Starting phenix.real_space_refine on Fri Jan 19 03:59:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky7_23070/01_2024/7ky7_23070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky7_23070/01_2024/7ky7_23070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky7_23070/01_2024/7ky7_23070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky7_23070/01_2024/7ky7_23070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky7_23070/01_2024/7ky7_23070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ky7_23070/01_2024/7ky7_23070_updated.pdb" } resolution = 3.08 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= 0.003 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 52 5.16 5 C 6683 2.51 5 N 1655 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ASP 702": "OD1" <-> "OD2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ASP 780": "OD1" <-> "OD2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 893": "NH1" <-> "NH2" Residue "A ASP 919": "OD1" <-> "OD2" Residue "A ASP 927": "OD1" <-> "OD2" Residue "A ASP 932": "OD1" <-> "OD2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "A ASP 1052": "OD1" <-> "OD2" Residue "A GLU 1054": "OE1" <-> "OE2" Residue "A GLU 1063": "OE1" <-> "OE2" Residue "A ASP 1064": "OD1" <-> "OD2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A GLU 1095": "OE1" <-> "OE2" Residue "A GLU 1127": "OE1" <-> "OE2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A ARG 1147": "NH1" <-> "NH2" 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 TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1261": "OE1" <-> "OE2" Residue "A ARG 1300": "NH1" <-> "NH2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A TYR 1335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1349": "OD1" <-> "OD2" Residue "A ARG 1351": "NH1" <-> "NH2" Residue "A ARG 1376": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1436": "NH1" <-> "NH2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A GLU 1452": "OE1" <-> "OE2" Residue "A ARG 1455": "NH1" <-> "NH2" Residue "A TYR 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1474": "OD1" <-> "OD2" Residue "B TYR 107": "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 ARG 187": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ASP 343": "OD1" <-> "OD2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10294 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 884, 7031 Classifications: {'peptide': 884} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 858} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2942 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 141 Unusual residues: {' MG': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.11, per 1000 atoms: 0.59 Number of scatterers: 10294 At special positions: 0 Unit cell: (148.176, 128.625, 98.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 Mg 1 11.99 O 1903 8.00 N 1655 7.00 C 6683 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=2.52 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG F 2 " - " MAN F 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN B 256 " " NAG D 1 " - " ASN B 298 " " NAG E 1 " - " ASN B 332 " " NAG F 1 " - " ASN B 240 " Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 1.8 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 7 sheets defined 44.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 283 through 298 Processing helix chain 'A' and resid 589 through 620 Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 641 through 653 Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.908A pdb=" N GLU A 667 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 756 through 778 removed outlier: 3.785A pdb=" N LYS A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 795 through 802 removed outlier: 4.100A pdb=" N LYS A 801 " --> pdb=" O VAL A 797 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 802 " --> pdb=" O GLU A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 821 Processing helix chain 'A' and resid 844 through 855 Processing helix chain 'A' and resid 934 through 949 removed outlier: 3.717A pdb=" N LEU A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 985 through 993 Processing helix chain 'A' and resid 1014 through 1023 Processing helix chain 'A' and resid 1037 through 1045 Processing helix chain 'A' and resid 1072 through 1086 Processing helix chain 'A' and resid 1095 through 1101 Processing helix chain 'A' and resid 1117 through 1121 Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1150 through 1161 Processing helix chain 'A' and resid 1175 through 1181 removed outlier: 3.708A pdb=" N ALA