Starting phenix.real_space_refine on Sun Jul 21 00:10:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/07_2024/7xmf_33295.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/07_2024/7xmf_33295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/07_2024/7xmf_33295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/07_2024/7xmf_33295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/07_2024/7xmf_33295.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/07_2024/7xmf_33295.cif" } resolution = 3.07 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= 0.026 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 924 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 7690 2.51 5 N 1851 2.21 5 O 2071 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A ASP 812": "OD1" <-> "OD2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A GLU 1195": "OE1" <-> "OE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A GLU 1217": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ASP 1267": "OD1" <-> "OD2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A TYR 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A ASP 1422": "OD1" <-> "OD2" Residue "A PHE 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1471": "OD1" <-> "OD2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A GLU 1477": "OE1" <-> "OE2" Residue "A TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ASP 1582": "OD1" <-> "OD2" Residue "A PHE 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1610": "NH1" <-> "NH2" Residue "A ARG 1613": "NH1" <-> "NH2" Residue "A ARG 1619": "NH1" <-> "NH2" Residue "A ARG 1622": "NH1" <-> "NH2" Residue "A TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A TYR 1739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1761": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11709 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9185 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1108} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'G2W': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.07, per 1000 atoms: 0.60 Number of scatterers: 11709 At special positions: 0 Unit cell: (130, 139.36, 114.4, 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 96 16.00 F 1 9.00 O 2071 8.00 N 1851 7.00 C 7690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.02 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.57 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2301 " - " ASN A1375 " " NAG A2302 " - " ASN A 283 " " NAG B 501 " - " ASN B 93 " " NAG B 502 " - " ASN B 110 " " NAG B 503 " - " ASN B 114 " " NAG B 504 " - " ASN B 135 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 1.9 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 66.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.848A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.070A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 188 through 204 removed outlier: 4.026A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.706A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 268 removed outlier: 3.666A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.707A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 417 removed outlier: 5.174A pdb=" N PHE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 769 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 821 Processing helix chain 'A' and resid 834 through 847 removed outlier: 3.579A pdb=" N PHE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.892A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.101A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.958A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 Processing helix chain 'A' and resid 1176 through 1191 removed outlier: 3.751A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 4.397A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 removed outlier: 4.040A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1290 Processing helix chain 'A' and resid 1291 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.613A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 3.953A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1467 removed outlier: 3.751A pdb=" N PHE A1446 " --> pdb=" O