Starting phenix.real_space_refine (version: dev) on Thu Dec 22 20:26:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtq_32795/12_2022/7wtq_32795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtq_32795/12_2022/7wtq_32795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtq_32795/12_2022/7wtq_32795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtq_32795/12_2022/7wtq_32795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtq_32795/12_2022/7wtq_32795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtq_32795/12_2022/7wtq_32795.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "SW TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51309 Number of models: 1 Model: "" Number of chains: 19 Chain: "C2" Number of atoms: 26763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1255, 26763 Classifications: {'RNA': 1255} Modifications used: {'rna2p_pur': 103, 'rna2p_pyr': 91, 'rna3p_pur': 573, 'rna3p_pyr': 488} Link IDs: {'rna2p': 194, 'rna3p': 1060} Chain breaks: 8 Chain: "SB" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "SE" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "SG" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "SH" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 171} Chain: "SI" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "SJ" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "SL" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "SN" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "SO" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "SW" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "SX" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "SY" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Sb" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Se" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 313 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 4, 'TRANS': 33} Chain: "CA" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "CB" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 302 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "CC" Number of atoms: 5346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5346 Classifications: {'peptide': 661} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 628} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "Sb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.80, per 1000 atoms: 0.56 Number of scatterers: 51309 At special positions: 0 Unit cell: (168.381, 234.039, 211.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 51 16.00 P 1255 15.00 O 13136 8.00 N 9343 7.00 C 27523 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: 26.32 Conformation dependent library (CDL) restraints added in 3.8 seconds 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 30 sheets defined 34.6% alpha, 19.8% beta 418 base pairs and 663 stacking pairs defined. Time for finding SS restraints: 19.49 Creating SS restraints... Processing helix chain 'SB' and resid 22 through 25 Processing helix chain 'SB' and resid 70 through 75 Processing helix chain 'SB' and resid 76 through 80 removed outlier: 3.957A pdb=" N HISSB 79 " --> pdb=" O SERSB 76 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SERSB 80 " --> pdb=" O GLUSB 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 76 through 80' Processing helix chain 'SB' and resid 106 through 114 removed outlier: 3.635A pdb=" N VALSB 114 " --> pdb=" O LEUSB 110 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 178 removed outlier: 3.909A pdb=" N GLYSB 178 " --> pdb=" O LYSSB 174 " (cutoff:3.500A) Processing helix chain 'SB' and resid 180 through 189 Processing helix chain 'SB' and resid 191 through 202 removed outlier: 3.524A pdb=" N LYSSB 202 " --> pdb=" O GLUSB 198 " (cutoff:3.500A) Processing helix chain 'SB' and resid 224 through 232 removed outlier: 3.896A pdb=" N LEUSB 228 " --> pdb=" O ASPSB 224 " (cutoff:3.500A) Processing helix chain 'SE' and resid 15 through 19 Processing helix chain 'SE' and resid 37 through 41 removed outlier: 3.628A pdb=" N SERSE 41 " --> pdb=" O LEUSE 38 " (cutoff:3.500A) Processing helix chain 'SE' and resid 44 through 50 Processing helix chain 'SE' and resid 57 through 66 Processing helix chain 'SE' and resid 133 through 135 No H-bonds generated for 'chain 'SE' and resid 133 through 135' Processing helix chain 'SE' and resid 239 through 243 removed outlier: 4.337A pdb=" N GLYSE 243 " --> pdb=" O LYSSE 240 " (cutoff:3.500A) Processing helix chain 'SE' and resid 247 through 258 Processing helix chain 'SG' and resid 20 through 28 removed outlier: 3.863A pdb=" N ARGSG 25 " --> pdb=" O HISSG 22 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VALSG 26 " --> pdb=" O ARGSG 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHESG 28 " --> pdb=" O ARGSG 25 " (cutoff:3.500A) Processing helix chain 'SG' and resid 42 through 46 removed outlier: 3.920A pdb=" N LYSSG 46 " --> pdb=" O ASPSG 43 " (cutoff:3.500A) Processing helix chain 'SG' and resid 137 through 146 Processing helix chain 'SG' and resid 180 through 217 removed outlier: 3.657A pdb=" N SERSG 217 " --> pdb=" O ALASG 213 " (cutoff:3.500A) Processing helix chain 'SH' and resid 14 through 29 Processing helix chain 'SH' and resid 31 through 39 removed outlier: 3.808A pdb=" N ARGSH 39 " --> pdb=" O LYSSH 35 " (cutoff:3.500A) Processing helix chain 'SH' and resid 66 through 74 removed outlier: 3.551A pdb=" N PHESH 70 " --> pdb=" O SERSH 66 " (cutoff:3.500A) Processing helix chain 'SH' and resid 75 through 85 Processing helix chain 'SH' and resid 117 through 130 removed outlier: 3.836A pdb=" N VALSH 130 " --> pdb=" O LEUSH 126 " (cutoff:3.500A) Processing helix chain 'SH' and resid 