Starting phenix.real_space_refine on Sun Feb 25 06:49:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/02_2024/7wtl_32790_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/02_2024/7wtl_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_32790/02_2024/7wtl_32790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/02_2024/7wtl_32790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/02_2024/7wtl_32790_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtl_32790/02_2024/7wtl_32790_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 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. 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-5238/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: 27.02, per 1000 atoms: 0.54 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: 26.43 Conformation dependent library (CDL) restraints added in 4.9 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: 25.09 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: 37.24 Time building geometry restraints manager: 26.73 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 SERSH 30 " pdb=" N SERSH 31 " pdb=" CA SERSH 31 " ideal model delta sigma weight residual 121.70 132.96 -11.26 1.80e+00 3.09e-01 3.91e+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 ... (remaining 76944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 30457 35.74 - 71.49: 2643 71.49 - 107.23: 272 107.23 - 142.98: 15 142.98 - 178.72: 17 Dihedral angle restraints: 33404 sinusoidal: 23884 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 33401 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 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.470 Check model and map are aligned: 0.800 Set scattering table: 0.510 Process input model: 161.030 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 : 21.472 178.722 27246 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.21 % Favored : 93.73 % Rotamer: Outliers : 0.04 % Allowed : 0.56 % Favored : 99.40 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPSB 117 HIS 0.008 0.001 HISSW 56 PHE 0.037 0.002 PHECL 226 TYR 0.020 0.002 TYRSL 35 ARG 0.011 0.001 ARGSI 194 *********************** 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 : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SE 254 ARG cc_start: 0.6980 (ttp-110) cc_final: 0.6738 (ttp80) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.6604 time to fit residues: 443.7574 Evaluate side-chains 306 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 4.379 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.8986 ------------------------------------------------------------------------------- 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: 0.7652 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 53067 Z= 0.305 Angle : 0.669 14.271 76949 Z= 0.339 Chirality : 0.040 0.273 9531 Planarity : 0.006 0.084 5697 Dihedral : 22.312 179.524 20511 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.55 % Favored : 93.33 % Rotamer: Outliers : 1.69 % Allowed : 8.44 % Favored : 89.87 % 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: -1.42 (0.14), residues: 3252 helix: -0.01 (0.16), residues: 1080 sheet: -0.88 (0.19), residues: 694 loop : -1.64 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPSN 139 HIS 0.009 0.001 HISCA 123 PHE 0.026 0.002 PHEJL 310 TYR 0.019 0.002 TYRCL 199 ARG 0.009 0.001 ARGCL 779 *********************** 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 381 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 333 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SE 121 TYR cc_start: 0.8061 (p90) cc_final: 0.7860 (p90) REVERT: SE 254 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6891 (ttp80) outliers start: 48 outliers final: 36 residues processed: 361 average time/residue: 0.6858 time to fit residues: 404.4867 Evaluate side-chains 340 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SE residue 120 SER Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 215 ASP Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SG residue 217 SER Chi-restraints excluded: chain SH residue 22 GLN Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 7 VAL Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 84 ILE Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SN residue 62 GLN Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 14 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 153 GLN Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain UC residue 550 LEU 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: 2.9990 chunk 326 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 50.0000 chunk 424 optimal weight: 9.9990 chunk 350 optimal weight: 3.9990 chunk 389 optimal weight: 40.0000 chunk 133 optimal weight: 0.5980 chunk 315 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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** SN 62 GLN 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 JL 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 53067 Z= 0.366 Angle : 0.701 14.099 76949 Z= 0.353 Chirality : 0.042 0.283 9531 Planarity : 0.006 0.082 5697 Dihedral : 22.330 179.715 20511 