Starting phenix.real_space_refine on Fri Mar 15 02:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/03_2024/7ky9_23072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/03_2024/7ky9_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_23072/03_2024/7ky9_23072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/03_2024/7ky9_23072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/03_2024/7ky9_23072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky9_23072/03_2024/7ky9_23072_updated.pdb" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 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. Process input model Symmetric amino acids flipped Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ASP 780": "OD1" <-> "OD2" Residue "A PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ASP 1012": "OD1" <-> "OD2" Residue "A GLU 1023": "OE1" <-> "OE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1099": "OE1" <-> "OE2" Residue "A GLU 1128": "OE1" <-> "OE2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1147": "NH1" <-> "NH2" Residue "A GLU 1194": "OE1" <-> "OE2" Residue "A ARG 1196": "NH1" <-> "NH2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A GLU 1229": "OE1" <-> "OE2" Residue "A PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1300": "NH1" <-> "NH2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A PHE 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1351": "NH1" <-> "NH2" Residue "A PHE 1353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1373": "OE1" <-> "OE2" Residue "A TYR 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1376": "NH1" <-> "NH2" Residue "A GLU 1407": "OE1" <-> "OE2" Residue "A TYR 1409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A PHE 1431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1436": "NH1" <-> "NH2" Residue "A PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A TYR 1447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1455": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 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: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.30, per 1000 atoms: 0.61 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 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=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: 4.66 Conformation dependent library (CDL) restraints added in 1.8 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: 2.25 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: 3.75 Time building geometry restraints manager: 5.02 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=" F1 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F4 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.686 1.785 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" F3 ALF A1702 " pdb="AL ALF A1702 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C5 MAN C 3 " pdb=" O5 MAN C 3 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.61e+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=" F1 ALF A1702 " pdb="AL ALF A1702 " pdb=" F2 ALF A1702 " ideal model delta sigma weight residual 108.68 179.87 -71.19 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F3 ALF A1702 " pdb="AL ALF A1702 " pdb=" F4 ALF A1702 " ideal model delta sigma weight residual 109.63 179.94 -70.31 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " pdb=" F4 ALF A1702 " ideal model delta sigma weight residual 110.21 90.13 20.08 3.00e+00 1.11e-01 4.48e+01 angle pdb=" F2 ALF A1702 " pdb="AL ALF A1702 " pdb=" F3 ALF A1702 " ideal model delta sigma weight residual 109.59 89.89 19.70 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F1 ALF A1702 " pdb="AL ALF A1702 " pdb=" F3 ALF A1702 " ideal model delta sigma weight residual 109.69 90.00 19.69 3.00e+00 1.11e-01 4.31e+01 ... (remaining 14358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 