165 through 175 Processing helix chain 'SI' and resid 49 through 51 No H-bonds generated for 'chain 'SI' and resid 49 through 51' Processing helix chain 'SI' and resid 88 through 94 removed outlier: 3.743A pdb=" N ARGSI 92 " --> pdb=" O ASNSI 88 " (cutoff:3.500A) Processing helix chain 'SI' and resid 106 through 117 Processing helix chain 'SI' and resid 136 through 146 Processing helix chain 'SI' and resid 153 through 163 removed outlier: 3.669A pdb=" N GLUSI 157 " --> pdb=" O GLUSI 153 " (cutoff:3.500A) Processing helix chain 'SI' and resid 172 through 177 Processing helix chain 'SI' and resid 186 through 200 Processing helix chain 'SJ' and resid 20 through 35 removed outlier: 3.562A pdb=" N LEUSJ 24 " --> pdb=" O GLUSJ 20 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 39 through 61 Processing helix chain 'SJ' and resid 66 through 83 Processing helix chain 'SJ' and resid 92 through 97 Processing helix chain 'SJ' and resid 101 through 107 removed outlier: 3.963A pdb=" N ARGSJ 107 " --> pdb=" O ASPSJ 103 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 108 through 116 Processing helix chain 'SJ' and resid 121 through 131 removed outlier: 3.627A pdb=" N GLNSJ 131 " --> pdb=" O VALSJ 127 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 152 through 154 No H-bonds generated for 'chain 'SJ' and resid 152 through 154' Processing helix chain 'SJ' and resid 162 through 166 Processing helix chain 'SJ' and resid 170 through 184 Processing helix chain 'SL' and resid 45 through 50 removed outlier: 3.941A pdb=" N ILESL 49 " --> pdb=" O PROSL 45 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLUSL 50 " --> pdb=" O LYSSL 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 45 through 50' Processing helix chain 'SN' and resid 30 through 44 Processing helix chain 'SN' and resid 46 through 58 removed outlier: 3.674A pdb=" N HISSN 58 " --> pdb=" O LEUSN 54 " (cutoff:3.500A) Processing helix chain 'SN' and resid 62 through 67 removed outlier: 3.583A pdb=" N ILESN 66 " --> pdb=" O GLNSN 62 " (cutoff:3.500A) Processing helix chain 'SN' and resid 70 through 78 Processing helix chain 'SN' and resid 85 through 105 Processing helix chain 'SN' and resid 108 through 132 Processing helix chain 'SN' and resid 144 through 151 removed outlier: 4.195A pdb=" N ALASN 148 " --> pdb=" O ALASN 144 " (cutoff:3.500A) Processing helix chain 'SO' and resid 56 through 75 Processing helix chain 'SO' and resid 95 through 108 removed outlier: 3.524A pdb=" N GLNSO 99 " --> pdb=" O GLYSO 95 " (cutoff:3.500A) Processing helix chain 'SW' and resid 5 through 20 Processing helix chain 'SW' and resid 31 through 44 Processing helix chain 'SW' and resid 82 through 84 No H-bonds generated for 'chain 'SW' and resid 82 through 84' Processing helix chain 'SW' and resid 85 through 94 Processing helix chain 'SW' and resid 113 through 120 Processing helix chain 'SX' and resid 11 through 25 Processing helix chain 'SX' and resid 27 through 35 removed outlier: 3.518A pdb=" N GLYSX 35 " --> pdb=" O LYSSX 31 " (cutoff:3.500A) Processing helix chain 'SX' and resid 35 through 40 Processing helix chain 'SX' and resid 91 through 95 Processing helix chain 'SX' and resid 132 through 137 Processing helix chain 'SY' and resid 36 through 48 removed outlier: 3.823A pdb=" N LEUSY 40 " --> pdb=" O SERSY 36 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYRSY 48 " --> pdb=" O LEUSY 44 " (cutoff:3.500A) Processing helix chain 'SY' and resid 51 through 53 No H-bonds generated for 'chain 'SY' and resid 51 through 53' Processing helix chain 'SY' and resid 78 through 86 removed outlier: 3.717A pdb=" N ALASY 82 " --> pdb=" O SERSY 78 " (cutoff:3.500A) Processing helix chain 'SY' and resid 87 through 94 Processing helix chain 'SY' and resid 104 through 116 Processing helix chain 'SY' and resid 122 through 135 Processing helix chain 'Sb' and resid 11 through 18 removed outlier: 3.549A pdb=" N GLUSb 15 " --> pdb=" O THRSb 11 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYSSb 18 " --> pdb=" O SERSb 14 " (cutoff:3.500A) Processing helix chain 'Se' and resid 32 through 44 Processing helix chain 'CA' and resid 102 through 112 Proline residue: CA 108 - end of helix removed outlier: 3.870A pdb=" N ASNCA 111 " --> pdb=" O THRCA 107 " (cutoff:3.500A) Processing helix chain 'CA' and resid 112 through 123 Proline residue: CA 118 - end of helix Processing helix chain 'CA' and resid 148 through 163 Processing helix chain 'CA' and resid 167 through 177 Processing helix chain 'CA' and resid 188 through 190 No H-bonds generated for 'chain 'CA' and resid 188 through 190' Processing helix chain 'CA' and resid 195 through 207 Processing helix chain 'CA' and resid 210 through 219 Processing helix chain 'CA' and resid 236 through 252 Processing helix chain 'CA' and resid 255 through 272 removed outlier: 3.593A pdb=" N VALCA 259 " --> pdb=" O PROCA 255 " (cutoff:3.500A) Processing helix chain 'CB' and resid 242 through 257 removed outlier: 4.026A pdb=" N GLUCB 251 " --> pdb=" O LEUCB 247 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEUCB 252 " --> pdb=" O ARGCB 248 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N METCB 253 " --> pdb=" O LYSCB 249 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYSCB 254 " --> pdb=" O LYSCB 250 " (cutoff:3.500A) Processing helix chain 'CC' and resid 23 through 33 Processing helix chain 'CC' and resid 50 through 71 removed outlier: 4.257A pdb=" N GLUCC 71 " --> pdb=" O LEUCC 67 " (cutoff:3.500A) Processing helix chain 'CC' and resid 96 through 107 removed outlier: 3.988A pdb=" N CYSCC 107 " --> pdb=" O LYSCC 103 " (cutoff:3.500A) Processing helix chain 'CC' and resid 