Starting phenix.real_space_refine (version: 1.20rc4) on Thu Dec 2 00:45:03 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/12_2021/7ky9_23072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/12_2021/7ky9_23072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/12_2021/7ky9_23072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/12_2021/7ky9_23072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/12_2021/7ky9_23072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/12_2021/7ky9_23072_updated.pdb" } resolution = 4.05 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 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 "A TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1409": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 10354 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7229 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 25, 'TRANS': 884} Chain breaks: 2 Chain: "B" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2959 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'NAG': 2, 'MAN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'ALF': 1, ' MG': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'NAG': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.38, per 1000 atoms: 0.62 Number of scatterers: 10354 At special positions: 0 Unit cell: (129.682, 114.814, 130.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 53 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1956 8.00 N 1690 7.00 C 6646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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=1, symmetry=0 Links applied ALPHA1-4 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B1001 " - " ASN B 298 " " NAG C 1 " - " ASN B 240 " " NAG D 1 " - " ASN B 256 " " NAG E 1 " - " ASN B 332 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 7 sheets defined 44.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 283 through 300 Processing helix chain 'A' and resid 589 through 615 removed outlier: 4.001A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 641 through 653 Processing helix chain 'A' and resid 662 through 678 removed outlier: 5.005A pdb=" N GLU A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 701 through 704 removed outlier: 3.694A pdb=" N GLY A 704 " --> pdb=" O ASP A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 704' Processing helix chain 'A' and resid 740 through 748 Processing helix chain 'A' and resid 755 through 778 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.535A pdb=" N GLU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 794 through 798' Processing helix chain 'A' and resid 806 through 820 Processing helix chain 'A' and resid 844 through 856 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 935 through 948 Processing helix chain 'A' and resid 963 through 976 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 1014 through 1023 Processing helix chain 'A' and resid 1037 through 1045 Processing helix chain 'A' and resid 1062 through 1068 removed outlier: 3.838A pdb=" N GLU A1067 " --> pdb=" O ASP A1064 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A1068 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1086 Processing helix chain 'A' and resid 1095 through 1103 Processing helix chain 'A' and resid 1117 through 1125 removed outlier: 3.782A pdb=" N LEU A1124 " --> pdb=" O LEU A1120 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN A1125 " --> pdb=" O LYS A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1178 through 1182 Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.792A pdb=" N GLN A1197 " --> pdb=" O GLU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1217 removed outlier: 3.774A pdb=" N THR A1213 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A1216 " --> pdb=" O THR A1213 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A1217 " --> pdb=" O ARG A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1250 Proline residue: A1232 - end of helix removed outlier: 3.712A pdb=" N VAL A1239 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A1240 " --> pdb=" O TYR A1236 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A1242 " --> pdb=" O ASN A1238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A1245 " --> pdb=" O PHE A1241 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 3.945A pdb=" N TYR A1268 " --> pdb=" O TYR A1264 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASN A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1282 Processing helix chain 'A' and resid 1289 through 1294 Processing helix chain 'A' and resid 1296 through 1304 removed outlier: 3.833A pdb=" N LEU A1304 " --> pdb=" O VAL A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1333 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1351 through 1373 Processing helix chain 'A' and resid 1381 through 1398 Processing helix chain 'A' and resid 1403 through 1405 No H-bonds generated for 'chain 'A' and resid 1403 through 1405' Processing helix chain 'A' and resid 1411 through 1415 Processing helix chain 'A' and resid 1419 through 1446 removed outlier: 3.807A pdb=" N VAL A1427 " --> pdb=" O ALA A1423 " (cutoff:3.500A) Proline residue: A1435 - end of helix Processing helix chain 'A' and resid 1450 through 1460 Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 72 through 99 Proline residue: B 77 - end of helix removed outlier: 4.030A pdb=" N LYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 309 through 315 removed outlier: 4.922A pdb=" N TRP B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 373 through 398 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing sheet with id= A, first strand: chain 'A' and resid 708 through 712 removed outlier: 7.455A pdb=" N LYS A1027 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N SER A 711 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP A1029 " --> pdb=" O SER A 711 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.775A pdb=" N LYS A 725 " --> pdb=" O ALA A1005 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 956 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A1003 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 954 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA A1005 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 952 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 858 through 860 Processing sheet with id= D, first strand: chain 'A' and resid 1055 through 1057 removed outlier: 7.467A pdb=" N ALA A1112 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA A1142 " --> pdb=" O VAL A1113 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ILE A1115 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A1144 " --> pdb=" O ILE A1115 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1188 through 1190 removed outlier: 6.932A pdb=" N TYR A1204 " --> pdb=" O GLY A1189 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 126 through 129 removed outlier: 6.068A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR B 324 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 141 through 145 412 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3265 1.34 - 1.46: 2385 1.46 - 1.58: 4853 1.58 - 1.69: 3 1.69 - 1.81: 80 Bond restraints: 10586 Sorted by residual: bond pdb=" CB MET B 169 " pdb=" CG MET B 169 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" CB ASN B 240 " pdb=" CG ASN B 240 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.21e+00 bond pdb=" SD MET B 169 " pdb=" CE MET B 169 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.18e+00 bond pdb=" CA LEU A1164 " pdb=" C LEU A1164 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.08e-02 8.57e+03 1.33e+00 bond pdb=" CG LEU A1259 " pdb=" CD2 LEU A1259 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 ... (remaining 10581 not shown) Histogram of bond angle deviations from ideal: 89.89 - 107.90: 373 107.90 - 125.91: 13827 125.91 - 143.92: 161 143.92 - 161.93: 0 161.93 - 179.94: 2 Bond angle restraints: 14363 Sorted by residual: angle pdb=" CB MET B 169 " pdb=" CG MET B 169 " pdb=" SD MET B 169 " ideal model delta sigma weight residual 112.70 97.45 15.25 3.00e+00 1.11e-01 2.58e+01 angle pdb=" N LEU A1164 " pdb=" CA LEU A1164 " pdb=" C LEU A1164 " ideal model delta sigma weight residual 111.02 105.13 5.89 1.25e+00 6.40e-01 2.22e+01 angle pdb=" N VAL A 792 " pdb=" CA VAL A 792 " pdb=" C VAL A 792 " ideal model delta sigma weight residual 113.71 109.75 3.96 9.50e-01 1.11e+00 1.74e+01 angle pdb=" CA LEU B 81 " pdb=" CB LEU B 81 " pdb=" CG LEU B 81 " ideal model delta sigma weight residual 116.30 125.70 -9.40 3.50e+00 8.16e-02 7.21e+00 angle pdb=" CA ARG A1130 " pdb=" CB ARG A1130 " pdb=" CG ARG A1130 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 ... (remaining 14358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 6055 28.79 - 57.58: 192 57.58 - 86.38: 12 86.38 - 115.17: 2 115.17 - 143.96: 1 Dihedral angle restraints: 6262 sinusoidal: 2545 harmonic: 3717 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -157.60 71.60 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" O1B ADP A1701 " pdb=" O3A ADP A1701 " pdb=" PB ADP A1701 " pdb=" PA ADP A1701 " ideal model delta sinusoidal sigma weight residual -60.00 83.96 -143.96 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O2A ADP A1701 " pdb=" O3A ADP A1701 " pdb=" PA ADP A1701 " pdb=" PB ADP A1701 " ideal model delta sinusoidal sigma weight residual -60.00 -150.44 90.44 1 2.00e+01 2.50e-03 2.42e+01 ... (remaining 6259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1622 0.165 - 0.329: 2 0.329 - 0.494: 0 0.494 - 0.659: 0 0.659 - 0.824: 1 Chirality restraints: 1625 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C1 MAN C 3 " pdb=" O4 NAG C 2 " pdb=" C2 MAN C 3 " pdb=" O5 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.36 0.04 2.00e-02 2.50e+03 4.03e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.09e+00 ... (remaining 1622 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 648 " 0.023 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP A 648 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 648 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 648 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 648 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 648 