Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 10:12:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s85_10116/04_2023/6s85_10116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s85_10116/04_2023/6s85_10116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s85_10116/04_2023/6s85_10116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s85_10116/04_2023/6s85_10116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s85_10116/04_2023/6s85_10116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s85_10116/04_2023/6s85_10116_updated.pdb" } resolution = 4.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4320 atoms to isotropic. 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 Mn 4 7.51 5 P 67 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7987 2.51 5 N 2293 2.21 5 O 2631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C TYR 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ASP 905": "OD1" <-> "OD2" Residue "C GLU 933": "OE1" <-> "OE2" Residue "C ARG 946": "NH1" <-> "NH2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 917": "NH1" <-> "NH2" Residue "D GLU 933": "OE1" <-> "OE2" Residue "D ARG 946": "NH1" <-> "NH2" Residue "D ASP 947": "OD1" <-> "OD2" Residue "D ARG 949": "NH1" <-> "NH2" Residue "D ARG 976": "NH1" <-> "NH2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 297": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13018 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2916 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2923 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 7, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3010 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2816 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 4 Chain: "E" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 659 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 9 not shown) Time building chain proxies: 7.25, per 1000 atoms: 0.56 Number of scatterers: 13018 At special positions: 0 Unit cell: (95.12, 102.5, 145.14, 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) Mn 4 24.99 S 34 16.00 P 67 15.00 Mg 2 11.99 O 2631 8.00 N 2293 7.00 C 7987 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: 6.28 Conformation dependent library (CDL) restraints added in 1.9 seconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 34.3% alpha, 12.7% beta 27 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.620A pdb=" N LEU C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 129 through 140 removed outlier: 4.186A pdb=" N GLU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.656A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 180 through 199 removed outlier: 3.512A pdb=" N GLY C 183 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE C 185 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 199 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 880 removed outlier: 4.416A pdb=" N TRP C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 876 through 880' Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 894 through 916 removed outlier: 4.432A pdb=" N LEU C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N HIS C 909 " --> pdb=" O ASP C 905 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 910 " --> pdb=" O ASN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 953 through 968 Processing helix chain 'C' and resid 993 through 1006 Processing helix chain 'C' and resid 1018 through 1023 Processing helix chain 'D' and resid 25 through 28 No H-bonds generated for 'chain 'D' and resid 25 through 28' Processing helix chain 'D' and resid 43 through 55 removed outlier: 4.562A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 158 through 162 removed outlier: 4.121A pdb=" N PHE D 161 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 162 " --> pdb=" O ALA D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 162' Processing helix chain 'D' and resid 167 through 176 removed outlier: 4.443A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.449A pdb=" N ALA D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 884 Processing helix chain 'D' and resid 893 through 918 removed outlier: 4.769A pdb=" N LEU D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 913 " --> pdb=" O HIS D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 950 No H-bonds generated for 'chain 'D' and resid 948 through 950' Processing helix chain 'D' and resid 953 through 970 Processing helix chain 'D' and resid 986 through 988 No H-bonds generated for 'chain 'D' and resid 986 through 988' Processing helix chain 'D' and resid 994 through 1006 removed outlier: 3.738A pdb=" N ALA D1003 " --> pdb=" O ASP D 999 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1020 No H-bonds generated for 'chain 'D' and resid 1018 through 1020' Processing helix chain 'A' and resid 21 through 38 removed outlier: 3.781A pdb=" N PHE A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.775A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.747A pdb=" N GLU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 146 through 172 removed outlier: 4.263A pdb=" N GLN A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 286 through 292 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 378 through 394 removed outlier: 4.069A pdb=" N HIS A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 38 removed outlier: 4.044A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.689A pdb=" N TYR B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 100 Processing helix chain 'B' and resid 152 through 172 removed outlier: 3.889A pdb=" N ILE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.654A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP B 296 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 