A1179 " --> pdb=" O SER A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1200 No H-bonds generated for 'chain 'A' and resid 1197 through 1200' Processing helix chain 'A' and resid 1210 through 1216 Processing helix chain 'A' and resid 1219 through 1249 Proline residue: A1232 - end of helix removed outlier: 3.911A pdb=" N PHE A1241 " --> pdb=" O LYS A1237 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A1244 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1254 removed outlier: 3.871A pdb=" N PHE A1254 " --> pdb=" O TYR A1251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1251 through 1254' Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 4.588A pdb=" N ASN A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1275 through 1283 Processing helix chain 'A' and resid 1289 through 1294 Processing helix chain 'A' and resid 1296 through 1303 removed outlier: 3.678A pdb=" N ILE A1303 " --> pdb=" O ARG A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1336 Proline residue: A1331 - end of helix Processing helix chain 'A' and resid 1351 through 1372 Processing helix chain 'A' and resid 1381 through 1400 Processing helix chain 'A' and resid 1411 through 1415 Processing helix chain 'A' and resid 1419 through 1446 removed outlier: 3.581A 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 'A' and resid 1462 through 1464 No H-bonds generated for 'chain 'A' and resid 1462 through 1464' Processing helix chain 'B' and resid 72 through 98 removed outlier: 3.774A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Proline residue: B 77 - end of helix removed outlier: 3.698A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 No H-bonds generated for 'chain 'B' and resid 110 through 113' 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 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 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 267 through 271 Processing helix chain 'B' and resid 309 through 314 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 374 through 397 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: 6.846A pdb=" N LYS A1027 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER A 711 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 6.821A 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 735 removed outlier: 6.870A pdb=" N ALA A1005 " --> pdb=" O LYS A 725 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N CYS A 727 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY A1003 " --> pdb=" O CYS A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 729 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU A1001 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 956 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A1003 " --> pdb=" O LEU A 954 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 954 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1005 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ARG A 952 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 870 through 872 Processing sheet with id= D, first strand: chain 'A' and resid 1055 through 1057 removed outlier: 6.783A pdb=" N ALA A1112 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A1142 " --> pdb=" O VAL A1113 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A1115 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 6.219A 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: 6.619A 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 127 through 129 removed outlier: 6.010A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU B 179 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.421A 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 145 378 hydrogen bonds defined for protein. 1074 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: 3.25 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3203 1.34 - 1.46: 2294 1.46 - 1.58: 4965 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 10537 Sorted by residual: bond pdb=" C1 MAN F 3 " pdb=" C2 MAN F 3 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.45e-02 4.76e+03 3.71e+00 bond pdb=" C1 MAN F 3 " pdb=" O5 MAN F 3 " ideal model delta sigma weight residual 1.399 1.433 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" N ASP A1462 " pdb=" CA ASP A1462 " ideal model delta sigma weight residual 1.459 1.477 -0.018 1.17e-02 7.31e+03 2.34e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 10532 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 257 106.51 - 113.40: 5879 113.40 - 120.28: 3953 120.28 - 127.16: 4131 127.16 - 134.05: 103 Bond angle restraints: 14323 Sorted by residual: angle pdb=" N LEU A1164 " pdb=" CA LEU A1164 " pdb=" C LEU A1164 " ideal model delta sigma weight residual 110.91 102.95 7.96 1.17e+00 7.31e-01 4.62e+01 angle pdb=" N ASP B 56 " pdb=" CA ASP B 56 " pdb=" CB ASP B 56 " ideal model delta sigma weight residual 114.10 110.08 4.02 1.00e+00 1.00e+00 1.62e+01 angle pdb=" C GLU B 55 " pdb=" N ASP B 56 " pdb=" CA ASP B 56 " ideal model delta sigma weight residual 126.86 121.69 5.17 1.57e+00 4.06e-01 1.09e+01 angle pdb=" C PHE A1408 " pdb=" N TYR A1409 " pdb=" CA TYR A1409 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 angle pdb=" OG1 THR A 991 " pdb=" CB THR A 991 " pdb=" CG2 THR A 991 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 ... (remaining 14318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.34: 6055 20.34 - 40.68: 501 40.68 - 61.02: 96 61.02 - 81.36: 11 81.36 - 101.71: 15 Dihedral angle restraints: 6678 sinusoidal: 3040 harmonic: 3638 Sorted by residual: dihedral pdb=" CA ASP A1349 " pdb=" C ASP A1349 " pdb=" N HIS A1350 " pdb=" CA HIS A1350 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS B 170 " pdb=" C LYS B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ILE A1250 " pdb=" C ILE A1250 " pdb=" N TYR A1251 " pdb=" CA TYR A1251 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 6675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1473 0.077 - 0.154: 144 0.154 - 0.231: 10 0.231 - 0.308: 7 0.308 - 0.385: 7 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C14 CLR A2005 " pdb=" C13 CLR A2005 " pdb=" C15 CLR A2005 " pdb=" C8 CLR A2005 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C14 CLR B 501 " pdb=" C13 CLR B 501 " pdb=" C15 CLR B 501 " pdb=" C8 CLR B 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C14 CLR B 502 " pdb=" C13 CLR B 502 " pdb=" C15 CLR B 502 " pdb=" C8 CLR B 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1638 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1461 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C GLY A1461 " -0.067 2.00e-02 2.50e+03 pdb=" O GLY A1461 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A1462 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PHE B 398 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE B 398 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY B 399 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 623 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 624 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 624 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 624 " 0.036 5.00e-02 4.00e+02 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 27 2.34 - 2.98: 5495 2.98 - 3.62: 15519 3.62 - 4.26: 25023 4.26 - 4.90: 40756 Nonbonded interactions: 86820 Sorted by model distance: nonbonded pdb=" OG1 THR A 714 " pdb="MG MG A2001 " model vdw 1.705 2.170 nonbonded pdb=" O ASP A1173 " pdb="MG MG A2001 " model vdw 1.938 2.170 nonbonded pdb=" O GLY A1013 " pdb=" OG SER A1017 " model vdw 2.208 2.440 nonbonded pdb=" O PHE A1272 " pdb=" OG SER A1388 " model vdw 2.220 2.440 nonbonded pdb=" O LEU A1136 " pdb=" ND2 ASN A1139 " model vdw 2.228 2.520 ... (remaining 86815 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 'C' and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or n \ ame O7 )) selection = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.370 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.043 10537 Z= 0.262 Angle : 0.705 9.123 14323 Z= 0.354 Chirality : 0.054 0.385 1641 Planarity : 0.003 0.064 1761 Dihedral : 15.490 101.706 4334 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.93 % Rotamer: Outliers : 1.01 % Allowed : 13.22 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.21), residues: 1231 helix: -1.61 (0.19), residues: 559 sheet: -2.24 (0.45), residues: 114 loop : -3.17 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1458 HIS 0.002 0.001 HIS A1336 PHE 0.023 0.001 PHE A1408 TYR 0.017 0.001 TYR B 280 ARG 0.003 0.000 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.078 Fit side-chains REVERT: A 647 PHE cc_start: 0.7965 (t80) cc_final: 0.7726 (t80) REVERT: A 894 MET cc_start: -0.0872 (pmm) cc_final: -0.2393 (tmm) REVERT: A 1095 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 1108 GLN cc_start: 0.7037 (mp10) cc_final: 0.6756 (mp10) REVERT: A 1129 MET cc_start: 0.8895 (tpp) cc_final: 0.8658 (tpp) outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.2253 time to fit residues: 37.4950 Evaluate side-chains 86 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 810 LYS Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN A 719 GLN A 730 ASN A 808 GLN A 888 ASN A1047 ASN