6163 28.79 - 57.58: 208 57.58 - 86.38: 18 86.38 - 115.17: 5 115.17 - 143.96: 2 Dihedral angle restraints: 6396 sinusoidal: 2679 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 6393 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.020 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.920 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.004 0.101 10586 Z= 0.254 Angle : 1.140 71.188 14363 Z= 0.474 Chirality : 0.049 0.824 1625 Planarity : 0.003 0.042 1802 Dihedral : 14.166 143.959 4006 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 % Allowed : 0.63 % Favored : 99.37 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 648 HIS 0.008 0.001 HIS B 363 PHE 0.027 0.002 PHE A1437 TYR 0.022 0.002 TYR B 79 ARG 0.019 0.001 ARG A1130 *********************** 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 : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 MET cc_start: -0.0507 (tmm) cc_final: -0.0782 (tmm) REVERT: A 784 PHE cc_start: 0.8947 (p90) cc_final: 0.8497 (t80) REVERT: A 1130 ARG cc_start: 0.9604 (ptp90) cc_final: 0.9308 (ptp90) REVERT: A 1200 MET cc_start: 0.9229 (mpp) cc_final: 0.8903 (mpp) REVERT: A 1213 THR cc_start: 0.8914 (m) cc_final: 0.8662 (t) REVERT: A 1421 TYR cc_start: 0.7916 (t80) cc_final: 0.7499 (t80) REVERT: A 1457 MET cc_start: 0.9097 (ppp) cc_final: 0.8592 (ppp) REVERT: B 179 LEU cc_start: 0.8636 (mp) cc_final: 0.8370 (mp) REVERT: B 182 PHE cc_start: 0.8497 (t80) cc_final: 0.7809 (t80) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2082 time to fit residues: 63.3382 Evaluate side-chains 171 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 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: 1.0798 ------------------------------------------------------------------------------- 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: 0.7242 moved from start: 0.0734 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= 0.154 Angle : 0.578 10.349 14363 Z= 0.282 Chirality : 0.042 0.168 1625 Planarity : 0.003 0.037 1802 Dihedral : 8.609 130.343 1606 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.44 % 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: -1.17 (0.24), residues: 1267 helix: 0.14 (0.22), residues: 574 sheet: -0.22 (0.43), residues: 143 loop : -1.94 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 648 HIS 0.003 0.001 HIS A 942 PHE 0.016 0.001 PHE A1330 TYR 0.018 0.001 TYR A 678 ARG 0.003 0.000 ARG A1130 *********************** 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: 1 poor density : 208 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 PHE cc_start: 0.8950 (p90) cc_final: 0.8481 (t80) REVERT: A 791 PHE cc_start: 0.8256 (t80) cc_final: 0.8021 (t80) REVERT: A 1111 PHE cc_start: 0.9442 (m-10) cc_final: 0.9116 (m-80) REVERT: A 1213 THR cc_start: 0.8970 (m) cc_final: 0.8726 (t) REVERT: A 1238 ASN cc_start: 0.8519 (t0) cc_final: 0.8181 (t0) REVERT: A 1317 MET cc_start: 0.8236 (ttp) cc_final: 0.8020 (tmm) REVERT: A 1329 PHE cc_start: 0.7695 (m-10) cc_final: 0.7383 (m-80) REVERT: A 1421 TYR cc_start: 0.8039 (t80) cc_final: 0.7552 (t80) REVERT: A 1457 MET cc_start: 0.9103 (ppp) cc_final: 0.8562 (ppp) REVERT: B 169 MET cc_start: 0.9041 (mmp) cc_final: 0.8724 (tpp) REVERT: B 181 LYS cc_start: 0.8921 (tmmt) cc_final: 0.8367 (tmtt) REVERT: B 182 PHE cc_start: 0.8679 (t80) cc_final: 0.7883 (t80) REVERT: B 333 ASP cc_start: 0.8634 (m-30) cc_final: 0.8359 (m-30) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2043 time to fit residues: 62.7092 Evaluate side-chains 170 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN A 942 HIS A 982 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10586 Z= 0.348 Angle : 0.727 9.781 14363 Z= 0.372 Chirality : 0.046 0.169 1625 Planarity : 0.005 0.045 1802 Dihedral : 8.207 119.381 1606 