330 removed outlier: 3.892A pdb=" N GLN B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 370 Processing helix chain 'B' and resid 378 through 393 removed outlier: 3.584A pdb=" N THR B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 389 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.616A pdb=" N LEU C 80 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 83 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 922 through 926 removed outlier: 3.598A pdb=" N ARG C 946 " --> pdb=" O VAL C 936 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 979 through 982 removed outlier: 6.576A pdb=" N THR C1010 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU C 982 " --> pdb=" O THR C1010 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY C1012 " --> pdb=" O LEU C 982 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.650A pdb=" N GLU D 84 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU D 6 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU D 82 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU D 8 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D 80 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG D 118 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 124 " --> pdb=" O ARG D 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.755A pdb=" N PHE D 33 " --> pdb=" O ILE D1011 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU D 980 " --> pdb=" O GLY D1012 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE D1014 " --> pdb=" O LEU D 980 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 982 " --> pdb=" O ILE D1014 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 922 through 926 Processing sheet with id= G, first strand: chain 'D' and resid 1030 through 1032 Processing sheet with id= H, first strand: chain 'A' and resid 264 through 272 removed outlier: 6.839A pdb=" N THR A 259 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 268 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 257 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN A 270 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 255 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA A 42 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR A 6 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 44 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 76 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 45 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 78 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 79 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 179 through 181 removed outlier: 8.471A pdb=" N ILE A 180 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 125 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 115 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL A 125 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLN A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 279 through 284 removed outlier: 6.531A pdb=" N TRP A 306 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU A 282 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP A 308 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY A 284 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU A 310 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 307 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 336 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE A 309 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL A 338 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 311 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 340 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.622A pdb=" N ILE A 229 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL A 235 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.728A pdb=" N ALA B 42 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR B 6 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 44 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N HIS B 76 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N VAL B 45 " --> pdb=" O HIS B 76 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 78 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 178 through 181 removed outlier: 6.572A pdb=" N LEU B 115 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL B 125 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN B 113 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 254 through 261 removed outlier: 3.504A pdb=" N SER B 267 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER B 261 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 6.37 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: 3340 1.33 - 1.45: 2779 1.45 - 1.57: 7078 1.57 - 1.69: 130 1.69 - 1.81: 52 Bond restraints: 13379 Sorted by residual: bond pdb=" C SER C 67 " pdb=" N GLN C 68 " ideal model delta sigma weight residual 1.333 1.397 -0.064 1.29e-02 6.01e+03 2.49e+01 bond pdb=" N VAL C 114 " pdb=" CA VAL C 114 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.30e+01 bond pdb=" N GLN C 155 " pdb=" CA GLN C 155 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.28e-02 6.10e+03 1.17e+01 bond pdb=" N THR D 177 " pdb=" CA THR D 177 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.22e-02 6.72e+03 9.63e+00 bond pdb=" N LYS D 894 " pdb=" CA LYS D 894 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.09e+00 ... (remaining 13374 not shown) Histogram of bond angle deviations from ideal: 92.28 - 101.20: 70 101.20 - 110.12: 3456 110.12 - 119.05: 8099 119.05 - 127.97: 6603 127.97 - 136.89: 187 Bond angle restraints: 18415 Sorted by residual: angle pdb=" N SER D 889 " pdb=" CA SER D 889 " pdb=" C SER D 889 " ideal model delta sigma weight residual 113.55 128.16 -14.61 1.26e+00 6.30e-01 1.34e+02 angle pdb=" N LYS D 