A1051 ASN A1182 GLN A1208 GLN A1219 HIS ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 GLN A1374 GLN B 61 GLN B 97 ASN B 131 HIS ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10537 Z= 0.423 Angle : 0.672 10.837 14323 Z= 0.332 Chirality : 0.047 0.207 1641 Planarity : 0.004 0.072 1761 Dihedral : 9.820 79.414 2000 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.47 % Favored : 92.45 % Rotamer: Outliers : 3.31 % Allowed : 17.17 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.23), residues: 1231 helix: -0.73 (0.21), residues: 568 sheet: -1.87 (0.49), residues: 104 loop : -2.88 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1458 HIS 0.005 0.001 HIS A1336 PHE 0.026 0.002 PHE A1408 TYR 0.026 0.002 TYR A1409 ARG 0.003 0.000 ARG A1414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 83 time to evaluate : 1.125 Fit side-chains REVERT: A 647 PHE cc_start: 0.7967 (t80) cc_final: 0.7667 (t80) REVERT: A 706 ILE cc_start: 0.8667 (mm) cc_final: 0.8394 (mm) REVERT: A 894 MET cc_start: -0.0773 (pmm) cc_final: -0.2506 (tmm) REVERT: A 1108 GLN cc_start: 0.7166 (mp10) cc_final: 0.6865 (mp10) REVERT: A 1129 MET cc_start: 0.8992 (tpp) cc_final: 0.8748 (tpp) REVERT: A 1445 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7301 (mp) REVERT: B 113 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7360 (t0) outliers start: 36 outliers final: 18 residues processed: 111 average time/residue: 0.1947 time to fit residues: 32.6750 Evaluate side-chains 97 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1379 TRP Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN A 807 HIS ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10537 Z= 0.201 Angle : 0.575 11.287 14323 Z= 0.286 Chirality : 0.043 0.237 1641 Planarity : 0.004 0.072 1761 Dihedral : 9.133 69.588 1995 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.39 % Allowed : 20.57 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 1231 helix: -0.28 (0.22), residues: 569 sheet: -1.72 (0.48), residues: 114 loop : -2.64 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1458 HIS 0.002 0.001 HIS A1336 PHE 0.023 0.001 PHE A1408 TYR 0.019 0.001 TYR A1332 ARG 0.002 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 1.026 Fit side-chains REVERT: A 625 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6812 (mtt-85) REVERT: A 647 PHE cc_start: 0.7972 (t80) cc_final: 0.7736 (t80) REVERT: A 745 LEU cc_start: 0.7894 (mt) cc_final: 0.7684 (pp) REVERT: A 1108 GLN cc_start: 0.7045 (mp10) cc_final: 0.6746 (mp10) REVERT: A 1129 MET cc_start: 0.8998 (tpp) cc_final: 0.8782 (tpp) REVERT: A 1270 LEU cc_start: 0.8347 (mp) cc_final: 0.8146 (mt) REVERT: B 113 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7301 (t0) REVERT: B 388 MET cc_start: 0.7133 (mmt) cc_final: 0.6847 (mmm) outliers start: 26 outliers final: 15 residues processed: 100 average time/residue: 0.2026 time to fit residues: 30.3120 Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1391 VAL Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 876 GLN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10537 Z= 0.329 Angle : 0.616 9.690 14323 Z= 0.306 Chirality : 0.045 0.214 1641 Planarity : 0.004 0.072 1761 Dihedral : 8.650 59.141 1995 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.07 % Favored : 92.85 % Rotamer: Outliers : 3.12 % Allowed : 20.48 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.93 (0.24), residues: 1231 helix: -0.05 (0.22), residues: 561 sheet: -1.63 (0.48), residues: 115 loop : -2.54 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1458 HIS 0.003 0.001 HIS A1336 PHE 0.025 0.002 PHE A1408 TYR 0.024 0.002 TYR A1409 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 77 time to evaluate : 1.443 Fit side-chains REVERT: A 619 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8579 (t80) REVERT: A 625 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6896 (mtt-85) REVERT: A 647 PHE cc_start: 0.7977 (t80) cc_final: 0.7675 (t80) REVERT: A 653 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7316 (tt) REVERT: A 1108 GLN cc_start: 0.7136 (mp10) cc_final: 0.6825 (mp10) REVERT: A 1129 MET cc_start: 0.9027 (tpp) cc_final: 0.8811 (tpp) REVERT: A 1270 LEU cc_start: 0.8427 (mp) cc_final: 0.8219 (mt) REVERT: B 113 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7315 (t0) REVERT: B 388 MET cc_start: 0.7262 (mmt) cc_final: 0.6950 (mmm) outliers start: 34 outliers final: 19 residues processed: 107 average time/residue: 0.2218 time to fit residues: 36.4142 Evaluate side-chains 101 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1338 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10537 Z= 0.196 Angle : 0.562 8.540 14323 Z= 0.281 Chirality : 0.042 0.212 1641 Planarity : 0.003 0.072 1761 Dihedral : 8.121 59.880 1995 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.94 % Allowed : 21.12 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.68 (0.24), residues: 1231 helix: 0.16 (0.22), residues: 564 sheet: -1.51 (0.48), residues: 115 loop : -2.