through 163 Processing sheet with id= J, first strand: chain 'SG' and resid 54 through 57 Processing sheet with id= K, first strand: chain 'SH' and resid 45 through 50 Processing sheet with id= L, first strand: chain 'SH' and resid 180 through 185 removed outlier: 4.732A pdb=" N GLNSH 180 " --> pdb=" O LYSSH 148 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'SI' and resid 63 through 67 Processing sheet with id= N, first strand: chain 'SI' and resid 181 through 183 removed outlier: 6.510A pdb=" N ASPSI 105 " --> pdb=" O ILESI 78 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILESI 78 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'SI' and resid 42 through 47 removed outlier: 6.880A pdb=" N HISSI 44 " --> pdb=" O ALASI 57 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALASI 57 " --> pdb=" O HISSI 44 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VALSI 46 " --> pdb=" O TYRSI 55 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYRSI 55 " --> pdb=" O VALSI 46 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'SJ' and resid 134 through 136 Processing sheet with id= Q, first strand: chain 'SL' and resid 99 through 110 removed outlier: 5.961A pdb=" N ARGSL 87 " --> pdb=" O VALSL 75 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VALSL 75 " --> pdb=" O ARGSL 87 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ALASL 89 " --> pdb=" O GLYSL 73 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLYSL 73 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 15.564A pdb=" N LEUSL 91 " --> pdb=" O LEUSL 71 " (cutoff:3.500A) removed outlier: 16.680A pdb=" N LEUSL 71 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASPSL 121 " --> pdb=" O VALSL 75 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLYSL 126 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VALSL 139 " --> pdb=" O GLYSL 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'SO' and resid 40 through 43 removed outlier: 3.648A pdb=" N ALASO 40 " --> pdb=" O VALSO 30 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VALSO 42 " --> pdb=" O VALSO 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALSO 28 " --> pdb=" O VALSO 42 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALASO 78 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALASO 17 " --> pdb=" O ALASO 78 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HISSO 80 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILESO 19 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYSSO 82 " --> pdb=" O ILESO 19 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALASO 21 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARGSO 84 " --> pdb=" O ALASO 21 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARGSO 111 " --> pdb=" O VALSO 79 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VALSO 81 " --> pdb=" O ARGSO 111 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLYSO 113 " --> pdb=" O VALSO 81 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ILESO 83 " --> pdb=" O GLYSO 113 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'SW' and resid 24 through 27 Processing sheet with id= T, first strand: chain 'SW' and resid 71 through 74 removed outlier: 6.901A pdb=" N ILESW 103 " --> pdb=" O LEUSW 126 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHESW 128 " --> pdb=" O TYRSW 101 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYRSW 101 " --> pdb=" O PHESW 128 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'SX' and resid 82 through 85 removed outlier: 6.427A pdb=" N GLNSX 75 " --> pdb=" O VALSX 53 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VALSX 53 " --> pdb=" O GLNSX 75 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALASX 105 " --> pdb=" O VALSX 124 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VALSX 124 " --> pdb=" O ALASX 105 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'SY' and resid 5 through 10 removed outlier: 6.895A pdb=" N LEUSY 74 " --> pdb=" O VALSY 57 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VALSY 57 " --> pdb=" O LEUSY 74 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYRSY 76 " --> pdb=" O VALSY 55 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VALSY 55 " --> pdb=" O TYRSY 76 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'SY' and resid 13 through 15 Processing sheet with id= X, first strand: chain 'Sb' and resid 43 through 47 Processing sheet with id= Y, first strand: chain 'CA' and resid 95 through 100 Processing sheet with id= Z, first strand: chain 'CA' and resid 181 through 186 Processing sheet with id= AA, first strand: chain 'CL' and resid 166 through 172 Processing sheet with id= AB, first strand: chain 'CL' and resid 294 through 297 removed outlier: 7.281A pdb=" N TYRCL 272 " --> pdb=" O ASPCL 247 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHECL 249 " --> pdb=" O ALACL 270 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALACL 270 " --> pdb=" O PHECL 249 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'CL' and