110 through 119 removed outlier: 3.970A pdb=" N METCC 114 " --> pdb=" O ASPCC 110 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASPCC 119 " --> pdb=" O VALCC 115 " (cutoff:3.500A) Processing helix chain 'CC' and resid 144 through 155 Processing helix chain 'CC' and resid 173 through 184 removed outlier: 3.607A pdb=" N GLYCC 184 " --> pdb=" O LEUCC 180 " (cutoff:3.500A) Processing helix chain 'CC' and resid 194 through 198 Processing helix chain 'CC' and resid 201 through 220 removed outlier: 3.572A pdb=" N GLNCC 205 " --> pdb=" O LYSCC 201 " (cutoff:3.500A) Processing helix chain 'CC' and resid 231 through 245 removed outlier: 3.620A pdb=" N ALACC 235 " --> pdb=" O LYSCC 231 " (cutoff:3.500A) Processing helix chain 'CC' and resid 250 through 255 Processing helix chain 'CC' and resid 351 through 357 removed outlier: 4.172A pdb=" N GLUCC 355 " --> pdb=" O PROCC 351 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRPCC 357 " --> pdb=" O GLYCC 353 " (cutoff:3.500A) Processing helix chain 'CC' and resid 462 through 482 Processing helix chain 'CC' and resid 493 through 498 removed outlier: 3.706A pdb=" N ARGCC 497 " --> pdb=" O SERCC 493 " (cutoff:3.500A) Processing helix chain 'CC' and resid 522 through 526 Processing helix chain 'CC' and resid 533 through 548 removed outlier: 3.617A pdb=" N THRCC 537 " --> pdb=" O ASNCC 533 " (cutoff:3.500A) Processing helix chain 'CC' and resid 566 through 571 removed outlier: 3.718A pdb=" N LYSCC 570 " --> pdb=" O LEUCC 567 " (cutoff:3.500A) Processing helix chain 'CC' and resid 723 through 730 Processing sheet with id=AA1, first strand: chain 'SB' and resid 42 through 49 removed outlier: 8.823A pdb=" N LEUSB 96 " --> pdb=" O TRPSB 29 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASPSB 31 " --> pdb=" O LEUSB 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'SB' and resid 66 through 69 removed outlier: 8.082A pdb=" N HISSB 101 " --> pdb=" O LEUSB 217 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ARGSB 213 " --> pdb=" O PHESB 105 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VALSB 212 " --> pdb=" O ILESB 140 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILESB 140 " --> pdb=" O VALSB 212 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VALSB 134 " --> pdb=" O LEUSB 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'SE' and resid 9 through 10 removed outlier: 4.340A pdb=" N LEUSE 9 " --> pdb=" O ALASE 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'SE' and resid 42 through 43 Processing sheet with id=AA5, first strand: chain 'SE' and resid 75 through 76 removed outlier: 3.577A pdb=" N GLUSE 97 " --> pdb=" O LEUSE 92 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASNSE 98 " --> pdb=" O ILESE 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'SE' and resid 102 through 103 removed outlier: 4.487A pdb=" N VALSE 102 " --> pdb=" O ALASE 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'SE' and resid 146 through 148 Processing sheet with id=AA8, first strand: chain 'SE' and resid 217 through 221 removed outlier: 6.124A pdb=" N LYSSE 211 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILESE 195 " --> pdb=" O LYSSE 211 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILESE 195 " --> pdb=" O LYSSE 179 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYSSE 179 " --> pdb=" O ILESE 195 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEUSE 180 " --> pdb=" O ILESE 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SG' and resid 12 through 17 removed outlier: 6.690A pdb=" N LYSSG 2 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEUSG 111 " --> pdb=" O LYSSG 2 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASNSG 4 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILESG 113 " --> pdb=" O ASNSG 4 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SERSG 6 " --> pdb=" O ILESG 113 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LYSSG 115 " --> pdb=" O SERSG 6 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASNSG 56 " --> pdb=" O ALASG 107 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEUSG 109 " --> pdb=" O GLYSG 54 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLYSG 54 " --> pdb=" O LEUSG 109 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEUSG 111 " --> pdb=" O ILESG 52 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILESG 52 " --> pdb=" O LEUSG 111 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILESG 113 " --> pdb=" O PHESG 50 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHESG 50 " --> pdb=" O ILESG 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SG' and resid 72 through 77 Processing sheet with id=AB2, first strand: chain 'SG' and resid 160 through 163 Processing sheet with id=AB3, first strand: chain 'SH' and resid 45 through 50 removed outlier: 6.585A pdb=" N LYSSH 56 " --> pdb=" O HISSH 89 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILESH 91 " --> pdb=" O LYSSH 56 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEUSH 58 " --> pdb=" O ILESH 91 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEUSH 93 " --> pdb=" O LEUSH 58 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILESH 60 " --> pdb=" O LEUSH 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'SH' and resid 181 through 184 removed outlier: 8.151A pdb=" N VALSH 182 " --> pdb=" O LYSSH 148 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLNSH 150 " --> pdb=" O VALSH 182 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLUSH 184 " --> pdb=" O GLNSH 150 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VALSH 152 " --> pdb=" O GLUSH 184 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHESW 50 " --> pdb=" O TYRSH 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'SI' and resid 3 through 4 removed outlier: 3.849A pdb=" N ILESI 3 " --> pdb=" O GLYSI 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'SI' and resid 37 through 38 removed outlier: 3.725A pdb=" N ILESI 60 " --> pdb=" O LYSSI 37 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYRSI 55 " --> pdb=" O VALSI 46 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VALSI 46 " --> pdb=" O TYRSI 55 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALASI 57 " --> pdb=" O HISSI 44 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HISSI 44 " --> pdb=" O ALASI 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'SI' and resid 72 through 75 removed outlier: 6.726A pdb=" N ASNSI 64 " --> pdb=" O GLYSI 181 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILESI 183 " --> pdb=" O ASNSI 64 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SERSI 66 " --> pdb=" O ILESI 183 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILESI 101 " --> pdb=" O VALSI 82 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASPSI 105 " --> pdb=" O ILESI 78 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILESI 78 " --> pdb=" O ASPSI 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'SJ' and resid 139 through 141 removed outlier: 4.631A pdb=" N ILESJ 134 " --> pdb=" O VALSJ 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'SL' and resid 70 through 77 removed outlier: 18.043A pdb=" N ILESL 70 " --> pdb=" O LEUSL 91 " (cutoff:3.500A) removed outlier: 14.892A pdb=" N LEUSL 91 " --> pdb=" O ILESL 70 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N THRSL 72 " --> pdb=" O ALASL 89 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALASL 89 " --> pdb=" O THRSL 72 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THRSL 74 " --> pdb=" O ARGSL 87 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VALSL 85 " --> pdb=" O VALSL 76 " (cutoff:3.500A) removed outlier: 16.122A pdb=" N VALSL 135 " --> pdb=" O HISSL 104 " (cutoff:3.500A) removed outlier: 13.889A pdb=" N ASNSL 106 " --> pdb=" O VALSL 135 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N PHESL 137 " --> pdb=" O ASNSL 106 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N VALSL 139 " --> pdb=" O PROSL 108 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N HISSL 110 " --> pdb=" O VALSL 139 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYSSL 141 " --> pdb=" O HISSL 110 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARGSL 136 " --> pdb=" O CYSSL 128 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THRSL 124 " --> pdb=" O VALSL 140 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VALSL 142 " --> pdb=" O ILESL 122 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILESL 122 " --> pdb=" O VALSL 142 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILESL 122 " --> pdb=" O GLYSL 73 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLYSL 73 " --> pdb=" O ILESL 122 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THRSL 124 " --> pdb=" O LEUSL 71 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEUSL 71 " --> pdb=" O THRSL 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'SO' and resid 38 through 42 removed outlier: 6.942A pdb=" N GLYSO 15 " --> pdb=" O HISSO 80 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LYSSO 82 " --> pdb=" O GLYSO 15 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALASO 17 " --> pdb=" O LYSSO 82 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ARGSO 84 " --> pdb=" O ALASO 17 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILESO 19 " --> pdb=" O ARGSO 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'SW' and resid 71 through 74 removed outlier: 3.658A pdb=" N GLYSW 123 " --> pdb=" O VALSW 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'SW' and resid 71 through 74 removed outlier: 5.361A pdb=" N ILESW 125 " --> pdb=" O THRSW 105 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THRSW 105 " --> pdb=" O ILESW 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'SX' and resid 49 through 57 removed outlier: 7.003A pdb=" N ARGSX 73 " --> pdb=" O LEUSX 54 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYSSX 56 " --> pdb=" O CYSSX 71 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N CYSSX 71 " --> pdb=" O LYSSX 56 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHESX 122 " --> pdb=" O THRSX 84 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VALSX 124 " --> pdb=" O PHESX 86 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VALSX 124 " --> pdb=" O ALASX 105 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALASX 105 " --> pdb=" O VALSX 124 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'SY' and resid 6 through 15 removed outlier: 5.812A pdb=" N ILESY 7 " --> pdb=" O LEUSY 28 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEUSY 28 " --> pdb=" O ILESY 7 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N THRSY 9 " --> pdb=" O ASPSY 26 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASPSY 26 " --> pdb=" O THRSY 9 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYSSY 11 " --> pdb=" O VALSY 24 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VALSY 24 " --> pdb=" O LYSSY 11 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYSSY 68 " --> pdb=" O THRSY 62 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N THRSY 62 " --> pdb=" O LYSSY 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VALSY 70 " --> pdb=" O PHESY 60 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHESY 60 " --> pdb=" O VALSY 70 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHESY 72 " --> pdb=" O PHESY 