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.80 % Favored : 93.08 % Rotamer: Outliers : 2.39 % Allowed : 12.49 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.32 (0.14), residues: 3252 helix: 0.21 (0.16), residues: 1078 sheet: -0.89 (0.19), residues: 690 loop : -1.65 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPSN 139 HIS 0.008 0.001 HISSW 113 PHE 0.023 0.002 PHEJL 310 TYR 0.025 0.002 TYRSN 18 ARG 0.007 0.001 ARGSI 141 *********************** 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 375 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 307 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: SE 90 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8277 (tp) REVERT: SE 254 ARG cc_start: 0.7165 (ttp-110) cc_final: 0.6947 (ttp80) REVERT: SN 49 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: JL 287 GLU cc_start: 0.6449 (pm20) cc_final: 0.6121 (pm20) outliers start: 68 outliers final: 57 residues processed: 354 average time/residue: 0.6531 time to fit residues: 381.6882 Evaluate side-chains 346 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 287 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 120 SER Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 215 ASP Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 125 THR Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 105 THR Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 7 VAL Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 84 ILE Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SN residue 49 GLN Chi-restraints excluded: chain SN residue 96 VAL Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SW residue 66 ASN Chi-restraints excluded: chain SW residue 90 THR Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 33 LEU Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain SY residue 131 ARG Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 14 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain JL residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 20.0000 chunk 295 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 394 optimal weight: 40.0000 chunk 417 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 373 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 53067 Z= 0.355 Angle : 0.690 12.054 76949 Z= 0.348 Chirality : 0.042 0.284 9531 Planarity : 0.006 0.085 5697 Dihedral : 22.324 179.905 20511 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 92.99 % Rotamer: Outliers : 3.24 % Allowed : 15.48 % Favored : 81.29 % 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: -1.24 (0.14), residues: 3252 helix: 0.36 (0.16), residues: 1073 sheet: -0.90 (0.19), residues: 690 loop : -1.63 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPSN 139 HIS 0.007 0.001 HISSW 113 PHE 0.017 0.002 PHESW 50 TYR 0.017 0.002 TYRSN 18 ARG 0.007 0.000 ARGSW 68 *********************** 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 402 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 310 time to evaluate : 4.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SE 90 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (tp) REVERT: SE 254 ARG cc_start: 0.7079 (ttp-110) cc_final: 0.6873 (ttp80) REVERT: SI 38 ILE cc_start: 0.8382 (mm) cc_final: 0.8067 (mm) REVERT: SY 68 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8499 (tptm) REVERT: CA 170 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6248 (m-30) REVERT: JL 261 MET cc_start: 0.5318 (pmm) cc_final: 0.4936 (pmm) REVERT: JL 287 GLU cc_start: 0.6571 (pm20) cc_final: 0.6278 (pm20) outliers start: 92 outliers final: 67 residues processed: 377 average time/residue: 0.6513 time to fit residues: 407.6782 Evaluate side-chains 358 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 288 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 215 ASP Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 81 VAL Chi-restraints excluded: chain SG residue 125 THR Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SG residue 217 SER Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 7 VAL Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 105 ASN Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SN residue 138 ASN Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SW residue 87 GLU Chi-restraints excluded: chain SW residue 90 THR Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 33 LEU Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 3 ASP Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 68 LYS Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 14 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 35 VAL Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 153 GLN Chi-restraints excluded: chain CA residue 170 ASP Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CA residue 231 ILE Chi-restraints excluded: chain CL residue 86 ILE Chi-restraints excluded: chain CL residue 105 ILE Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 198 VAL Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain JL residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** SI 64 ASN ** 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** JL 36 GLN ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 