resid 869 through 871 removed outlier: 7.349A pdb=" N THRCL 863 " --> pdb=" O TYRCL 880 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N TYRCL 880 " --> pdb=" O THRCL 863 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARGCL 828 " --> pdb=" O VALCL 919 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VALCL 919 " --> pdb=" O ARGCL 828 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ARGCL 830 " --> pdb=" O GLYCL 917 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLYCL 917 " --> pdb=" O ARGCL 830 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLYCL 898 " --> pdb=" O ALACL 914 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THRCL 916 " --> pdb=" O PHECL 896 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHECL 896 " --> pdb=" O THRCL 916 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASPCL 843 " --> pdb=" O PROCL 858 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'CL' and resid 966 through 968 removed outlier: 4.381A pdb=" N ILECL 928 " --> pdb=" O VALCL1009 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHECL 947 " --> pdb=" O TYRCL 939 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILECL 941 " --> pdb=" O THRCL 945 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THRCL 945 " --> pdb=" O ILECL 941 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALACL 990 " --> pdb=" O ILECL 976 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILECL 976 " --> pdb=" O ALACL 990 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'JL' and resid 183 through 191 removed outlier: 7.209A pdb=" N VALJL 206 " --> pdb=" O ILEJL 188 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYSJL 190 " --> pdb=" O SERJL 204 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SERJL 204 " --> pdb=" O LYSJL 190 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASNJL 80 " --> pdb=" O VALJL 60 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLUJL 62 " --> pdb=" O ASNJL 80 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VALJL 82 " --> pdb=" O GLUJL 62 " (cutoff:3.500A) 966 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 861 hydrogen bonds 1334 hydrogen bond angles 0 basepair planarities 360 basepair parallelities 568 stacking parallelities Total time for adding SS restraints: 34.81 Time building geometry restraints manager: 26.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9982 1.33 - 1.46: 18153 1.46 - 1.58: 22609 1.58 - 1.70: 2201 1.70 - 1.82: 122 Bond restraints: 53067 Sorted by residual: bond pdb=" CG ARGSI 141 " pdb=" CD ARGSI 141 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.93e+00 bond pdb=" C PROCA 118 " pdb=" N PROCA 119 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.58e+00 bond pdb=" C LYSSI 137 " pdb=" O LYSSI 137 " ideal model delta sigma weight residual 1.236 1.259 -0.023 1.28e-02 6.10e+03 3.28e+00 bond pdb=" C3' UC2 272 " pdb=" O3' UC2 272 " ideal model delta sigma weight residual 1.427 1.452 -0.025 1.50e-02 4.44e+03 2.71e+00 bond pdb=" C3' GC2 42 " pdb=" O3' GC2 42 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.63e+00 ... (remaining 53062 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.89: 5276 104.89 - 112.52: 29411 112.52 - 120.16: 21623 120.16 - 127.80: 18588 127.80 - 135.44: 2051 Bond angle restraints: 76949 Sorted by residual: angle pdb=" C TYRSY 48 " pdb=" N LYSSY 49 " pdb=" CA LYSSY 49 " ideal model delta sigma weight residual 121.33 130.46 -9.13 1.40e+00 5.10e-01 4.26e+01 angle pdb=" C GLUSI 140 " pdb=" N ARGSI 141 " pdb=" CA ARGSI 141 " ideal model delta sigma weight residual 120.29 112.05 8.24 1.42e+00 4.96e-01 3.36e+01 angle pdb=" N ARGSI 141 " pdb=" CA ARGSI 141 " pdb=" CB ARGSI 141 " ideal model delta sigma weight residual 110.16 118.52 -8.36 1.48e+00 4.57e-01 3.19e+01 angle pdb=" CA LEUSG 69 " pdb=" CB LEUSG 69 " pdb=" CG LEUSG 69 " ideal model delta sigma weight residual 116.30 135.44 -19.14 3.50e+00 8.16e-02 2.99e+01 angle pdb=" CA LYSSY 49 " pdb=" CB LYSSY 49 " pdb=" CG LYSSY 49 " ideal model delta sigma weight residual 114.10 124.65 -10.55 2.00e+00 2.50e-01 2.78e+01 ... (remaining 76944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 28655 35.74 - 71.49: 976 71.49 - 107.23: 85 107.23 - 142.98: 15 142.98 - 178.72: 17 Dihedral angle restraints: 29748 sinusoidal: 20228 harmonic: 9520 Sorted by residual: dihedral pdb=" O4' UC2 767 " pdb=" C1' UC2 767 " pdb=" N1 UC2 767 " pdb=" C2 UC2 767 " ideal model delta sinusoidal sigma weight residual -160.00 1.39 -161.39 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" O4' UC2 260 " pdb=" C1' UC2 260 " pdb=" N1 UC2 260 " pdb=" C2 UC2 260 " ideal model delta sinusoidal sigma weight residual 200.00 39.63 160.37 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" CA LEUSH 9 " pdb=" C LEUSH 9 " pdb=" N SERSH 10 " pdb=" CA SERSH 10 " ideal model delta harmonic sigma weight residual 180.00 134.65 45.35 0 5.00e+00 4.00e-02 8.23e+01 ... (remaining 29745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 8424 0.064 - 0.128: 937 0.128 - 0.193: 134 