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Sb' and resid 43 through 47 Processing sheet with id=AC7, first strand: chain 'Sb' and resid 64 through 65 Processing sheet with id=AC8, first strand: chain 'CA' and resid 95 through 100 Processing sheet with id=AC9, first strand: chain 'CA' and resid 181 through 186 Processing sheet with id=AD1, first strand: chain 'CC' and resid 123 through 128 removed outlier: 6.458A pdb=" N ILECC 86 " --> pdb=" O ILECC 138 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VALCC 158 " --> pdb=" O ILECC 189 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VALCC 191 " --> pdb=" O VALCC 158 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N PHECC 160 " --> pdb=" O VALCC 191 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'CC' and resid 336 through 338 removed outlier: 11.593A pdb=" N PHECC 301 " --> pdb=" O PROCC 564 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEUCC 303 " --> pdb=" O ARGCC 562 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARGCC 562 " --> pdb=" O LEUCC 303 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASPCC 275 " --> pdb=" O VALCC 267 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THRCC 281 " --> pdb=" O ALACC 261 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALACC 261 " --> pdb=" O THRCC 281 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARGCC 283 " --> pdb=" O VALCC 259 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VALCC 259 " --> pdb=" O ARGCC 283 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'CC' and resid 707 through 710 removed outlier: 6.771A pdb=" N LYSCC 756 " --> pdb=" O LYSCC 746 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HISCC 640 " --> pdb=" O ILECC 696 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARGCC 700 " --> pdb=" O TYRCC 642 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYSCC 641 " --> pdb=" O GLNCC 631 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLNCC 631 " --> pdb=" O LYSCC 641 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHECC 629 " --> pdb=" O GLUCC 643 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASNCC 595 " --> pdb=" O LEUCC 689 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THRCC 687 " --> pdb=" O SERCC 597 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEUCC 682 " --> pdb=" O LYSCC 671 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYSCC 671 " --> pdb=" O LEUCC 682 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2745 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1005 hydrogen bonds 1562 hydrogen bond angles 0 basepair planarities 418 basepair parallelities 663 stacking parallelities Total time for adding SS restraints: 36.55 Time building geometry restraints manager: 28.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 3273 1.24 - 1.38: 16094 1.38 - 1.53: 30294 1.53 - 1.68: 5186 1.68 - 1.82: 81 Bond restraints: 54928 Sorted by residual: bond pdb=" CG PROCC 45 " pdb=" CD PROCC 45 " ideal model delta sigma weight residual 1.503 1.089 0.414 3.40e-02 8.65e+02 1.48e+02 bond pdb=" N PROCC 45 " pdb=" CD PROCC 45 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" C SERCC 461 " pdb=" N PROCC 462 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.23e-02 6.61e+03 8.65e+00 bond pdb=" C GLNSX 63 " pdb=" N PROSX 64 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.90e+00 bond pdb=" C SERSH 31 " pdb=" N PROSH 32 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.86e+00 ... (remaining 54923 not shown) Histogram of bond angle deviations from ideal: 80.22 - 91.43: 2 91.43 - 102.65: 1962 102.65 - 113.86: 38587 113.86 - 125.07: 34564 125.07 - 136.28: 5092 Bond angle restraints: 80207 Sorted by residual: angle pdb=" N PROCC 45 " pdb=" CD PROCC 45 " pdb=" CG PROCC 45 " ideal model delta sigma weight residual 103.20 80.22 22.98 1.50e+00 4.44e-01 2.35e+02 angle pdb=" CA PROCC 45 " pdb=" CB PROCC 45 " pdb=" CG PROCC 45 " ideal model delta sigma weight residual 104.50 88.93 15.57 1.90e+00 2.77e-01 6.71e+01 angle pdb=" CA PROCC 45 " pdb=" N PROCC 45 " pdb=" CD PROCC 45 " ideal model delta sigma weight residual 112.00 102.37 9.63 1.40e+00 5.10e-01 4.73e+01 angle pdb=" C SERSb 58 " pdb=" N CYSSb 59 " pdb=" CA CYSSb 59 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.93e+01 angle pdb=" C PHESY 58 " pdb=" N GLYSY 59 " pdb=" CA GLYSY 59 " ideal model delta sigma weight residual 122.20 117.16 5.04 9.50e-01 1.11e+00 2.81e+01 ... (remaining 80202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 29178 35.80 - 71.60: 1119 71.60 - 107.40: 110 107.40 - 143.21: 8 143.21 - 179.01: 18 Dihedral angle restraints: 30433 sinusoidal: 21556 harmonic: 8877 Sorted by residual: dihedral pdb=" CA GLNSX 63 " pdb=" C GLNSX 63 " pdb=" N PROSX 64 " pdb=" CA PROSX 64 " ideal model delta harmonic sigma weight residual -180.00 -125.99 -54.01 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" O4' UC2 767 " pdb=" C1' UC2 767 " pdb=" N1 UC2 767 " pdb=" C2 UC2 767 " ideal model delta sinusoidal sigma weight residual 200.00 35.45 164.55 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' CC2 934 " pdb=" C1' CC2 934 " pdb=" N1 CC2 934 " pdb=" C2 CC2 934 " ideal model delta sinusoidal sigma weight residual 200.00 43.38 156.62 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 30430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 9580 0.107 - 0.215: 371 0.215 - 0.322: 28 0.322 - 0.429: 2 0.429 - 0.536: 1 Chirality restraints: 9982 Sorted by residual: chirality pdb=" CB ILESL 54 " pdb=" CA ILESL 54 " pdb=" CG1 ILESL 54 " pdb=" CG2 ILESL 54 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" C1' CC2 191 " pdb=" O4' CC2 191 " pdb=" C2' CC2 191 " pdb=" N1 CC2 191 " both_signs ideal model delta sigma weight residual False 2.45 2.10 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILESX 59 " pdb=" CA ILESX 59 " pdb=" CG1 ILESX 59 " pdb=" CG2 ILESX 59 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 9979 not shown) Planarity restraints: 5563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GC2 689 " 0.039 2.00e-02 2.50e+03 2.59e-02 2.01e+01 pdb=" N9 GC2 689 " -0.026 2.00e-02 2.50e+03 pdb=" C8 GC2 689 " -0.008 2.00e-02 2.50e+03 pdb=" N7 GC2 689 " 0.003 2.00e-02 2.50e+03 pdb=" C5 GC2 689 " -0.003 2.00e-02 2.50e+03 pdb=" C6 GC2 689 " -0.012 2.00e-02 2.50e+03 pdb=" O6 GC2 689 " 0.029 2.00e-02 2.50e+03 pdb=" N1 GC2 689 " 0.006 2.00e-02 2.50e+03 pdb=" C2 GC2 689 " -0.059 2.00e-02 2.50e+03 pdb=" N2 GC2 689 " 0.035 2.00e-02 2.50e+03 pdb=" N3 GC2 689 " -0.002 2.00e-02 2.50e+03 pdb=" C4 GC2 689 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GC21141 " -0.042 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" N9 GC21141 " 0.029 2.00e-02 2.50e+03 pdb=" C8 GC21141 " 0.004 2.00e-02 2.50e+03 pdb=" N7 GC21141 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GC21141 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GC21141 " 0.014 2.00e-02 2.50e+03 pdb=" O6 GC21141 " -0.030 2.00e-02 2.50e+03 pdb=" N1 GC21141 " -0.011 2.00e-02 2.50e+03 pdb=" C2 GC21141 " 0.056 2.00e-02 2.50e+03 pdb=" N2 GC21141 " -0.030 2.00e-02 2.50e+03 pdb=" N3 GC21141 " 0.004 2.00e-02 2.50e+03 pdb=" C4 GC21141 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' CC21675 " 0.007 2.00e-02 2.50e+03 2.92e-02 1.91e+01 pdb=" N1 CC21675 " 0.003 2.00e-02 2.50e+03 pdb=" C2 CC21675 " -0.072 2.00e-02 2.50e+03 pdb=" O2 CC21675 " 0.043 2.00e-02 2.50e+03 pdb=" N3 CC21675 " 0.002 2.00e-02 2.50e+03 pdb=" C4 CC21675 " -0.014 2.00e-02 2.50e+03 pdb=" N4 CC21675 " 0.016 2.00e-02 2.50e+03 pdb=" C5 CC21675 " 0.010 2.00e-02 2.50e+03 pdb=" C6 CC21675 " 0.004 2.00e-02 2.50e+03 ... (remaining 5560 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3216 2.70 - 3.25: 45044 3.25 - 3.80: 96275 3.80 - 4.35: 121390 4.35 - 4.90: 172341 Nonbonded interactions: 438266 Sorted by model distance: nonbonded pdb=" O4 UC21656 " pdb=" O6 GC21745 " model vdw 2.146 2.432 nonbonded pdb=" O4 UC2 229 " pdb=" O6 GC2 235 " model vdw 2.149 3.040 nonbonded pdb=" O4 UC2 873 " pdb=" O6 GC2 954 " model vdw 2.162 3.040 nonbonded pdb=" O2 UC2 227 " pdb=" O6 GC2 834 " model vdw 2.183 2.432 nonbonded pdb=" O2' GC21064 " pdb=" O ILESB 204 " model vdw 2.185 2.440 ... (remaining 438261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1255 5.49 5 S 51 5.16 5 C 27523 2.51 5 N 9343 2.21 5 O 13136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.060 Extract box with map and model: 14.540 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.430 Process input model: 159.860 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.414 54928 Z= 0.338 Angle : 0.902 22.979 80207 Z= 0.464 Chirality : 0.047 0.536 9982 Planarity : 0.008 0.130 5563 Dihedral : 16.333 179.008 24697 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.03 % Favored : 91.83 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 2.31 % Twisted General : 0.17 % 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: -1.90 (0.14), residues: 3037 helix: -0.52 (0.16), residues: 918 sheet: -0.71 (0.21), residues: 616 loop : -1.97 (0.14), residues: 1503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 501 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 502 average time/residue: 0.6051 time to fit residues: 512.3949 Evaluate side-chains 373 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 4.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 358 optimal weight: 40.0000 chunk 322 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 333 optimal weight: 0.0170 chunk 128 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 247 optimal weight: 0.3980 chunk 385 optimal weight: 10.0000 overall best weight: 2.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SG 80 ASN SI 111 GLN ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 133 HIS ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 24 ASN SO 65 GLN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 54928 Z= 0.219 Angle : 0.647 16.192 80207 Z= 0.328 Chirality : 0.038 0.345 9982 Planarity : 0.005 0.077 5563 Dihedral : 15.995 179.831 18440 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.97 % Favored : 91.93 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 1.54 % 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: -1.36 (0.15), residues: 3037 helix: 0.27 (0.17), residues: 949 sheet: -0.64 (0.21), residues: 593 loop : -1.80 (0.15), residues: 1495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 412 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 32 residues processed: 436 average time/residue: 0.6094 time to fit residues: 450.1930 Evaluate side-chains 400 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 368 time to evaluate : 4.000 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5073 time to fit residues: 36.4456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 214 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 321 optimal weight: 0.5980 chunk 262 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 386 optimal weight: 0.9990 chunk 417 optimal weight: 30.0000 chunk 344 optimal weight: 5.9990 chunk 383 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SB 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SB 183 GLN ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SI 88 ASN ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 24 ASN SO 65 GLN SO 99 GLN SW 80 