53067 Z= 0.357 Angle : 0.696 14.854 76949 Z= 0.350 Chirality : 0.042 0.283 9531 Planarity : 0.006 0.085 5697 Dihedral : 22.324 179.963 20511 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 3.90 % Allowed : 16.43 % Favored : 79.67 % 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: -1.25 (0.15), residues: 3252 helix: 0.37 (0.16), residues: 1084 sheet: -0.97 (0.19), residues: 692 loop : -1.64 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPSN 139 HIS 0.007 0.001 HISSW 113 PHE 0.023 0.002 PHESG 156 TYR 0.017 0.002 TYRSN 18 ARG 0.005 0.000 ARGSI 56 *********************** 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 409 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 298 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 110 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8252 (mt) REVERT: SE 90 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8332 (tp) REVERT: SE 128 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7934 (ptmt) REVERT: SE 254 ARG cc_start: 0.7080 (ttp-110) cc_final: 0.6873 (ttp80) REVERT: SO 61 MET cc_start: 0.7289 (tmm) cc_final: 0.6976 (tmm) REVERT: SO 128 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8215 (pttp) REVERT: SY 68 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8459 (tptm) REVERT: Sb 26 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: CA 170 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6286 (m-30) REVERT: JL 287 GLU cc_start: 0.6494 (pm20) cc_final: 0.6267 (pm20) outliers start: 111 outliers final: 80 residues processed: 385 average time/residue: 0.6539 time to fit residues: 418.2415 Evaluate side-chains 372 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 285 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 110 LEU Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 173 THR Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 128 LYS Chi-restraints excluded: chain SE residue 140 VAL Chi-restraints excluded: chain SE residue 164 LEU Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 215 ASP Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 71 THR Chi-restraints excluded: chain SG residue 81 VAL Chi-restraints excluded: chain SG residue 125 THR Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SG residue 217 SER Chi-restraints excluded: chain SH residue 41 LEU Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 36 THR Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 130 THR Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 7 VAL Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 109 VAL Chi-restraints excluded: chain SL residue 117 VAL Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 96 VAL Chi-restraints excluded: chain SN residue 105 ASN Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SN residue 138 ASN Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 43 THR Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SO residue 128 LYS Chi-restraints excluded: chain SW residue 66 ASN Chi-restraints excluded: chain SW residue 87 GLU Chi-restraints excluded: chain SW residue 90 THR Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 33 LEU Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 3 ASP Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 68 LYS Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 14 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain CA residue 107 THR Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 170 ASP Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CA residue 231 ILE Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CL residue 86 ILE Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 198 VAL Chi-restraints excluded: chain CL residue 244 MET Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain CL residue 792 VAL Chi-restraints excluded: chain CL residue 918 ILE Chi-restraints excluded: chain JL residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.9990 chunk 376 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 0.0870 chunk 103 optimal weight: 9.9990 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- 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 48 GLN SL 138 ASN ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 239 ASN JL 36 GLN ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 53067 Z= 0.152 Angle : 0.583 12.088 76949 Z= 0.296 Chirality : 0.036 0.261 9531 Planarity : 0.004 0.070 5697 Dihedral : 22.229 179.630 20511 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 2.39 % Allowed : 18.43 % Favored : 79.18 % 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: 0.67 (0.16), residues: 1072 sheet: -0.81 (0.20), residues: 669 loop : -1.43 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPSB 117 HIS 0.004 0.001 HISCL 192 PHE 0.024 0.001 PHECA 158 TYR 0.015 0.001 TYRSN 18 ARG 0.006 0.000 ARGSG 23 *********************** 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 390 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 322 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 210 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8063 (mp) REVERT: SE 128 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7656 (ptmt) REVERT: SE 254 