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: -1.37 (0.24), residues: 1267 helix: 0.05 (0.22), residues: 571 sheet: -0.54 (0.41), residues: 144 loop : -2.04 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1399 HIS 0.009 0.002 HIS A1350 PHE 0.028 0.002 PHE A1426 TYR 0.026 0.002 TYR B 278 ARG 0.010 0.001 ARG B 162 *********************** 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 197 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 PHE cc_start: 0.9034 (p90) cc_final: 0.8509 (t80) REVERT: A 1199 VAL cc_start: 0.8957 (m) cc_final: 0.8706 (m) REVERT: A 1213 THR cc_start: 0.9251 (m) cc_final: 0.9025 (t) REVERT: A 1238 ASN cc_start: 0.8566 (t0) cc_final: 0.8274 (t0) REVERT: A 1254 PHE cc_start: 0.8648 (m-80) cc_final: 0.7892 (t80) REVERT: A 1255 ASP cc_start: 0.7970 (t0) cc_final: 0.7691 (t0) REVERT: A 1299 TYR cc_start: 0.9134 (t80) cc_final: 0.8655 (t80) REVERT: A 1303 ILE cc_start: 0.9418 (mm) cc_final: 0.9169 (mm) REVERT: A 1457 MET cc_start: 0.9137 (ppp) cc_final: 0.8883 (ppp) REVERT: B 173 VAL cc_start: 0.9568 (t) cc_final: 0.9366 (t) REVERT: B 176 ASN cc_start: 0.9333 (m-40) cc_final: 0.9030 (m-40) REVERT: B 182 PHE cc_start: 0.8831 (t80) cc_final: 0.8132 (t80) REVERT: B 239 PHE cc_start: 0.8261 (t80) cc_final: 0.8027 (t80) REVERT: B 333 ASP cc_start: 0.8897 (m-30) cc_final: 0.8597 (m-30) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2058 time to fit residues: 59.6452 Evaluate side-chains 158 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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: 9.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10586 Z= 0.269 Angle : 0.649 8.988 14363 Z= 0.331 Chirality : 0.045 0.147 1625 Planarity : 0.004 0.048 1802 Dihedral : 7.744 115.968 1606 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % 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: 0.11 (0.22), residues: 566 sheet: -0.49 (0.41), residues: 143 loop : -1.91 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 308 HIS 0.005 0.001 HIS A1350 PHE 0.021 0.002 PHE A1431 TYR 0.024 0.002 TYR A1316 ARG 0.006 0.001 ARG B 162 *********************** 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 197 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.318 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: A 784 PHE cc_start: 0.8999 (p90) cc_final: 0.8444 (t80) REVERT: A 1199 VAL cc_start: 0.8782 (m) cc_final: 0.8504 (m) REVERT: A 1213 THR cc_start: 0.9201 (m) cc_final: 0.8962 (t) REVERT: A 1254 PHE cc_start: 0.8683 (m-80) cc_final: 0.7810 (t80) REVERT: A 1299 TYR cc_start: 0.9050 (t80) cc_final: 0.8696 (t80) REVERT: A 1303 ILE cc_start: 0.9431 (mm) cc_final: 0.9223 (mm) REVERT: A 1457 MET cc_start: 0.9179 (ppp) cc_final: 0.8925 (ppp) REVERT: B 182 PHE cc_start: 0.8830 (t80) cc_final: 0.7785 (t80) REVERT: B 333 ASP cc_start: 0.8412 (m-30) cc_final: 0.8159 (m-30) REVERT: B 357 LYS cc_start: 0.9193 (pttp) cc_final: 0.8671 (pttp) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2038 time to fit residues: 58.2493 Evaluate side-chains 163 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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: 0.5980 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 110 optimal weight: 0.0030 chunk 30 optimal weight: 20.0000 overall best weight: 3.