ASN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 54928 Z= 0.359 Angle : 0.731 15.478 80207 Z= 0.368 Chirality : 0.042 0.341 9982 Planarity : 0.006 0.078 5563 Dihedral : 16.213 179.674 18440 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.82 % Favored : 91.08 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 1.54 % Twisted General : 0.07 % 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: -1.28 (0.15), residues: 3037 helix: 0.51 (0.17), residues: 953 sheet: -0.63 (0.21), residues: 604 loop : -1.88 (0.15), residues: 1480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 400 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 45 residues processed: 437 average time/residue: 0.5990 time to fit residues: 446.9182 Evaluate side-chains 412 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 367 time to evaluate : 4.304 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4290 time to fit residues: 42.1310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 382 optimal weight: 30.0000 chunk 290 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 410 optimal weight: 10.0000 chunk 202 optimal weight: 0.2980 chunk 367 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 160 HIS SB 183 GLN ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 78 ASN SO 24 ASN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 54928 Z= 0.230 Angle : 0.638 15.546 80207 Z= 0.322 Chirality : 0.038 0.330 9982 Planarity : 0.005 0.077 5563 Dihedral : 16.057 179.362 18440 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.26 % Favored : 91.64 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 1.54 % 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: -1.09 (0.15), residues: 3037 helix: 0.74 (0.17), residues: 961 sheet: -0.65 (0.21), residues: 605 loop : -1.77 (0.15), residues: 1471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 393 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 420 average time/residue: 0.6087 time to fit residues: 438.1128 Evaluate side-chains 393 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 369 time to evaluate : 4.036 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4547 time to fit residues: 25.1697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 342 optimal weight: 9.9990 chunk 233 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 350 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 368 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 153 HIS SB 183 GLN SB 211 HIS ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SH 74 GLN ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SN 151 ASN SO 24 ASN SW 113 HIS ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 54928 Z= 0.343 Angle : 0.712 14.069 80207 Z= 0.358 Chirality : 0.041 0.399 9982 Planarity : 0.006 0.077 5563 Dihedral : 16.204 179.486 18440 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.88 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.77 % Twisted General : 0.07 % 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: -1.16 (0.15), residues: 3037 helix: 0.76 (0.17), residues: 959 sheet: -0.84 (0.21), residues: 611 loop : -1.81 (0.15), residues: 1467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 389 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 38 residues processed: 430 average time/residue: 0.6082 time to fit residues: 449.7278 Evaluate side-chains 405 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 367 time to evaluate : 3.989 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4373 time to fit residues: 36.8547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 138 optimal weight: 5.9990 chunk 369 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 241 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 411 optimal weight: 9.9990 chunk 341 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 183 GLN ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 24 ASN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 54928 Z= 0.355 Angle : 0.732 13.865 80207 Z= 0.368 Chirality : 0.042 0.420 9982 Planarity : 0.006 0.078 5563 Dihedral : 16.285 179.783 18440 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.38 % Favored : 90.55 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.77 % Twisted General : 0.07 % 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: -1.29 (0.15), residues: 3037 helix: 0.67 (0.17), residues: 966 sheet: -1.03 (0.20), residues: 622 loop : -1.86 (0.15), residues: 1449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 384 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 42 residues processed: 419 average time/residue: 0.5981 time to fit residues: 428.3235 Evaluate side-chains 397 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 355 time to evaluate : 4.025 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.4982 time to fit residues: 43.8004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 396 optimal weight: 40.0000 chunk 46 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 346 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 409 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 183 GLN ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 24 ASN SW 98 GLN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Sb 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 54928 Z= 0.176 Angle : 0.621 14.274 80207 Z= 0.314 Chirality : 0.037 0.357 9982 Planarity : 0.005 0.076 5563 Dihedral : 15.979 179.357 18440 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.77 % 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: -0.98 (0.15), residues: 3037 helix: 0.91 (0.17), residues: 964 sheet: -0.76 (0.21), residues: 597 loop : -1.69 (0.15), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 415 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 434 average time/residue: 0.6298 time to fit residues: 466.6324 Evaluate side-chains 383 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 370 time to evaluate : 4.328 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5988 time to fit residues: 18.6460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 253 optimal weight: 0.2980 chunk 163 optimal weight: 0.0270 chunk 244 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 overall best weight: 2.