ARG cc_start: 0.7027 (ttp-110) cc_final: 0.6815 (ttp80) REVERT: SO 61 MET cc_start: 0.7280 (tmm) cc_final: 0.7008 (tmm) REVERT: SW 41 MET cc_start: 0.8296 (mtt) cc_final: 0.7999 (mtt) REVERT: CA 170 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5752 (m-30) outliers start: 68 outliers final: 52 residues processed: 371 average time/residue: 0.6573 time to fit residues: 404.8920 Evaluate side-chains 353 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 298 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SB residue 210 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 128 LYS Chi-restraints excluded: chain SE residue 169 ILE Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 117 VAL Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 62 LEU Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SW residue 66 ASN Chi-restraints excluded: chain SW residue 87 GLU Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 3 ASP Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 131 ARG Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain CA residue 107 THR Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 170 ASP Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CA residue 231 ILE Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CL residue 105 ILE Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 223 LEU Chi-restraints excluded: chain CL residue 244 MET Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain CL residue 792 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 236 optimal weight: 0.0170 chunk 351 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 416 optimal weight: 0.2980 chunk 260 optimal weight: 0.2980 chunk 253 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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 48 GLN ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 157 ASN CL 239 ASN JL 36 GLN ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 53067 Z= 0.159 Angle : 0.575 13.747 76949 Z= 0.291 Chirality : 0.036 0.259 9531 Planarity : 0.004 0.072 5697 Dihedral : 22.124 179.725 20511 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 2.81 % Allowed : 18.89 % Favored : 78.30 % 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: -0.82 (0.15), residues: 3252 helix: 0.76 (0.16), residues: 1074 sheet: -0.77 (0.20), residues: 682 loop : -1.38 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPCL 834 HIS 0.003 0.001 HISCL 192 PHE 0.020 0.001 PHECA 158 TYR 0.015 0.001 TYRCA 117 ARG 0.008 0.000 ARGSG 23 *********************** 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 386 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 306 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 110 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8067 (mt) REVERT: SB 210 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7990 (mp) REVERT: SE 90 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8230 (tp) REVERT: SE 128 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7757 (ptmt) REVERT: SE 254 ARG cc_start: 0.7092 (ttp-110) cc_final: 0.6862 (ttp80) REVERT: SO 61 MET cc_start: 0.7211 (tmm) cc_final: 0.6947 (tmm) REVERT: SW 41 MET cc_start: 0.8388 (mtt) cc_final: 0.8167 (mtt) outliers start: 80 outliers final: 62 residues processed: 366 average time/residue: 0.6476 time to fit residues: 392.0337 Evaluate side-chains 356 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 290 time to evaluate : 4.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 110 LEU Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SB residue 210 ILE Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 128 LYS Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SH residue 41 LEU Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 24 LEU Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 117 VAL Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 62 LEU Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 66 ASN Chi-restraints excluded: chain SW residue 87 GLU Chi-restraints excluded: chain SW residue 90 THR Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 3 ASP Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain CA residue 107 THR Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CA residue 231 ILE Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CL residue 105 ILE Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 223 LEU Chi-restraints excluded: chain CL residue 244 MET Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain CL residue 792 VAL 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: 1.9990 chunk 248 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 48 GLN ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 39 GLN ** SW 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 239 ASN CL 276 HIS ** CL 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JL 36 GLN ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 53067 Z= 0.199 Angle : 0.588 14.076 76949 Z= 0.298 Chirality : 0.036 0.257 9531 Planarity : 0.005 0.071 5697 Dihedral : 22.092 179.975 20511 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.73 % Favored : 93.17 % Rotamer: Outliers : 3.38 % Allowed : 18.85 % Favored : 77.77 % 