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 648 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 648 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 648 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 648 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 240 " -0.002 2.00e-02 2.50e+03 2.93e-02 1.07e+01 pdb=" CG ASN B 240 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 240 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 240 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 240 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C ASN B 240 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN B 240 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP B 241 " 0.014 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1161 2.74 - 3.28: 11273 3.28 - 3.82: 17886 3.82 - 4.36: 20291 4.36 - 4.90: 33103 Nonbonded interactions: 83714 Sorted by model distance: nonbonded pdb=" OD1 ASP B 304 " pdb=" N ILE B 305 " model vdw 2.206 2.520 nonbonded pdb=" OE1 GLU A1193 " pdb=" F3 ALF A1702 " model vdw 2.216 2.390 nonbonded pdb=" OG1 THR A 718 " pdb=" O ARG A1009 " model vdw 2.218 2.440 nonbonded pdb=" O ARG B 188 " pdb=" OG SER B 192 " model vdw 2.224 2.440 nonbonded pdb=" CG2 THR A1342 " pdb=" O LEU A1346 " model vdw 2.244 3.460 ... (remaining 83709 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 'D' selection = chain 'E' } 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 53 5.16 5 C 6646 2.51 5 N 1690 2.21 5 O 1956 1.98 5 F 4 1.80 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 Write .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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.360 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.090 Process input model: 31.510 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10586 Z= 0.179 Angle : 0.676 15.247 14363 Z= 0.363 Chirality : 0.049 0.824 1625 Planarity : 0.003 0.042 1802 Dihedral : 13.425 143.959 3872 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: -1.25 (0.24), residues: 1267 helix: 0.13 (0.22), residues: 568 sheet: -0.22 (0.42), residues: 143 loop : -2.01 (0.28), residues: 556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2069 time to fit residues: 63.7536 Evaluate side-chains 171 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.0070 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 115 optimal weight: 0.0970 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 10586 Z= 0.153 Angle : 0.561 9.928 14363 Z= 0.279 Chirality : 0.042 0.256 1625 Planarity : 0.003 0.037 1802 Dihedral : 7.211 129.220 1472 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % 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: -1.15 (0.24), residues: 1267 helix: 0.13 (0.22), residues: 576 sheet: -0.21 (0.43), residues: 143 loop : -1.88 (0.28), residues: 548 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.277 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: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1995 time to fit residues: 61.1978 Evaluate side-chains 173 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 115 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN A 942 HIS ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 10586 Z= 0.299 Angle : 0.683 9.732 14363 Z= 0.353 Chirality : 0.046 0.213 1625 Planarity : 0.004 0.042 1802 Dihedral : 7.238 117.719 1472 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer Outliers : 0.09 % 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: -1.34 (0.24), residues: 1267 helix: 0.06 (0.22), residues: 574 sheet: -0.43 (0.41), residues: 143 loop : -2.05 (0.27), residues: 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.267 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: 1 residues processed: 199 average time/residue: 0.1982 time to fit residues: 58.0647 Evaluate side-chains 157 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0943 time to fit residues: 1.8801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 GLN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 10586 Z= 0.232 Angle : 0.624 9.186 14363 Z= 0.317 Chirality : 0.044 0.161 1625 Planarity : 0.004 0.044 1802 Dihedral : 7.104 114.736 1472 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.09 % 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: -1.29 (0.24), residues: 1267 helix: 0.14 (0.22), residues: 569 sheet: -0.46 (0.42), residues: 143 loop : -2.03 (0.27), residues: 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.344 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: 198 average time/residue: 0.1990 time to fit residues: 58.0544 Evaluate side-chains 160 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.0770 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 110 optimal weight: 0.2980 chunk 30 optimal weight: 20.0000 overall best weight: 5.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1297 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.089 10586 Z= 0.432 Angle : 0.807 10.918 14363 Z= 0.420 Chirality : 0.048 0.177 1625 Planarity : 0.005 0.057 1802 Dihedral : 7.579 113.164 1472 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 29.