0.193 - 0.257: 27 0.257 - 0.321: 9 Chirality restraints: 9531 Sorted by residual: chirality pdb=" CB ILESG 52 " pdb=" CA ILESG 52 " pdb=" CG1 ILESG 52 " pdb=" CG2 ILESG 52 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILESG 5 " pdb=" CA ILESG 5 " pdb=" CG1 ILESG 5 " pdb=" CG2 ILESG 5 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB VALSH 64 " pdb=" CA VALSH 64 " pdb=" CG1 VALSH 64 " pdb=" CG2 VALSH 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 9528 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CC2 962 " 0.033 2.00e-02 2.50e+03 3.38e-02 2.58e+01 pdb=" N1 CC2 962 " -0.024 2.00e-02 2.50e+03 pdb=" C2 CC2 962 " -0.080 2.00e-02 2.50e+03 pdb=" O2 CC2 962 " 0.040 2.00e-02 2.50e+03 pdb=" N3 CC2 962 " 0.007 2.00e-02 2.50e+03 pdb=" C4 CC2 962 " -0.009 2.00e-02 2.50e+03 pdb=" N4 CC2 962 " 0.023 2.00e-02 2.50e+03 pdb=" C5 CC2 962 " 0.008 2.00e-02 2.50e+03 pdb=" C6 CC2 962 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CC2 224 " 0.002 2.00e-02 2.50e+03 2.71e-02 1.66e+01 pdb=" N1 CC2 224 " 0.008 2.00e-02 2.50e+03 pdb=" C2 CC2 224 " -0.066 2.00e-02 2.50e+03 pdb=" O2 CC2 224 " 0.040 2.00e-02 2.50e+03 pdb=" N3 CC2 224 " 0.005 2.00e-02 2.50e+03 pdb=" C4 CC2 224 " -0.015 2.00e-02 2.50e+03 pdb=" N4 CC2 224 " 0.011 2.00e-02 2.50e+03 pdb=" C5 CC2 224 " 0.014 2.00e-02 2.50e+03 pdb=" C6 CC2 224 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC2 689 " -0.033 2.00e-02 2.50e+03 2.35e-02 1.66e+01 pdb=" N9 GC2 689 " 0.024 2.00e-02 2.50e+03 pdb=" C8 GC2 689 " 0.007 2.00e-02 2.50e+03 pdb=" N7 GC2 689 " -0.003 2.00e-02 2.50e+03 pdb=" C5 GC2 689 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GC2 689 " 0.012 2.00e-02 2.50e+03 pdb=" O6 GC2 689 " -0.025 2.00e-02 2.50e+03 pdb=" N1 GC2 689 " -0.005 2.00e-02 2.50e+03 pdb=" C2 GC2 689 " 0.055 2.00e-02 2.50e+03 pdb=" N2 GC2 689 " -0.033 2.00e-02 2.50e+03 pdb=" N3 GC2 689 " 0.001 2.00e-02 2.50e+03 pdb=" C4 GC2 689 " 0.000 2.00e-02 2.50e+03 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1537 2.66 - 3.22: 40693 3.22 - 3.78: 91091 3.78 - 4.34: 119719 4.34 - 4.90: 171222 Nonbonded interactions: 424262 Sorted by model distance: nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.096 3.040 nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.110 3.040 nonbonded pdb=" O3A GTPCL2001 " pdb="MG MGCL2002 " model vdw 2.126 2.170 nonbonded pdb=" OG1 THRCL 83 " pdb="MG MGCL2002 " model vdw 2.187 2.170 nonbonded pdb=" O2B GTPCL2001 " pdb="MG MGCL2002 " model vdw 2.192 2.170 ... (remaining 424257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1105 5.49 5 Mg 1 5.21 5 S 73 5.16 5 C 27202 2.51 5 N 9055 2.21 5 O 12374 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 14.910 Check model and map are aligned: 0.720 Convert atoms to be neutral: 0.400 Process input model: 157.490 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.003 0.067 53067 Z= 0.208 Angle : 0.796 19.140 76949 Z= 0.404 Chirality : 0.043 0.321 9531 Planarity : 0.006 0.078 5697 Dihedral : 15.891 178.722 23590 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.73 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3252 helix: -0.62 (0.15), residues: 1065 sheet: -1.02 (0.19), residues: 695 loop : -1.64 (0.15), residues: 1492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 412 time to evaluate : 4.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.6195 time to fit residues: 416.7018 Evaluate side-chains 306 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 4.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 338 optimal weight: 50.0000 chunk 131 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 252 optimal weight: 0.5980 chunk 392 optimal weight: 40.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 157 ASN SH 22 GLN SI 44 HIS ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 138 ASN SN 62 GLN ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SX 21 ASN ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 123 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 53067 Z= 0.262 Angle : 0.635 13.578 76949 Z= 0.321 Chirality : 0.039 0.270 9531 Planarity : 0.005 0.079 5697 Dihedral : 15.092 179.994 16855 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.37 % Favored : 93.54 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3252 helix: -0.00 (0.16), residues: 1080 sheet: -0.90 (0.19), residues: 706 loop : -1.60 (0.15), residues: 1466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 333 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 33 residues processed: 353 average time/residue: 0.6461 time to fit residues: 373.6831 Evaluate side-chains 343 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 310 time to evaluate : 4.049 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4366 time to fit residues: 32.2632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 326 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 0.2980 chunk 424 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 chunk 389 optimal weight: 50.0000 chunk 133 