ILE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1487 Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1502 through 1514 Processing helix chain 'A' and resid 1514 through 1534 Processing helix chain 'A' and resid 1540 through 1569 Processing helix chain 'A' and resid 1572 through 1575 removed outlier: 3.712A pdb=" N THR A1575 " --> pdb=" O TYR A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1572 through 1575' Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1616 through 1622 removed outlier: 3.929A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1626 removed outlier: 3.525A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1623 through 1626' Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.550A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.109A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1705 Processing helix chain 'A' and resid 1732 through 1768 Processing helix chain 'B' and resid 153 through 191 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA2, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.946A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 54 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.115A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.302A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 48 757 hydrogen bonds defined for protein. 2172 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: 3.71 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3549 1.35 - 1.51: 4364 1.51 - 1.68: 3915 1.68 - 1.84: 153 1.84 - 2.01: 1 Bond restraints: 11982 Sorted by residual: bond pdb=" C17 G2W A2303 " pdb=" N05 G2W A2303 " ideal model delta sigma weight residual 1.322 1.472 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C17 G2W A2303 " pdb=" N06 G2W A2303 " ideal model delta sigma weight residual 1.334 1.480 -0.146 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C24 G2W A2303 " pdb=" C26 G2W A2303 " ideal model delta sigma weight residual 1.391 1.534 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C21 G2W A2303 " pdb=" C22 G2W A2303 " ideal model delta sigma weight residual 1.379 1.520 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C25 G2W A2303 " pdb=" C27 G2W A2303 " ideal model delta sigma weight residual 1.383 1.523 -0.140 2.00e-02 2.50e+03 4.88e+01 ... (remaining 11977 not shown) Histogram of bond angle deviations from ideal: 81.13 - 92.64: 5 92.64 - 104.15: 147 104.15 - 115.66: 7516 115.66 - 127.17: 8455 127.17 - 138.68: 113 Bond angle restraints: 16236 Sorted by residual: angle pdb=" C ASP A 799 " pdb=" CA ASP A 799 " pdb=" CB ASP A 799 " ideal model delta sigma weight residual 110.17 136.07 -25.90 1.97e+00 2.58e-01 1.73e+02 angle pdb=" N ASP A 799 " pdb=" CA ASP A 799 " pdb=" C ASP A 799 " ideal model delta sigma weight residual 109.81 81.13 28.68 2.21e+00 2.05e-01 1.68e+02 angle pdb=" C MET C 85 " pdb=" CA MET C 85 " pdb=" CB MET C 85 " ideal model delta sigma weight residual 111.23 94.71 16.52 1.63e+00 3.76e-01 1.03e+02 angle pdb=" C ASN C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.66 114.07 5.59 7.20e-01 1.93e+00 6.03e+01 angle pdb=" CA CYS C 127 " pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 114.40 128.18 -13.78 2.30e+00 1.89e-01 3.59e+01 ... (remaining 16231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 6600 23.88 - 47.76: 500 47.76 - 71.64: 79 71.64 - 95.52: 17 95.52 - 119.40: 3 Dihedral angle restraints: 7199 sinusoidal: 2999 harmonic: 4200 Sorted by residual: dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual -86.00 -162.02 76.02 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" C MET C 85 " pdb=" N MET C 85 " pdb=" CA MET C 85 " pdb=" CB MET C 85 " ideal model delta harmonic sigma weight residual -122.60 -106.78 -15.82 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" CB CYS A 275 " pdb=" SG CYS A 275 " pdb=" SG CYS A 315 " pdb=" CB CYS A 315 " ideal model delta sinusoidal sigma weight residual -86.00 -136.23 50.23 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 7196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1735 0.084 - 0.168: 143 0.168 - 0.253: 8 0.253 - 0.337: 5 0.337 - 0.421: 1 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA ASP A 799 " pdb=" N ASP A 799 " pdb=" C