890 " pdb=" CA LYS D 890 " pdb=" C LYS D 890 " ideal model delta sigma weight residual 109.24 92.28 16.96 1.67e+00 3.59e-01 1.03e+02 angle pdb=" C SER D 889 " pdb=" CA SER D 889 " pdb=" CB SER D 889 " ideal model delta sigma weight residual 109.34 94.92 14.42 1.55e+00 4.16e-01 8.66e+01 angle pdb=" O3' DG F 70 " pdb=" C3' DG F 70 " pdb=" C2' DG F 70 " ideal model delta sigma weight residual 111.50 101.35 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" N SER C 154 " pdb=" CA SER C 154 " pdb=" C SER C 154 " ideal model delta sigma weight residual 110.55 117.57 -7.02 1.35e+00 5.49e-01 2.71e+01 ... (remaining 18410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 6473 16.64 - 33.29: 831 33.29 - 49.93: 368 49.93 - 66.58: 121 66.58 - 83.22: 30 Dihedral angle restraints: 7823 sinusoidal: 3520 harmonic: 4303 Sorted by residual: dihedral pdb=" CD ARG D 946 " pdb=" NE ARG D 946 " pdb=" CZ ARG D 946 " pdb=" NH1 ARG D 946 " ideal model delta sinusoidal sigma weight residual 0.00 -74.04 74.04 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" C ASP B 376 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual -122.60 -137.83 15.23 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" CA GLU C 25 " pdb=" C GLU C 25 " pdb=" N PRO C 26 " pdb=" CA PRO C 26 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 7820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1882 0.094 - 0.189: 222 0.189 - 0.283: 14 0.283 - 0.377: 1 0.377 - 0.472: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CA ASP B 376 " pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CB ASP B 376 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CA ASP D 893 " pdb=" N ASP D 893 " pdb=" C ASP D 893 " pdb=" CB ASP D 893 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA GLU B 302 " pdb=" N GLU B 302 " pdb=" C GLU B 302 " pdb=" CB GLU B 302 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2117 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 946 " -1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG D 946 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG D 946 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 946 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 946 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 248 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C GLU B 248 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU B 248 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS B 249 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D1028 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C ILE D1028 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE D1028 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS D1029 " 0.015 2.00e-02 2.50e+03 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 94 2.40 - 3.03: 7022 3.03 - 3.65: 20596 3.65 - 4.28: 29990 4.28 - 4.90: 46705 Nonbonded interactions: 104407 Sorted by model distance: nonbonded pdb=" OP1 DG F 76 " pdb="MN MN A 501 " model vdw 1.775 2.320 nonbonded pdb=" O PHE B 246 " pdb=" SG CYS B 249 " model vdw 1.782 3.400 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.808 2.320 nonbonded pdb=" CB PHE D 190 " pdb=" O SER D 889 " model vdw 1.823 3.440 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 502 " model vdw 1.836 2.320 ... (remaining 104402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 105 or resid 109 through 137 or resid 151 throug \ h 188 or resid 205 through 342 or resid 354 through 395 or resid 501 through 502 \ )) selection = (chain 'B' and (resid 1 through 188 or resid 205 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 201 or resid 875 through 1047 or resid 1101 thro \ ugh 1102)) } 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=0.28 max=1.00 mean=0.99 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 6.870 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.350 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 53.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.008 0.064 13379 Z= 0.501 Angle : 1.013 16.962 18415 Z= 0.614 Chirality : 0.060 0.472 2120 Planarity : 0.012 0.475 2153 Dihedral : 19.018 83.221 5029 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.79 % Favored : 91.87 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.59 (0.19), residues: 1464 helix: -2.64 (0.19), residues: 479 sheet: -2.41 (0.29), residues: 269 loop : -2.08 (0.21), residues: 716 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 191 average time/residue: 0.3114 time to fit residues: 82.4508 Evaluate side-chains 115 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.423 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2360 time to fit residues: 3.1537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 30.0000 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 103 ASN C 906 ASN C 909 HIS C 914 GLN ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN D 875 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN B 71 GLN B 76 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13379 Z= 0.182 Angle : 0.602 7.406 18415 Z= 0.320 Chirality : 0.041 0.231 2120 Planarity : 0.004 0.040 2153 Dihedral : 19.274 88.853 2241 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.34 (0.21), residues: 1464 helix: -1.09 (0.21), residues: 490 sheet: -2.00 (0.30), residues: 262 loop : -1.61 (0.23), residues: 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.420 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 outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2653 time to fit residues: 64.3316 Evaluate side-chains 110 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 110 GLN ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN A 325 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 13379 Z= 0.313 Angle : 0.658 6.122 18415 Z= 0.348 Chirality : 0.042 0.169 2120 Planarity : 0.004 0.038 2153 Dihedral : 19.154 86.013 2241 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.80 (0.22), residues: 1464 helix: -0.45 (0.22), residues: 493 sheet: -2.04 (0.31), residues: 261 loop : -1.29 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2557 time to fit residues: 46.4204 Evaluate side-chains 91 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 8.9990 chunk 104 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 39 optimal weight: 0.0070 chunk 123 optimal weight: 7.