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 22 GLN ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 138 ASN ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 80 HIS ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 66 ASN ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 145 ASN CL 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 53067 Z= 0.203 Angle : 0.595 12.837 76949 Z= 0.302 Chirality : 0.037 0.259 9531 Planarity : 0.005 0.069 5697 Dihedral : 15.025 179.952 16855 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.57 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3252 helix: 0.40 (0.16), residues: 1072 sheet: -0.80 (0.19), residues: 692 loop : -1.53 (0.15), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 321 time to evaluate : 4.049 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 342 average time/residue: 0.6218 time to fit residues: 351.7826 Evaluate side-chains 313 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 298 time to evaluate : 3.806 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5038 time to fit residues: 17.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 40.0000 chunk 295 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 263 optimal weight: 10.0000 chunk 394 optimal weight: 50.0000 chunk 417 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 373 optimal weight: 0.0270 chunk 112 optimal weight: 4.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 138 ASN ** SN 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 239 ASN JL 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 53067 Z= 0.308 Angle : 0.653 12.507 76949 Z= 0.330 Chirality : 0.040 0.271 9531 Planarity : 0.005 0.081 5697 Dihedral : 15.124 179.908 16855 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3252 helix: 0.52 (0.16), residues: 1070 sheet: -0.81 (0.19), residues: 684 loop : -1.56 (0.15), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 312 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 39 residues processed: 346 average time/residue: 0.6189 time to fit residues: 356.6366 Evaluate side-chains 332 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 293 time to evaluate : 4.004 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4267 time to fit residues: 36.2746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 356 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 0.9990 chunk 374 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 138 ASN ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 53067 Z= 0.213 Angle : 0.603 13.454 76949 Z= 0.305 Chirality : 0.037 0.260 9531 Planarity : 0.005 0.070 5697 Dihedral : 15.036 179.568 16855 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.57 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3252 helix: 0.65 (0.16), residues: 1070 sheet: -0.81 (0.19), residues: 694 loop : -1.47 (0.15), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 321 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 348 average time/residue: 0.6328 time to fit residues: 365.2090 Evaluate side-chains 310 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 289 time to evaluate : 4.170 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4842 time to fit residues: 23.8363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.8980 chunk 376 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 417 optimal weight: 0.4980 chunk 346 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 122 HIS SL 138 ASN ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 15 ASN SY 110 GLN Sb 42 ASN CA 111 ASN CL 239 ASN CL 276 HIS JL 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 53067 Z= 0.150 Angle : 0.566 15.014 76949 Z= 0.286 Chirality : 0.035 0.245 9531 Planarity : 0.004 0.069 5697 Dihedral : 14.894 179.851 16855 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.30 % Favored : 93.60 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3252 helix: 0.75 (0.16), residues: 1072 sheet: -0.68 (0.20), residues: 681 loop : -1.38 (0.16), residues: 1499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 327 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 349 average time/residue: 0.6214 time to fit residues: 359.8308 Evaluate side-chains 318 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 299 time to evaluate : 3.999 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4194 time to fit residues: 20.1562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 305 optimal weight: 0.0370 chunk 236 optimal weight: 0.0070 chunk 351 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 416 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 44 HIS SI 64 ASN SL 138 ASN SW 39 GLN CL 157 ASN CL 239 ASN JL 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 53067 Z= 0.188 Angle : 0.586 15.964 76949 Z= 0.295 Chirality : 0.036 0.249 9531 Planarity : 0.004 0.069 5697 Dihedral : 14.858 179.838 16855 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.55 % Favored : 93.36 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 