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1458 HIS 0.006 0.001 HIS A 942 PHE 0.022 0.001 PHE A1408 TYR 0.028 0.001 TYR B 136 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 1.212 Fit side-chains REVERT: A 647 PHE cc_start: 0.7946 (t80) cc_final: 0.7661 (t80) REVERT: A 653 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7220 (tt) REVERT: A 1108 GLN cc_start: 0.7073 (mp10) cc_final: 0.6753 (mp10) REVERT: A 1129 MET cc_start: 0.8992 (tpp) cc_final: 0.8775 (tpp) REVERT: A 1450 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: B 113 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7296 (t0) REVERT: B 348 TRP cc_start: 0.9159 (OUTLIER) cc_final: 0.8637 (t60) REVERT: B 388 MET cc_start: 0.7238 (mmt) cc_final: 0.6940 (mmm) outliers start: 32 outliers final: 17 residues processed: 107 average time/residue: 0.1988 time to fit residues: 32.5296 Evaluate side-chains 97 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1309 ASN Chi-restraints excluded: chain A residue 1338 ASN Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 20.0000 chunk 107 optimal weight: 0.0170 chunk 23 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1338 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.185 Angle : 0.554 7.959 14323 Z= 0.277 Chirality : 0.042 0.187 1641 Planarity : 0.004 0.069 1761 Dihedral : 7.806 59.531 1993 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.75 % Allowed : 21.49 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.53 (0.24), residues: 1231 helix: 0.28 (0.22), residues: 567 sheet: -1.34 (0.49), residues: 115 loop : -2.38 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1458 HIS 0.002 0.000 HIS A1336 PHE 0.022 0.001 PHE A1408 TYR 0.030 0.001 TYR B 136 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 1.006 Fit side-chains REVERT: A 625 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6805 (mtt-85) REVERT: A 647 PHE cc_start: 0.7944 (t80) cc_final: 0.7667 (t80) REVERT: A 1108 GLN cc_start: 0.7021 (mp10) cc_final: 0.6713 (mp10) REVERT: A 1129 MET cc_start: 0.8988 (tpp) cc_final: 0.8772 (tpp) REVERT: A 1450 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: B 113 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7285 (t0) REVERT: B 388 MET cc_start: 0.7245 (mmt) cc_final: 0.6948 (mmm) outliers start: 30 outliers final: 19 residues processed: 102 average time/residue: 0.1909 time to fit residues: 29.3054 Evaluate side-chains 97 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1338 ASN Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.166 Angle : 0.551 10.171 14323 Z= 0.275 Chirality : 0.041 0.169 1641 Planarity : 0.003 0.069 1761 Dihedral : 7.580 58.323 1993 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.94 % Allowed : 20.84 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1231 helix: 0.33 (0.22), residues: 567 sheet: -1.18 (0.50), residues: 115 loop : -2.31 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1458 HIS 0.001 0.000 HIS A1336 PHE 0.022 0.001 PHE A1408 TYR 0.032 0.001 TYR B 136 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 1.283 Fit side-chains REVERT: A 625 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6752 (mtt-85) REVERT: A 647 PHE cc_start: 0.7954 (t80) cc_final: 0.7670 (t80) REVERT: A 799 ASP cc_start: 0.3858 (OUTLIER) cc_final: 0.3323 (p0) REVERT: A 1108 GLN cc_start: 0.6997 (mp10) cc_final: 0.6668 (mp10) REVERT: A 1129 MET cc_start: 0.8976 (tpp) cc_final: 0.8775 (tpp) REVERT: A 1450 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: B 113 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7269 (t0) REVERT: B 348 TRP cc_start: 0.9159 (OUTLIER) cc_final: 0.8519 (t60) REVERT: B 388 MET cc_start: 0.7243 (mmt) cc_final: 0.6956 (mmm) REVERT: B 397 LEU cc_start: 0.7562 (tt) cc_final: 0.6837 (mt) outliers start: 32 outliers final: 20 residues processed: 103 average time/residue: 0.2064 time to fit residues: 32.0668 Evaluate side-chains 97 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1338 ASN Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 75 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.199 Angle : 0.548 7.225 14323 Z= 0.277 Chirality : 0.042 0.171 1641 Planarity : 0.004 