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10586 Z= 0.317 Angle : 0.708 9.741 14363 Z= 0.364 Chirality : 0.046 0.181 1625 Planarity : 0.004 0.047 1802 Dihedral : 7.757 113.515 1606 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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: -1.43 (0.24), residues: 1267 helix: -0.02 (0.21), residues: 572 sheet: -0.58 (0.41), residues: 144 loop : -2.05 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 266 HIS 0.008 0.002 HIS A1350 PHE 0.032 0.002 PHE A1330 TYR 0.026 0.002 TYR B 378 ARG 0.014 0.001 ARG A1414 *********************** 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 196 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.296 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: A 610 PHE cc_start: 0.7365 (t80) cc_final: 0.7138 (t80) REVERT: A 784 PHE cc_start: 0.8983 (p90) cc_final: 0.8431 (t80) REVERT: A 1199 VAL cc_start: 0.8724 (m) cc_final: 0.8481 (m) REVERT: A 1229 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8508 (tm-30) REVERT: A 1299 TYR cc_start: 0.9075 (t80) cc_final: 0.8645 (t80) REVERT: A 1303 ILE cc_start: 0.9457 (mm) cc_final: 0.9211 (mm) REVERT: A 1457 MET cc_start: 0.9152 (ppp) cc_final: 0.8883 (ppp) REVERT: B 176 ASN cc_start: 0.9244 (m-40) cc_final: 0.8928 (m-40) REVERT: B 182 PHE cc_start: 0.8672 (t80) cc_final: 0.8006 (t80) REVERT: B 257 TYR cc_start: 0.8447 (t80) cc_final: 0.7924 (t80) REVERT: B 326 LEU cc_start: 0.9267 (tp) cc_final: 0.9053 (tp) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2101 time to fit residues: 60.5651 Evaluate side-chains 159 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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: 40.0000 chunk 110 optimal weight: 0.3980 chunk 24 optimal weight: 30.0000 chunk 72 optimal weight: 0.0970 chunk 30 optimal weight: 30.0000 chunk 122 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- 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** ** 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 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: 0.7374 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10586 Z= 0.189 Angle : 0.636 10.853 14363 Z= 0.319 Chirality : 0.044 0.201 1625 Planarity : 0.004 0.042 1802 Dihedral : 7.242 110.221 1606 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -1.17 (0.24), residues: 1267 helix: 0.19 (0.22), residues: 555 sheet: -0.41 (0.42), residues: 143 loop : -1.86 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 308 HIS 0.002 0.001 HIS A1104 PHE 0.016 0.002 PHE A1431 TYR 0.021 0.002 TYR A 678 ARG 0.005 0.000 ARG B 187 *********************** 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 202 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.156 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: A 610 PHE cc_start: 0.7329 (t80) cc_final: 0.7094 (t80) REVERT: A 784 PHE cc_start: 0.8990 (p90) cc_final: 0.8417 (t80) REVERT: A 1180 MET cc_start: 0.8244 (mmp) cc_final: 0.8006 (mmm) REVERT: A 1213 THR cc_start: 0.9160 (m) cc_final: 0.8937 (t) REVERT: A 1299 TYR cc_start: 0.8959 (t80) cc_final: 0.8640 (t80) REVERT: A 1313 PHE cc_start: 0.6935 (m-10) cc_final: 0.6709 (m-10) REVERT: A 1457 MET cc_start: 0.9131 (ppp) cc_final: 0.8833 (ppp) REVERT: B 172 ASN cc_start: 0.9160 (t0) cc_final: 0.8811 (t0) REVERT: B 182 PHE cc_start: 0.8665 (t80) cc_final: 0.7967 (t80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1969 time to fit residues: 57.7722 Evaluate side-chains 166 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10586 Z= 0.167 Angle : 0.630 11.201 14363 Z= 0.312 Chirality : 0.044 0.176 1625 Planarity : 0.004 0.038 1802 Dihedral : 6.832 103.075 1606 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.18 (0.24), residues: 1267 helix: 0.08 (0.22), residues: 567 sheet: -0.42 (0.41), residues: 148 loop : -1.79 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1308 HIS 0.002 0.001 HIS A1104 PHE 0.032 0.001 PHE A1330 TYR 0.027 0.001 TYR B 278 ARG 0.003 0.000 ARG A1130 *********************** 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 : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7413 (t80) cc_final: 0.7151 (t80) REVERT: A 706 ILE cc_start: 0.8377 (mm) cc_final: 0.8111 (tp) REVERT: A 784 PHE cc_start: 0.8984 (p90) cc_final: 0.8405 (t80) REVERT: A 1200 MET cc_start: 0.9224 (mmp) cc_final: 0.8957 (mmm) REVERT: A 1213 THR