3252 helix: 0.77 (0.16), residues: 1076 sheet: -0.64 (0.20), residues: 678 loop : -1.38 (0.16), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 307 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 329 average time/residue: 0.6519 time to fit residues: 354.5648 Evaluate side-chains 318 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 303 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5400 time to fit residues: 19.0229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 283 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 327 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 48 GLN ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 239 ASN ** CL 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JL 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 53067 Z= 0.181 Angle : 0.577 16.098 76949 Z= 0.291 Chirality : 0.036 0.247 9531 Planarity : 0.004 0.068 5697 Dihedral : 14.823 179.745 16855 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.55 % Favored : 93.36 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3252 helix: 0.81 (0.16), residues: 1077 sheet: -0.65 (0.20), residues: 678 loop : -1.37 (0.16), residues: 1497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 306 time to evaluate : 3.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 325 average time/residue: 0.6623 time to fit residues: 353.7116 Evaluate side-chains 303 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 4.241 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4354 time to fit residues: 15.8174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 10.0000 chunk 398 optimal weight: 2.9990 chunk 363 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 304 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 350 optimal weight: 0.8980 chunk 366 optimal weight: 30.0000 chunk 386 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 118 GLN ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 48 GLN SL 138 ASN ** CL 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JL 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 53067 Z= 0.217 Angle : 0.602 18.319 76949 Z= 0.303 Chirality : 0.037 0.253 9531 Planarity : 0.004 0.070 5697 Dihedral : 14.830 179.945 16855 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.23 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 3252 helix: 0.81 (0.16), residues: 1069 sheet: -0.69 (0.20), residues: 682 loop : -1.36 (0.16), residues: 1501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 302 time to evaluate : 4.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 312 average time/residue: 0.6664 time to fit residues: 341.1511 Evaluate side-chains 301 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 293 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6357 time to fit residues: 12.9836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 0.9980 chunk 410 optimal weight: 5.9990 chunk 250 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 430 optimal weight: 8.9990 chunk 396 optimal weight: 20.0000 chunk 342 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 138 ASN SW 15 ASN ** CL 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 53067 Z= 0.261 Angle : 0.634 18.858 76949 Z= 0.318 Chirality : 0.038 0.261 9531 Planarity : 0.005 0.073 5697 Dihedral : 14.908 179.421 16855 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.23 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3252 helix: 0.74 (0.16), residues: 1069 sheet: -0.80 (0.20), residues: 696 loop : -1.37 (0.16), residues: 1487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 298 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 301 average time/residue: 0.6540 time to fit residues: 321.8484 Evaluate side-chains 294 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 289 time to evaluate : 3.948 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4535 time to fit residues: 9.1096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.8980 chunk 365 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 352 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SB 220 GLN ** SH 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 26 GLN ** CL 986 HIS ** 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 = 0.3940 r_free = 0.3940 target = 0.132216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113095 restraints weight = 100992.088| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 0.99 r_work: 0.3285 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 53067 Z= 0.301 Angle : 0.662 19.346 76949 Z= 0.333 Chirality : 0.040 0.269 9531 Planarity : 0.005 0.074 5697 Dihedral : 15.018 179.077 16855 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3252 helix: 0.66 (0.16), residues: 1075 sheet: -0.87 (0.19), residues: 696 loop : -1.39 (0.16), residues: 1481 =============================================================================== Job complete usr+sys time: 8660.83 seconds wall clock time: 159 minutes 52.43 seconds (9592.43 seconds total)