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer Outliers : 0.09 % 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: -1.66 (0.23), residues: 1267 helix: -0.18 (0.21), residues: 572 sheet: -0.69 (0.41), residues: 143 loop : -2.21 (0.26), residues: 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.312 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: 1 outliers final: 1 residues processed: 189 average time/residue: 0.1975 time to fit residues: 55.1661 Evaluate side-chains 148 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.363 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1474 time to fit residues: 2.0271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 0.0980 chunk 30 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN A1297 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10586 Z= 0.244 Angle : 0.680 10.578 14363 Z= 0.346 Chirality : 0.046 0.208 1625 Planarity : 0.004 0.054 1802 Dihedral : 7.313 111.957 1472 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % 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: -1.54 (0.24), residues: 1267 helix: -0.16 (0.21), residues: 581 sheet: -0.52 (0.41), residues: 143 loop : -2.11 (0.28), residues: 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.304 Fit side-chains 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: 199 average time/residue: 0.2067 time to fit residues: 60.3805 Evaluate side-chains 161 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10586 Z= 0.164 Angle : 0.633 11.220 14363 Z= 0.315 Chirality : 0.043 0.155 1625 Planarity : 0.004 0.043 1802 Dihedral : 6.940 106.601 1472 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % 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: -1.19 (0.24), residues: 1267 helix: 0.10 (0.22), residues: 559 sheet: -0.49 (0.42), residues: 148 loop : -1.78 (0.28), residues: 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.253 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: 204 average time/residue: 0.1950 time to fit residues: 59.3327 Evaluate side-chains 164 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 0.0470 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 10586 Z= 0.219 Angle : 0.652 11.092 14363 Z= 0.327 Chirality : 0.044 0.166 1625 Planarity : 0.004 0.039 1802 Dihedral : 6.876 99.222 1472 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: -1.14 (0.24), residues: 1267 helix: 0.18 (0.22), residues: 560 sheet: -0.47 (0.42), residues: 148 loop : -1.80 (0.28), residues: 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.169 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: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1987 time to fit residues: 57.7610 Evaluate side-chains 157 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.0370 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10586 Z= 0.177 Angle : 0.650 11.335 14363 Z= 0.324 Chirality : 0.044 0.176 1625 Planarity : 0.004 0.039 1802 Dihedral : 6.754 90.873 1472 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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: -1.15 (0.24), residues: 1267 helix: 0.16 (0.22), residues: 554 sheet: -0.45 (0.42), residues: 148 loop : -1.78 (0.28), residues: 565 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.277 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: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2016 time to fit residues: 59.6431 Evaluate side-chains 163 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 116 optimal weight: 0.0470 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1233 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 10586 Z= 0.168 Angle : 0.669 11.753 14363 Z= 0.328 Chirality : 0.044 0.165 1625 Planarity : 0.004 0.039 1802 Dihedral : 6.482 86.464 1472 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: -1.09 (0.24), residues: 1267 helix: 0.20 (0.22), residues: 550 sheet: -0.41 (0.42), residues: 148 loop : -1.73 (0.28), residues: 569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.237 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: 199 average time/residue: 0.1972 time to fit residues: 58.8058 Evaluate side-chains 167 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 92 optimal weight: 0.0770 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.097925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075240 restraints weight = 44819.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.077784 restraints weight = 26260.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.079616 restraints weight = 18079.283| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 10586 Z= 0.279 Angle : 0.702 10.810 14363 Z= 0.358 Chirality : 0.046 0.235 1625 Planarity : 0.004 0.042 1802 Dihedral : 6.641 89.794 1472 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % 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 (0.24), residues: 1267 helix: 0.18 (0.22), residues: 554 sheet: -0.50 (0.42), residues: 148 loop : -1.86 (0.27), residues: 565 =============================================================================== Job complete usr+sys time: 2272.31 seconds wall clock time: 43 minutes 44.16 seconds (2624.16 seconds total)