cc_start: 0.9171 (m) cc_final: 0.8968 (t) REVERT: A 1299 TYR cc_start: 0.8937 (t80) cc_final: 0.8608 (t80) REVERT: A 1380 PHE cc_start: 0.8621 (t80) cc_final: 0.8166 (t80) REVERT: A 1457 MET cc_start: 0.9070 (ppp) cc_final: 0.8783 (ppp) REVERT: B 172 ASN cc_start: 0.9127 (t0) cc_final: 0.8714 (t0) REVERT: B 182 PHE cc_start: 0.8624 (t80) cc_final: 0.8009 (t80) REVERT: B 189 TYR cc_start: 0.8144 (t80) cc_final: 0.7912 (t80) REVERT: B 257 TYR cc_start: 0.8443 (t80) cc_final: 0.7957 (t80) REVERT: B 357 LYS cc_start: 0.9147 (pttp) cc_final: 0.8685 (pttp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2011 time to fit residues: 59.9972 Evaluate side-chains 160 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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: 0.2980 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 0.0870 chunk 77 optimal weight: 0.0970 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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** ** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10586 Z= 0.147 Angle : 0.648 11.731 14363 Z= 0.315 Chirality : 0.044 0.175 1625 Planarity : 0.004 0.036 1802 Dihedral : 6.355 91.486 1606 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: -1.04 (0.24), residues: 1267 helix: 0.19 (0.22), residues: 558 sheet: -0.34 (0.42), residues: 146 loop : -1.68 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1308 HIS 0.002 0.000 HIS B 363 PHE 0.041 0.001 PHE A1426 TYR 0.028 0.001 TYR B 278 ARG 0.007 0.000 ARG A1414 *********************** 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 202 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7385 (t80) cc_final: 0.7126 (t80) REVERT: A 653 LEU cc_start: 0.7738 (mt) cc_final: 0.7491 (mt) REVERT: A 706 ILE cc_start: 0.8392 (mm) cc_final: 0.8151 (tp) REVERT: A 784 PHE cc_start: 0.9001 (p90) cc_final: 0.8443 (t80) REVERT: A 1136 LEU cc_start: 0.9540 (pp) cc_final: 0.9155 (tp) REVERT: A 1200 MET cc_start: 0.9212 (mmp) cc_final: 0.8943 (mmm) REVERT: A 1213 THR cc_start: 0.9166 (m) cc_final: 0.8963 (t) REVERT: A 1229 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 1255 ASP cc_start: 0.7697 (t0) cc_final: 0.7459 (t0) REVERT: A 1299 TYR cc_start: 0.8924 (t80) cc_final: 0.8675 (t80) REVERT: A 1380 PHE cc_start: 0.8720 (t80) cc_final: 0.8141 (t80) REVERT: A 1457 MET cc_start: 0.9078 (ppp) cc_final: 0.8780 (ppp) REVERT: B 181 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7278 (tmtt) REVERT: B 182 PHE cc_start: 0.8558 (t80) cc_final: 0.7940 (t80) REVERT: B 189 TYR cc_start: 0.8102 (t80) cc_final: 0.7877 (t80) REVERT: B 357 LYS cc_start: 0.9132 (pttp) cc_final: 0.8635 (pttp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2001 time to fit residues: 59.6861 Evaluate side-chains 164 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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: 0.4980 chunk 117 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 0.4980 chunk 68 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10586 Z= 0.162 Angle : 0.640 11.482 14363 Z= 0.311 Chirality : 0.044 0.279 1625 Planarity : 0.003 0.036 1802 Dihedral : 5.988 79.276 1606 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -1.08 (0.24), residues: 1267 helix: 0.23 (0.22), residues: 558 sheet: -0.38 (0.41), residues: 148 loop : -1.79 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1308 HIS 0.002 0.000 HIS B 363 PHE 0.028 0.001 PHE A1313 TYR 0.015 0.001 TYR A 678 ARG 0.003 0.000 ARG A1130 *********************** 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 201 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7381 (t80) cc_final: 0.7122 (t80) REVERT: A 706 ILE cc_start: 0.8378 (mm) cc_final: 0.8119 (tp) REVERT: A 784 PHE cc_start: 0.9003 (p90) cc_final: 0.8446 (t80) REVERT: A 1136 LEU cc_start: 0.9544 (pp) cc_final: 0.9228 (tp) REVERT: A 1200 MET cc_start: 0.9231 (mmp) cc_final: 0.8977 (mmm) REVERT: A 1213 THR cc_start: 0.9171 (m) cc_final: 0.8960 (t) REVERT: A 1229 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 1255 ASP cc_start: 0.7790 (t0) cc_final: 0.7458 (t0) REVERT: A 1299 TYR cc_start: 0.8905 (t80) cc_final: 0.8652 (t80) REVERT: A 1380 PHE cc_start: 0.8531 (t80) cc_final: 0.8092 (t80) REVERT: A 1457 MET cc_start: 0.9069 (ppp) cc_final: 0.8766 (ppp) REVERT: B 111 MET cc_start: 0.9048 (ppp) cc_final: 0.8756 (ppp) REVERT: B 182 PHE cc_start: 0.8539 (t80) cc_final: 0.7956 (t80) REVERT: B 189 TYR cc_start: 0.8049 (t80) cc_final: 0.7838 (t80) REVERT: B 357 LYS cc_start: 0.9177 (pttp) cc_final: 0.8662 (pttp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1995 time to fit residues: 59.3590 Evaluate side-chains 167 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 4.9990 chunk 120 optimal weight: 8.9990 chunk 73 optimal weight: 0.0970 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10586 Z= 0.147 Angle : 0.644 11.692 14363 Z= 0.310 Chirality : 0.044 0.147 1625 Planarity : 0.003 0.039 1802 Dihedral : 5.434 62.425 1606 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.00 (0.24), residues: 1267 helix: 0.36 (0.22), residues: 545 sheet: -0.32 (0.42), residues: 148 loop : -1.77 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1308 HIS 0.003 0.000 HIS B 363 PHE 0.011 0.001 PHE B 320 TYR 0.017 0.001 TYR A 678 ARG 0.007 0.000 ARG B 199 ********************** 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 201 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.7391 (t80) cc_final: 0.7122 (t80) REVERT: A 706 ILE cc_start: 0.8391 (mm) cc_final: 0.8137 (tp) REVERT: A 784 PHE cc_start: 0.9020 (p90) cc_final: 0.8463 (t80) REVERT: A 1136 LEU cc_start: 0.9534 (pp) cc_final: 0.9222 (tp) REVERT: A 1200 MET cc_start: 0.9220 (mmp) cc_final: 0.8986 (mmm) REVERT: A 1213 THR cc_start: 0.9022 (m) cc_final: 0.8804 (t) REVERT: A 1229 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 1255 ASP cc_start: 0.7633 (t0) cc_final: 0.7394 (t0) REVERT: A 1258 TYR cc_start: 0.7936 (t80) cc_final: 0.7451 (t80) REVERT: A 1299 TYR cc_start: 0.8897 (t80) cc_final: 0.8682 (t80) REVERT: A 1308 TRP cc_start: 0.7470 (t-100) cc_final: 0.7264 (t-100) REVERT: A 1457 MET cc_start: 0.9065 (ppp) cc_final: 0.8750 (ppp) REVERT: B 111 MET cc_start: 0.9052 (ppp) cc_final: 0.8755 (ppp) REVERT: B 181 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7562 (tptt) REVERT: B 182 PHE cc_start: 0.8529 (t80) cc_final: 0.7902 (t80) REVERT: B 189 TYR cc_start: 0.8053 (t80) cc_final: 0.7832 (t80) REVERT: B 357 LYS cc_start: 0.9181 (pttp) cc_final: 0.8660 (pttp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1971 time to fit residues: 59.6687 Evaluate side-chains 174 residues out of total 1113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** ** A1350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.102355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.079697 restraints weight = 42564.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.082210 restraints weight = 25681.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.083834 restraints weight = 17894.362| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10586 Z= 0.193 Angle : 0.648 11.280 14363 Z= 0.317 Chirality : 0.044 0.167 1625 Planarity : 0.004 0.037 1802 Dihedral : 5.112 49.085 1606 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -0.96 (0.24), residues: 1267 helix: 0.33 (0.22), residues: 561 sheet: -0.45 (0.41), residues: 149 loop : -1.69 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1308 HIS 0.003 0.001 HIS A1350 PHE 0.016 0.001 PHE A1384 TYR 0.018 0.001 TYR A 678 ARG 0.007 0.000 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.82 seconds wall clock time: 45 minutes 33.12 seconds (2733.12 seconds total)