0.068 1761 Dihedral : 7.398 56.751 1993 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.85 % Allowed : 21.30 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1231 helix: 0.36 (0.22), residues: 573 sheet: -0.80 (0.57), residues: 92 loop : -2.34 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1458 HIS 0.002 0.001 HIS A 942 PHE 0.023 0.001 PHE A1408 TYR 0.033 0.001 TYR B 136 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 1.253 Fit side-chains REVERT: A 625 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6793 (mtt-85) REVERT: A 799 ASP cc_start: 0.3766 (OUTLIER) cc_final: 0.3146 (p0) REVERT: A 952 ARG cc_start: 0.8233 (mmt-90) cc_final: 0.7166 (mmm160) REVERT: A 1108 GLN cc_start: 0.7009 (mp10) cc_final: 0.6680 (mp10) REVERT: A 1299 TYR cc_start: 0.8526 (t80) cc_final: 0.8123 (t80) REVERT: B 113 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7299 (t0) REVERT: B 348 TRP cc_start: 0.9164 (OUTLIER) cc_final: 0.8505 (t60) REVERT: B 388 MET cc_start: 0.7257 (mmt) cc_final: 0.6937 (mmm) REVERT: B 397 LEU cc_start: 0.7525 (tt) cc_final: 0.6810 (mt) outliers start: 31 outliers final: 19 residues processed: 107 average time/residue: 0.2170 time to fit residues: 34.4453 Evaluate side-chains 94 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.0060 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A1252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10537 Z= 0.169 Angle : 0.537 7.209 14323 Z= 0.274 Chirality : 0.041 0.177 1641 Planarity : 0.003 0.070 1761 Dihedral : 7.285 59.212 1993 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.57 % Allowed : 21.67 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -1.23 (0.24), residues: 1231 helix: 0.47 (0.22), residues: 574 sheet: -0.66 (0.57), residues: 92 loop : -2.28 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 411 HIS 0.001 0.000 HIS A1336 PHE 0.027 0.001 PHE A 647 TYR 0.034 0.001 TYR B 136 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 1.085 Fit side-chains REVERT: A 625 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6819 (mtt-85) REVERT: A 799 ASP cc_start: 0.3745 (OUTLIER) cc_final: 0.3129 (p0) REVERT: A 952 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.7201 (mmm160) REVERT: A 1108 GLN cc_start: 0.6987 (mp10) cc_final: 0.6660 (mp10) REVERT: A 1299 TYR cc_start: 0.8462 (t80) cc_final: 0.8097 (t80) REVERT: B 113 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7289 (t0) REVERT: B 348 TRP cc_start: 0.9129 (OUTLIER) cc_final: 0.8491 (t60) REVERT: B 376 ILE cc_start: 0.8503 (mt) cc_final: 0.8278 (mt) REVERT: B 388 MET cc_start: 0.7225 (mmt) cc_final: 0.6904 (mmm) REVERT: B 397 LEU cc_start: 0.7501 (tt) cc_final: 0.6794 (mt) outliers start: 28 outliers final: 21 residues processed: 101 average time/residue: 0.2176 time to fit residues: 32.6057 Evaluate side-chains 95 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1044 PHE Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1176 ASN Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1371 PHE Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 401 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6672 > 50: distance: 153 - 157: 34.576 distance: 157 - 158: 41.743 distance: 158 - 159: 48.938 distance: 158 - 161: 15.316 distance: 159 - 160: 39.150 distance: 159 - 166: 39.813 distance: 162 - 163: 40.067 distance: 164 - 165: 41.062 distance: 167 - 168: 40.129 distance: 168 - 171: 39.313 distance: 171 - 172: 41.114 distance: 172 - 175: 55.779 distance: 173 - 178: 38.840 distance: 175 - 176: 56.901 distance: 175 - 177: 39.753 distance: 178 - 179: 56.546 distance: 179 - 180: 56.910 distance: 179 - 182: 7.212 distance: 182 - 183: 32.911 distance: 186 - 187: 39.032 distance: 187 - 188: 41.222 distance: 187 - 190: 38.790 distance: 188 - 192: 56.515 distance: 190 - 191: 57.008 distance: 193 - 194: 39.310 distance: 194 - 198: 56.366 distance: 196 - 197: 41.581 distance: 199 - 200: 39.423 distance: 199 - 202: 39.571 distance: 200 - 201: 40.841 distance: 200 - 209: 40.911 distance: 202 - 203: 70.114 distance: 205 - 206: 40.850 distance: 206 - 207: 38.727 distance: 206 - 208: 56.852 distance: 209 - 210: 56.186 distance: 210 - 211: 39.853 distance: 211 - 212: 41.039 distance: 211 - 216: 40.142 distance: 213 - 214: 38.635 distance: 213 - 215: 55.582 distance: 216 - 217: 38.822 distance: 217 - 220: 40.937 distance: 220 - 221: 38.975 distance: 222 - 223: 39.037 distance: 222 - 228: 39.612 distance: 223 - 224: 41.311 distance: 223 - 226: 39.684 distance: 224 - 229: 33.990 distance: 225 - 251: 36.027 distance: 226 - 227: 40.642 distance: 227 - 228: 56.004