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 183 GLN ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SO 24 ASN SO 99 GLN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.171 54928 Z= 0.273 Angle : 0.668 14.089 80207 Z= 0.337 Chirality : 0.039 0.338 9982 Planarity : 0.005 0.078 5563 Dihedral : 16.025 179.107 18440 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.82 % Favored : 91.08 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.77 % 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: -1.00 (0.15), residues: 3037 helix: 0.91 (0.17), residues: 961 sheet: -0.71 (0.21), residues: 597 loop : -1.74 (0.15), residues: 1479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 382 time to evaluate : 4.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 394 average time/residue: 0.5978 time to fit residues: 403.9910 Evaluate side-chains 384 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 365 time to evaluate : 4.048 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4602 time to fit residues: 21.4430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 372 optimal weight: 5.9990 chunk 392 optimal weight: 40.0000 chunk 358 optimal weight: 7.9990 chunk 381 optimal weight: 0.7980 chunk 229 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 344 optimal weight: 1.9990 chunk 361 optimal weight: 6.9990 chunk 380 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 183 GLN ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 98 GLN ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.162 54928 Z= 0.202 Angle : 0.634 17.319 80207 Z= 0.318 Chirality : 0.037 0.360 9982 Planarity : 0.005 0.076 5563 Dihedral : 15.929 178.915 18440 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.46 % Favored : 91.44 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % 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: -0.91 (0.15), residues: 3037 helix: 1.00 (0.17), residues: 961 sheet: -0.78 (0.21), residues: 611 loop : -1.65 (0.16), residues: 1465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 383 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 393 average time/residue: 0.5951 time to fit residues: 403.5721 Evaluate side-chains 376 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 369 time to evaluate : 4.157 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5207 time to fit residues: 11.4583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 250 optimal weight: 8.9990 chunk 403 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 280 optimal weight: 0.4980 chunk 423 optimal weight: 9.9990 chunk 389 optimal weight: 50.0000 chunk 337 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 183 GLN ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.162 54928 Z= 0.327 Angle : 0.721 16.451 80207 Z= 0.361 Chirality : 0.041 0.320 9982 Planarity : 0.006 0.078 5563 Dihedral : 16.126 178.768 18440 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.52 % Favored : 90.39 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.11 (0.15), residues: 3037 helix: 0.82 (0.17), residues: 965 sheet: -0.85 (0.21), residues: 585 loop : -1.78 (0.15), residues: 1487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 374 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 384 average time/residue: 0.6294 time to fit residues: 416.5134 Evaluate side-chains 378 residues out of total 2651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 364 time to evaluate : 4.007 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4640 time to fit residues: 16.9465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 267 optimal weight: 6.9990 chunk 359 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 337 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: SB 177 GLN SB 183 GLN SB 220 GLN ** SE 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SE 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SG 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SH 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SH 122 HIS SH 170 GLN SJ 48 GLN ** SJ 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Sb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.111923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077664 restraints weight = 143608.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076872 restraints weight = 136376.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077437 restraints weight = 89644.102| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.161 54928 Z= 0.530 Angle : 0.900 16.663 80207 Z= 0.446 Chirality : 0.048 0.320 9982 Planarity : 0.007 0.098 5563 Dihedral : 16.725 179.814 18440 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.41 % Favored : 89.50 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.65 (0.15), residues: 3037 helix: 0.32 (0.17), residues: 962 sheet: -1.22 (0.21), residues: 607 loop : -2.02 (0.15), residues: 1468 =============================================================================== Job complete usr+sys time: 8490.55 seconds wall clock time: 156 minutes 34.18 seconds (9394.18 seconds total)