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN A 38 HIS A 39 GLN ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13379 Z= 0.207 Angle : 0.583 6.696 18415 Z= 0.306 Chirality : 0.040 0.166 2120 Planarity : 0.003 0.043 2153 Dihedral : 18.882 85.930 2241 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1464 helix: -0.05 (0.23), residues: 500 sheet: -1.79 (0.31), residues: 270 loop : -1.14 (0.25), residues: 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2630 time to fit residues: 53.1642 Evaluate side-chains 98 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 909 HIS ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN D 193 HIS ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS B 36 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 13379 Z= 0.204 Angle : 0.578 8.974 18415 Z= 0.300 Chirality : 0.040 0.149 2120 Planarity : 0.003 0.029 2153 Dihedral : 18.770 83.666 2241 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.33 % Favored : 94.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.20 (0.23), residues: 1464 helix: 0.15 (0.23), residues: 502 sheet: -1.69 (0.30), residues: 274 loop : -1.03 (0.26), residues: 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2506 time to fit residues: 51.6687 Evaluate side-chains 101 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 142 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13379 Z= 0.170 Angle : 0.564 9.208 18415 Z= 0.292 Chirality : 0.040 0.146 2120 Planarity : 0.003 0.028 2153 Dihedral : 18.606 80.938 2241 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.01 (0.23), residues: 1464 helix: 0.28 (0.23), residues: 504 sheet: -1.55 (0.31), residues: 272 loop : -0.92 (0.26), residues: 688 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2587 time to fit residues: 56.6565 Evaluate side-chains 105 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 0.0000 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 147 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13379 Z= 0.172 Angle : 0.572 9.533 18415 Z= 0.293 Chirality : 0.040 0.192 2120 Planarity : 0.003 0.045 2153 Dihedral : 18.529 78.040 2241 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.81 (0.23), residues: 1464 helix: 0.41 (0.24), residues: 499 sheet: -1.45 (0.31), residues: 272 loop : -0.74 (0.26), residues: 693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2455 time to fit residues: 52.3956 Evaluate side-chains 107 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 0.0060 chunk 44 optimal weight: 0.0020 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.7808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13379 Z= 0.141 Angle : 0.560 9.890 18415 Z= 0.283 Chirality : 0.039 0.177 2120 Planarity : 0.003 0.041 2153 Dihedral : 18.392 74.724 2241 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.69 (0.23), residues: 1464 helix: 0.54 (0.24), residues: 500 sheet: -1.32 (0.31), residues: 272 loop : -0.74 (0.26), residues: 692 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2343 time to fit residues: 53.1817 Evaluate side-chains 104 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 13379 Z= 0.337 Angle : 0.680 10.048 18415 Z= 0.348 Chirality : 0.043 0.155 2120 Planarity : 0.004 0.069 2153 Dihedral : 18.625 79.819 2241 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.88 (0.23), residues: 1464 helix: 0.22 (0.23), residues: 502 sheet: -1.46 (0.31), residues: 267 loop : -0.70 (0.26), residues: 695 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.491 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2444 time to fit residues: 48.7074 Evaluate side-chains 93 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN D 941 GLN ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 13379 Z= 0.223 Angle : 0.611 8.836 18415 Z= 0.313 Chirality : 0.041 0.161 2120 Planarity : 0.003 0.042 2153 Dihedral : 18.544 77.030 2241 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1464 helix: 0.44 (0.24), residues: 500 sheet: -1.36 (0.32), residues: 263 loop : -0.73 (0.26), residues: 701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.462 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2324 time to fit residues: 46.8712 Evaluate side-chains 97 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.074908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.060047 restraints weight = 50426.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.061585 restraints weight = 32614.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062670 restraints weight = 23679.522| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 13379 Z= 0.411 Angle : 0.746 11.263 18415 Z= 0.382 Chirality : 0.045 0.179 2120 Planarity : 0.004 0.069 2153 Dihedral : 18.817 80.872 2241 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.58 % Favored : 92.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.13 (0.23), residues: 1464 helix: -0.01 (0.23), residues: 503 sheet: -1.48 (0.33), residues: 245 loop : -0.91 (0.25), residues: 716 =============================================================================== Job complete usr+sys time: 2169.04 seconds wall clock time: 40 minutes 48.64 seconds (2448.64 seconds total)