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: 0.79 (0.16), residues: 1073 sheet: -0.74 (0.20), residues: 680 loop : -1.37 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPCL 237 HIS 0.004 0.001 HISSE 8 PHE 0.019 0.001 PHECA 158 TYR 0.015 0.001 TYRCA 117 ARG 0.010 0.000 ARGSG 23 *********************** 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 396 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 300 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 110 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8124 (mt) REVERT: SB 210 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7962 (mp) REVERT: SE 90 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8275 (tp) REVERT: SE 128 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7846 (ptmt) REVERT: SE 254 ARG cc_start: 0.7087 (ttp-110) cc_final: 0.6869 (ttp80) REVERT: SI 137 LYS cc_start: 0.7123 (pttp) cc_final: 0.6770 (pttp) REVERT: SW 41 MET cc_start: 0.8375 (mtt) cc_final: 0.8170 (mtt) REVERT: SY 68 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8432 (tptm) REVERT: Sb 26 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7772 (pt0) outliers start: 96 outliers final: 78 residues processed: 374 average time/residue: 0.6345 time to fit residues: 393.5285 Evaluate side-chains 372 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 288 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 110 LEU Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SB residue 210 ILE Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 120 SER Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 128 LYS Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 215 ASP Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SH residue 41 LEU Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 78 THR Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SI residue 96 LEU Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 24 LEU Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 117 VAL Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SL residue 124 THR Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 66 ASN Chi-restraints excluded: chain SW residue 87 GLU Chi-restraints excluded: chain SW residue 90 THR Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 3 ASP Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 68 LYS Chi-restraints excluded: chain SY residue 131 ARG Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 14 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain CA residue 107 THR Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 157 ASP Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CA residue 231 ILE Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CL residue 74 VAL Chi-restraints excluded: chain CL residue 105 ILE Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 223 LEU Chi-restraints excluded: chain CL residue 244 MET Chi-restraints excluded: chain CL residue 276 HIS Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain CL residue 321 GLU Chi-restraints excluded: chain CL residue 792 VAL Chi-restraints excluded: chain JL residue 75 LEU Chi-restraints excluded: chain JL residue 261 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 9.9990 chunk 398 optimal weight: 40.0000 chunk 363 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 0.0670 chunk 304 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 350 optimal weight: 7.9990 chunk 366 optimal weight: 30.0000 chunk 386 optimal weight: 1.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- 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** ** SJ 123 HIS ** 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 CL 276 HIS ** CL 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JL 36 GLN ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 53067 Z= 0.304 Angle : 0.661 16.112 76949 Z= 0.331 Chirality : 0.040 0.272 9531 Planarity : 0.005 0.078 5697 Dihedral : 22.129 179.649 20511 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 3.41 % Allowed : 19.10 % Favored : 77.49 % 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: 0.70 (0.16), residues: 1075 sheet: -0.87 (0.20), residues: 678 loop : -1.43 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPSN 139 HIS 0.030 0.001 HISCL 276 PHE 0.018 0.002 PHECA 158 TYR 0.015 0.001 TYRCA 117 ARG 0.006 0.000 ARGSG 23 *********************** 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 388 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 291 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 110 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8197 (mt) REVERT: SB 210 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8020 (mp) REVERT: SE 90 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8305 (tp) REVERT: SE 128 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7880 (ptmt) REVERT: SE 254 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6857 (ttp80) REVERT: SO 61 MET cc_start: 0.7152 (tmm) cc_final: 0.6920 (tmm) REVERT: SW 41 MET cc_start: 0.8327 (mtt) cc_final: 0.8041 (mtt) REVERT: SY 68 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8464 (tptm) REVERT: Sb 26 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7735 (pt0) outliers start: 97 outliers final: 82 residues processed: 366 average time/residue: 0.6719 time to fit residues: 408.3311 Evaluate side-chains 376 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 288 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 110 LEU Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SB residue 210 ILE Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 120 SER Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 128 LYS Chi-restraints excluded: chain SE residue 164 LEU Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 215 ASP Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 52 ILE Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 81 VAL Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SH residue 41 LEU Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 78 THR Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 24 LEU Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 7 VAL Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 117 VAL Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SL residue 124 THR Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 66 ASN Chi-restraints excluded: chain SW residue 87 GLU Chi-restraints excluded: chain SW residue 90 THR Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 3 ASP Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 68 LYS Chi-restraints excluded: chain SY residue 118 ILE Chi-restraints excluded: chain SY residue 131 ARG Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 14 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain CA residue 107 THR Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CA residue 231 ILE Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CL residue 74 VAL Chi-restraints excluded: chain CL residue 105 ILE Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 207 LEU Chi-restraints excluded: chain CL residue 223 LEU Chi-restraints excluded: chain CL residue 244 MET Chi-restraints excluded: chain CL residue 276 HIS Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain CL residue 792 VAL Chi-restraints excluded: chain JL residue 36 GLN Chi-restraints excluded: chain JL residue 75 LEU Chi-restraints excluded: chain JL residue 138 VAL Chi-restraints excluded: chain JL residue 261 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 0.9990 chunk 410 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 chunk 430 optimal weight: 20.0000 chunk 396 optimal weight: 3.9990 chunk 342 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 42 ASN ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 276 HIS ** CL 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JL 36 GLN ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 53067 Z= 0.237 Angle : 0.625 21.483 76949 Z= 0.315 Chirality : 0.038 0.271 9531 Planarity : 0.005 0.072 5697 Dihedral : 22.130 179.988 20511 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.77 % Favored : 93.14 % Rotamer: Outliers : 3.20 % Allowed : 19.52 % Favored : 77.28 % 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: -0.87 (0.15), residues: 3252 helix: 0.73 (0.16), residues: 1074 sheet: -0.79 (0.20), residues: 658 loop : -1.42 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPSI 143 HIS 0.013 0.001 HISCL 276 PHE 0.018 0.001 PHECA 158 TYR 0.022 0.001 TYRUC 542 ARG 0.008 0.000 ARGSI 141 ********************** 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 386 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 295 time to evaluate : 3.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: SB 110 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8145 (mt) REVERT: SB 210 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7988 (mp) REVERT: SE 90 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8287 (tp) REVERT: SE 128 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7911 (ptmt) REVERT: SE 254 ARG cc_start: 0.7059 (ttp-110) cc_final: 0.6844 (ttp80) REVERT: SO 61 MET cc_start: 0.7125 (tmm) cc_final: 0.6863 (tmm) REVERT: SW 41 MET cc_start: 0.8331 (mtt) cc_final: 0.8117 (mtt) REVERT: SY 68 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8456 (tptm) REVERT: Sb 26 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7716 (pt0) outliers start: 91 outliers final: 81 residues processed: 366 average time/residue: 0.6589 time to fit residues: 401.3400 Evaluate side-chains 376 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 289 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain SB residue 42 ASN Chi-restraints excluded: chain SB residue 108 ASP Chi-restraints excluded: chain SB residue 110 LEU Chi-restraints excluded: chain SB residue 159 SER Chi-restraints excluded: chain SB residue 199 ASN Chi-restraints excluded: chain SB residue 210 ILE Chi-restraints excluded: chain SE residue 90 ILE Chi-restraints excluded: chain SE residue 97 GLU Chi-restraints excluded: chain SE residue 126 VAL Chi-restraints excluded: chain SE residue 128 LYS Chi-restraints excluded: chain SE residue 164 LEU Chi-restraints excluded: chain SE residue 181 VAL Chi-restraints excluded: chain SE residue 215 ASP Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 53 SER Chi-restraints excluded: chain SG residue 81 VAL Chi-restraints excluded: chain SG residue 128 THR Chi-restraints excluded: chain SG residue 129 VAL Chi-restraints excluded: chain SG residue 168 THR Chi-restraints excluded: chain SG residue 175 ILE Chi-restraints excluded: chain SH residue 41 LEU Chi-restraints excluded: chain SH residue 67 LEU Chi-restraints excluded: chain SH residue 78 THR Chi-restraints excluded: chain SH residue 147 ASN Chi-restraints excluded: chain SH residue 177 THR Chi-restraints excluded: chain SI residue 4 SER Chi-restraints excluded: chain SI residue 46 VAL Chi-restraints excluded: chain SJ residue 19 TYR Chi-restraints excluded: chain SJ residue 122 VAL Chi-restraints excluded: chain SJ residue 140 ILE Chi-restraints excluded: chain SJ residue 161 THR Chi-restraints excluded: chain SL residue 6 THR Chi-restraints excluded: chain SL residue 7 VAL Chi-restraints excluded: chain SL residue 21 ASN Chi-restraints excluded: chain SL residue 60 PHE Chi-restraints excluded: chain SL residue 76 VAL Chi-restraints excluded: chain SL residue 117 VAL Chi-restraints excluded: chain SL residue 122 ILE Chi-restraints excluded: chain SL residue 124 THR Chi-restraints excluded: chain SL residue 131 ILE Chi-restraints excluded: chain SN residue 46 THR Chi-restraints excluded: chain SN residue 132 VAL Chi-restraints excluded: chain SO residue 24 ASN Chi-restraints excluded: chain SO residue 56 SER Chi-restraints excluded: chain SO residue 71 CYS Chi-restraints excluded: chain SO residue 81 VAL Chi-restraints excluded: chain SO residue 86 THR Chi-restraints excluded: chain SO residue 119 THR Chi-restraints excluded: chain SW residue 65 LEU Chi-restraints excluded: chain SW residue 66 ASN Chi-restraints excluded: chain SW residue 87 GLU Chi-restraints excluded: chain SW residue 90 THR Chi-restraints excluded: chain SW residue 102 VAL Chi-restraints excluded: chain SX residue 81 LYS Chi-restraints excluded: chain SY residue 3 ASP Chi-restraints excluded: chain SY residue 13 ILE Chi-restraints excluded: chain SY residue 17 LEU Chi-restraints excluded: chain SY residue 24 VAL Chi-restraints excluded: chain SY residue 26 ASP Chi-restraints excluded: chain SY residue 27 VAL Chi-restraints excluded: chain SY residue 35 VAL Chi-restraints excluded: chain SY residue 68 LYS Chi-restraints excluded: chain Sb residue 11 THR Chi-restraints excluded: chain Sb residue 14 SER Chi-restraints excluded: chain Sb residue 23 THR Chi-restraints excluded: chain Sb residue 26 GLN Chi-restraints excluded: chain Sb residue 45 THR Chi-restraints excluded: chain Sb residue 62 ILE Chi-restraints excluded: chain CA residue 107 THR Chi-restraints excluded: chain CA residue 117 TYR Chi-restraints excluded: chain CA residue 192 THR Chi-restraints excluded: chain CA residue 193 LEU Chi-restraints excluded: chain CA residue 231 ILE Chi-restraints excluded: chain CA residue 260 TYR Chi-restraints excluded: chain CL residue 74 VAL Chi-restraints excluded: chain CL residue 105 ILE Chi-restraints excluded: chain CL residue 116 THR Chi-restraints excluded: chain CL residue 170 VAL Chi-restraints excluded: chain CL residue 207 LEU Chi-restraints excluded: chain CL residue 244 MET Chi-restraints excluded: chain CL residue 276 HIS Chi-restraints excluded: chain CL residue 288 VAL Chi-restraints excluded: chain CL residue 792 VAL Chi-restraints excluded: chain JL residue 36 GLN Chi-restraints excluded: chain JL residue 75 LEU Chi-restraints excluded: chain JL residue 138 VAL Chi-restraints excluded: chain JL residue 261 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 3.9990 chunk 365 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 316 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 343 optimal weight: 0.4980 chunk 143 optimal weight: 4.9990 chunk 352 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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** ** SW 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 42 ASN ** CA 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CL 276 HIS ** CL 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JL 36 GLN ** JL 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JL 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.131957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112223 restraints weight = 100936.731| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.07 r_work: 0.3275 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 53067 Z= 0.308 Angle : 0.667 20.457 76949 Z= 0.334 Chirality : 0.040 0.282 9531 Planarity : 0.005 0.084 5697 Dihedral : 22.140 179.666 20511 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.77 % Rotamer: Outliers : 3.34 % Allowed : 19.66 % Favored : 77.00 % 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: -0.95 (0.15), residues: 3252 helix: 0.66 (0.16), residues: 1082 sheet: -0.88 (0.20), residues: 667 loop : -1.46 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPSN 139 HIS 0.013 0.001 HISCL 276 PHE 0.031 0.002 PHESI 191 TYR 0.022 0.001 TYRUC 542 ARG 0.025 0.000 ARGSI 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9614.05 seconds wall clock time: 180 minutes 39.90 seconds (10839.90 seconds total)