ASP A 799 " pdb=" CB ASP A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.51e+00 ... (remaining 1889 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 799 " 0.030 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C ASP A 799 " -0.105 2.00e-02 2.50e+03 pdb=" O ASP A 799 " 0.040 2.00e-02 2.50e+03 pdb=" N PRO A 800 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 104 " 0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO C 105 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 132 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO C 133 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " 0.042 5.00e-02 4.00e+02 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 87 2.54 - 3.13: 9584 3.13 - 3.72: 18467 3.72 - 4.31: 25841 4.31 - 4.90: 42467 Nonbonded interactions: 96446 Sorted by model distance: nonbonded pdb=" N ASP A 799 " pdb=" O ASP A 799 " model vdw 1.953 2.496 nonbonded pdb=" O GLY A1444 " pdb=" OG1 THR A1448 " model vdw 2.045 2.440 nonbonded pdb=" O PHE A1738 " pdb=" OG SER A1742 " model vdw 2.069 2.440 nonbonded pdb=" CD2 TYR C 128 " pdb=" NH2 ARG C 137 " model vdw 2.087 3.420 nonbonded pdb=" O GLN C 62 " pdb=" CD PRO C 132 " model vdw 2.107 3.440 ... (remaining 96441 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=0.41 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: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.920 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.199 11982 Z= 0.481 Angle : 0.868 28.675 16236 Z= 0.485 Chirality : 0.051 0.421 1892 Planarity : 0.005 0.093 1981 Dihedral : 16.545 119.403 4458 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.56 % Favored : 94.09 % Rotamer: Outliers : 3.37 % Allowed : 19.03 % Favored : 77.60 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -2.41 (0.20), residues: 1421 helix: -1.18 (0.15), residues: 873 sheet: -1.36 (0.45), residues: 137 loop : -2.23 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 67 HIS 0.004 0.001 HIS A 766 PHE 0.018 0.002 PHE C 80 TYR 0.018 0.002 TYR C 125 ARG 0.003 0.001 ARG A1622 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6706 (tt) cc_final: 0.6244 (mt) REVERT: A 254 PHE cc_start: 0.8027 (t80) cc_final: 0.7803 (t80) REVERT: A 279 SER cc_start: 0.8583 (t) cc_final: 0.8304 (p) REVERT: A 405 TYR cc_start: 0.7166 (t80) cc_final: 0.6960 (t80) REVERT: A 794 LYS cc_start: 0.6091 (mmmt) cc_final: 0.4868 (tttm) REVERT: A 796 ILE cc_start: 0.7027 (pp) cc_final: 0.6760 (pt) REVERT: A 1251 LYS cc_start: 0.7693 (tttt) cc_final: 0.7412 (mptt) REVERT: A 1252 THR cc_start: 0.8608 (p) cc_final: 0.8245 (t) REVERT: A 1424 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7495 (tp-100) REVERT: A 1519 ILE cc_start: 0.8581 (pt) cc_final: 0.8337 (tp) REVERT: A 1541 GLN cc_start: 0.7787 (tp40) cc_final: 0.7494 (mm-40) REVERT: A 1579 ASN cc_start: 0.7970 (m-40) cc_final: 0.7735 (m-40) REVERT: A 1720 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7716 (t) REVERT: B 118 ASP cc_start: 0.7125 (m-30) cc_final: 0.6720 (m-30) outliers start: 43 outliers final: 23 residues processed: 264 average time/residue: 0.2238 time to fit residues: 85.3478 Evaluate side-chains 202 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 146 ASN A 265 GLN A 282 ASN A 360 GLN A 365 ASN A 395 ASN A 409 ASN A 765 HIS A 861 ASN A 941 GLN A1459 ASN A1463 GLN A1528 ASN B 61 GLN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11982 Z= 0.236 Angle : 0.652 10.833 16236 Z= 0.335 Chirality : 0.043 0.319 1892 Planarity : 0.005 0.067 1981 Dihedral : 10.070 110.732 1810 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.15 % Allowed : 20.44 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.92 (0.22), residues: 1421 helix: 0.09 (0.17), residues: 869 sheet: -1.22 (0.45), residues: 129 loop : -1.69 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 67 HIS 0.003 0.001 HIS A 766 PHE 0.015 0.001 PHE A1440 TYR 0.014 0.001 TYR A1548 ARG 0.007 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6714 (tt) cc_final: 0.6257 (mt) REVERT: A 130 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5814 (tpp) REVERT: A 207 LEU cc_start: 0.4024 (OUTLIER) cc_final: 0.3764 (tp) REVERT: A 279 SER cc_start: 0.8565 (t) cc_final: 0.8258 (p) REVERT: A 742 MET cc_start: 0.6232 (ttm) cc_final: 0.5824 (ttm) REVERT: A 794 LYS cc_start: 0.6247 (mmmt) cc_final: 0.5227 (tttm) REVERT: A 837 PHE cc_start: 0.7560 (m-10) cc_final: 0.7030 (m-10) REVERT: A 1251 LYS cc_start: 0.7576 (tttt) cc_final: 0.7304 (mptt) REVERT: A 1252 THR cc_start: 0.8599 (p) cc_final: 0.8258 (t) REVERT: A 1424 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7740 (tp-100) REVERT: A 1541 GLN cc_start: 0.7682 (tp40) cc_final: 0.7404 (mm-40) REVERT: A 1579 ASN cc_start: 0.7995 (m-40) cc_final: 0.7775 (m-40) REVERT: A 1768 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5162 (mp0) REVERT: C 79 MET cc_start: -0.0250 (ppp) cc_final: -0.2265 (mmm) REVERT: C 85 MET cc_start: 0.5161 (mpp) cc_final: 0.4862 (mtm) outliers start: 53 outliers final: 31 residues processed: 225 average time/residue: 0.2062 time to fit residues: 69.3475 Evaluate side-chains 195 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.0070 chunk 40 optimal weight: 0.0570 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 115 optimal weight: 0.1980 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A 766 HIS A 956 ASN A1463 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11982 Z= 0.163 Angle : 0.600 9.921 16236 Z= 0.305 Chirality : 0.041 0.261 1892 Planarity : 0.004 0.042 1981 Dihedral : 10.479 118.166 1794 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.99 % Allowed : 21.53 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.29 (0.22), residues: 1421 helix: 0.67 (0.17), residues: 869 sheet: -1.18 (0.45), residues: 131 loop : -1.55 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.002 0.000 HIS A 909 PHE 0.015 0.001 PHE A1440 TYR 0.020 0.001 TYR A1548 ARG 0.004 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6320 (mt) REVERT: A 207 LEU cc_start: 0.4082 (OUTLIER) cc_final: 0.3841 (tp) REVERT: A 243 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7178 (tppt) REVERT: A 364 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: A 742 MET cc_start: 0.6089 (ttm) cc_final: 0.5745 (ttm) REVERT: A 796 ILE cc_start: 0.7145 (pp) cc_final: 0.6899 (pt) REVERT: A 1251 LYS cc_start: 0.7416 (tttt) cc_final: 0.7201 (mptt) REVERT: A 1477 GLU cc_start: 0.7235 (tp30) cc_final: 0.6935 (tp30) REVERT: A 1556 ILE cc_start: 0.8012 (tp) cc_final: 0.7764 (tp) REVERT: A 1720 VAL cc_start: 0.7976 (m) cc_final: 0.7762 (t) REVERT: B 68 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7711 (p) REVERT: C 79 MET cc_start: -0.0187 (ppp) cc_final: -0.2111 (mmm) outliers start: 51 outliers final: 28 residues processed: 215 average time/residue: 0.2061 time to fit residues: 66.3499 Evaluate side-chains 196 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A 909 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11982 Z= 0.385 Angle : 0.686 12.622 16236 Z= 0.350 Chirality : 0.046 0.358 1892 Planarity : 0.004 0.044 1981 Dihedral : 10.361 120.294 1785 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.25 % Allowed : 21.30 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.20 (0.22), residues: 1421 helix: 0.74 (0.17), residues: 858 sheet: -0.97 (0.46), residues: 128 loop : -1.52 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 933 HIS 0.002 0.001 HIS A 909 PHE 0.020 0.002 PHE A 963 TYR 0.022 0.002 TYR A1548 ARG 0.004 0.001 ARG A 907 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 171 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.4163 (OUTLIER) cc_final: 0.3926 (tp) REVERT: A 243 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7317 (tppt) REVERT: A 742 MET cc_start: 0.6210 (ttm) cc_final: 0.5790 (ttm) REVERT: A 794 LYS cc_start: 0.6319 (OUTLIER) cc_final: 0.5187 (mmmt) REVERT: A 796 ILE cc_start: 0.7211 (pp) cc_final: 0.6999 (pt) REVERT: A 1251 LYS cc_start: 0.7475 (tttt) cc_final: 0.7227 (mptt) REVERT: A 1431 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8178 (tp) REVERT: A 1556 ILE cc_start: 0.7946 (tp) cc_final: 0.7705 (tp) REVERT: A 1668 TYR cc_start: 0.8037 (m-80) cc_final: 0.7769 (m-80) REVERT: A 1720 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7803 (t) REVERT: A 1768 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.3934 (tm-30) REVERT: B 68 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7983 (m) REVERT: C 79 MET cc_start: -0.0107 (ppp) cc_final: -0.2078 (mmm) outliers start: 67 outliers final: 43 residues processed: 230 average time/residue: 0.1966 time to fit residues: 68.4580 Evaluate side-chains 206 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1523 VAL Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.0010 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 ASN A1709 ASN B 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11982 Z= 0.175 Angle : 0.594 11.353 16236 Z= 0.299 Chirality : 0.041 0.270 1892 Planarity : 0.004 0.040 1981 Dihedral : 9.843 119.648 1781 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.99 % Allowed : 22.63 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.18 (0.23), residues: 1421 helix: 1.04 (0.17), residues: 863 sheet: -0.96 (0.46), residues: 129 loop : -1.34 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.001 0.000 HIS B 134 PHE 0.015 0.001 PHE A 963 TYR 0.022 0.001 TYR A1548 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7233 (tppt) REVERT: A 364 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: A 405 TYR cc_start: 0.6993 (t80) cc_final: 0.6696 (t80) REVERT: A 742 MET cc_start: 0.6033 (ttm) cc_final: 0.5674 (ttm) REVERT: A 794 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.5755 (mmmt) REVERT: A 796 ILE cc_start: 0.7179 (pp) cc_final: 0.6922 (pt) REVERT: A 837 PHE cc_start: 0.7585 (m-10) cc_final: 0.7175 (m-10) REVERT: A 861 ASN cc_start: 0.6089 (m-40) cc_final: 0.5453 (m-40) REVERT: A 1276 ASN cc_start: 0.8028 (t0) cc_final: 0.7604 (m-40) REVERT: A 1470 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.6726 (mp10) REVERT: A 1556 ILE cc_start: 0.7880 (tp) cc_final: 0.7653 (tp) REVERT: A 1720 VAL cc_start: 0.7960 (m) cc_final: 0.7757 (t) REVERT: C 79 MET cc_start: -0.0160 (ppp) cc_final: -0.2222 (mmm) outliers start: 51 outliers final: 33 residues processed: 210 average time/residue: 0.2058 time to fit residues: 65.0337 Evaluate side-chains 194 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 138 optimal weight: 40.0000 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11982 Z= 0.211 Angle : 0.604 10.088 16236 Z= 0.304 Chirality : 0.042 0.277 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.761 118.944 1781 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.99 % Allowed : 22.79 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.30 (0.23), residues: 1421 helix: 1.13 (0.17), residues: 864 sheet: -0.95 (0.46), residues: 131 loop : -1.27 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1700 HIS 0.002 0.000 HIS A 766 PHE 0.024 0.001 PHE A 183 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7213 (tppt) REVERT: A 364 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: A 742 MET cc_start: 0.6017 (ttm) cc_final: 0.5773 (tpp) REVERT: A 794 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.5956 (mmtp) REVERT: A 796 ILE cc_start: 0.7186 (pp) cc_final: 0.6900 (pt) REVERT: A 837 PHE cc_start: 0.7549 (m-10) cc_final: 0.7128 (m-10) REVERT: A 861 ASN cc_start: 0.6172 (m-40) cc_final: 0.5539 (m-40) REVERT: A 1230 ASP cc_start: 0.7857 (t0) cc_final: 0.7342 (m-30) REVERT: A 1276 ASN cc_start: 0.8050 (t0) cc_final: 0.7614 (m-40) REVERT: A 1470 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: A 1556 ILE cc_start: 0.7838 (tp) cc_final: 0.7609 (tp) REVERT: A 1720 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7781 (t) REVERT: A 1768 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.3988 (tm-30) REVERT: C 79 MET cc_start: -0.0019 (ppp) cc_final: -0.2141 (mmm) outliers start: 51 outliers final: 39 residues processed: 205 average time/residue: 0.2077 time to fit residues: 63.8903 Evaluate side-chains 203 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 159 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 137 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 84 optimal weight: 0.0020 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11982 Z= 0.203 Angle : 0.593 12.037 16236 Z= 0.298 Chirality : 0.041 0.268 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.616 117.518 1781 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 4.46 % Allowed : 22.24 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.38 (0.23), residues: 1421 helix: 1.18 (0.17), residues: 869 sheet: -0.88 (0.45), residues: 135 loop : -1.26 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.001 0.000 HIS C 139 PHE 0.014 0.001 PHE A 963 TYR 0.033 0.001 TYR A1573 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 166 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7216 (tppt) REVERT: A 364 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: A 742 MET cc_start: 0.5970 (ttm) cc_final: 0.5731 (tpp) REVERT: A 794 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6178 (mmtp) REVERT: A 796 ILE cc_start: 0.7166 (pp) cc_final: 0.6879 (pt) REVERT: A 837 PHE cc_start: 0.7448 (m-10) cc_final: 0.7015 (m-10) REVERT: A 861 ASN cc_start: 0.6187 (m-40) cc_final: 0.5594 (m-40) REVERT: A 1230 ASP cc_start: 0.7823 (t0) cc_final: 0.7346 (m-30) REVERT: A 1276 ASN cc_start: 0.8024 (t0) cc_final: 0.7626 (m-40) REVERT: A 1470 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.6790 (mp10) REVERT: A 1556 ILE cc_start: 0.7823 (tp) cc_final: 0.7597 (tp) REVERT: A 1691 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 1720 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7806 (t) REVERT: A 1768 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.3577 (tm-30) REVERT: B 159 SER cc_start: 0.8765 (t) cc_final: 0.8369 (m) REVERT: C 79 MET cc_start: 0.0088 (ppp) cc_final: -0.2138 (mmm) outliers start: 57 outliers final: 41 residues processed: 212 average time/residue: 0.2104 time to fit residues: 66.6879 Evaluate side-chains 206 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** A1579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11982 Z= 0.173 Angle : 0.590 10.802 16236 Z= 0.294 Chirality : 0.041 0.248 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.467 116.191 1780 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 3.84 % Allowed : 22.55 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.48 (0.23), residues: 1421 helix: 1.26 (0.17), residues: 869 sheet: -0.87 (0.45), residues: 137 loop : -1.21 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 PHE 0.014 0.001 PHE A 963 TYR 0.041 0.001 TYR A1573 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7191 (tppt) REVERT: A 364 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: A 742 MET cc_start: 0.6076 (ttm) cc_final: 0.5815 (tpp) REVERT: A 794 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6064 (mmtp) REVERT: A 796 ILE cc_start: 0.7328 (pp) cc_final: 0.7094 (pt) REVERT: A 841 ARG cc_start: 0.7220 (mmm-85) cc_final: 0.6871 (mmm-85) REVERT: A 861 ASN cc_start: 0.6197 (m-40) cc_final: 0.5625 (m-40) REVERT: A 1230 ASP cc_start: 0.7763 (t0) cc_final: 0.7227 (m-30) REVERT: A 1276 ASN cc_start: 0.7971 (t0) cc_final: 0.7604 (m-40) REVERT: A 1470 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: A 1556 ILE cc_start: 0.7824 (tp) cc_final: 0.7594 (tp) REVERT: A 1691 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7907 (mp) REVERT: A 1768 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.3511 (tm-30) REVERT: B 159 SER cc_start: 0.8715 (t) cc_final: 0.8323 (m) REVERT: C 79 MET cc_start: 0.0066 (ppp) cc_final: -0.2005 (mmm) REVERT: C 130 MET cc_start: 0.0742 (ppp) cc_final: 0.0276 (pmm) outliers start: 49 outliers final: 38 residues processed: 203 average time/residue: 0.2151 time to fit residues: 64.9943 Evaluate side-chains 205 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 ASN A1762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11982 Z= 0.332 Angle : 0.656 11.412 16236 Z= 0.329 Chirality : 0.044 0.322 1892 Planarity : 0.004 0.042 1981 Dihedral : 9.638 115.292 1780 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.35 % Favored : 94.51 % Rotamer: Outliers : 3.92 % Allowed : 22.63 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.29 (0.23), residues: 1421 helix: 1.09 (0.17), residues: 864 sheet: -0.80 (0.45), residues: 135 loop : -1.24 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 933 HIS 0.002 0.001 HIS A 915 PHE 0.026 0.002 PHE A 183 TYR 0.063 0.002 TYR A1573 ARG 0.003 0.000 ARG A 907 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8360 (mtmm) REVERT: A 243 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7236 (tppt) REVERT: A 279 SER cc_start: 0.8391 (t) cc_final: 0.8004 (p) REVERT: A 364 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: A 742 MET cc_start: 0.6207 (ttm) cc_final: 0.5909 (tpp) REVERT: A 796 ILE cc_start: 0.7332 (pp) cc_final: 0.7056 (pt) REVERT: A 837 PHE cc_start: 0.7405 (m-10) cc_final: 0.7061 (m-10) REVERT: A 841 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6944 (mmm-85) REVERT: A 861 ASN cc_start: 0.6200 (m-40) cc_final: 0.5645 (m-40) REVERT: A 1230 ASP cc_start: 0.7944 (t0) cc_final: 0.7433 (m-30) REVERT: A 1276 ASN cc_start: 0.8006 (t0) cc_final: 0.7623 (m-40) REVERT: A 1343 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: A 1470 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: A 1556 ILE cc_start: 0.7828 (tp) cc_final: 0.7613 (tp) REVERT: A 1573 TYR cc_start: 0.7635 (t80) cc_final: 0.7352 (t80) REVERT: A 1668 TYR cc_start: 0.8021 (m-80) cc_final: 0.7729 (m-80) REVERT: A 1691 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7964 (mp) REVERT: A 1768 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.3506 (tm-30) REVERT: B 159 SER cc_start: 0.8756 (t) cc_final: 0.8344 (m) REVERT: C 79 MET cc_start: 0.0127 (ppp) cc_final: -0.1980 (mmm) outliers start: 50 outliers final: 38 residues processed: 205 average time/residue: 0.2366 time to fit residues: 72.6135 Evaluate side-chains 204 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 911 ASN A1579 ASN A1762 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11982 Z= 0.155 Angle : 0.597 10.357 16236 Z= 0.295 Chirality : 0.041 0.245 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.374 114.094 1780 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 3.13 % Allowed : 23.41 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.52 (0.23), residues: 1421 helix: 1.36 (0.17), residues: 857 sheet: -0.84 (0.45), residues: 136 loop : -1.27 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 PHE 0.013 0.001 PHE A1440 TYR 0.037 0.001 TYR A1573 ARG 0.003 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6107 (mp) REVERT: A 243 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7200 (tppt) REVERT: A 364 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7514 (pm20) REVERT: A 794 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6302 (mmtp) REVERT: A 796 ILE cc_start: 0.7544 (pp) cc_final: 0.7317 (pt) REVERT: A 798 MET cc_start: 0.6792 (tpp) cc_final: 0.6571 (ptm) REVERT: A 837 PHE cc_start: 0.7371 (m-10) cc_final: 0.7029 (m-10) REVERT: A 841 ARG cc_start: 0.7254 (mmm-85) cc_final: 0.6958 (mmm-85) REVERT: A 861 ASN cc_start: 0.6198 (m-40) cc_final: 0.5620 (m-40) REVERT: A 952 MET cc_start: 0.7069 (tpt) cc_final: 0.6812 (tpt) REVERT: A 1230 ASP cc_start: 0.7777 (t0) cc_final: 0.7239 (m-30) REVERT: A 1276 ASN cc_start: 0.7923 (t0) cc_final: 0.7570 (m-40) REVERT: A 1470 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.6750 (mp10) REVERT: A 1556 ILE cc_start: 0.7883 (tp) cc_final: 0.7654 (tp) REVERT: A 1574 PHE cc_start: 0.7901 (m-80) cc_final: 0.7687 (m-10) REVERT: A 1691 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 1768 GLU cc_start: 0.5636 (OUTLIER) cc_final: 0.3243 (tm-30) REVERT: B 159 SER cc_start: 0.8748 (t) cc_final: 0.8398 (m) REVERT: C 79 MET cc_start: 0.0066 (ppp) cc_final: -0.2057 (mmm) REVERT: C 130 MET cc_start: 0.0658 (ppp) cc_final: 0.0155 (pmm) outliers start: 40 outliers final: 33 residues processed: 198 average time/residue: 0.2232 time to fit residues: 65.6810 Evaluate side-chains 202 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 162 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 ASN ** B 61 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 = 0.4248 r_free = 0.4248 target = 0.181541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125820 restraints weight = 14621.830| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.92 r_work: 0.3455 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11982 Z= 0.166 Angle : 0.598 10.254 16236 Z= 0.295 Chirality : 0.041 0.246 1892 Planarity : 0.004 0.042 1981 Dihedral : 9.282 112.924 1780 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.37 % Allowed : 23.26 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.59 (0.23), residues: 1421 helix: 1.41 (0.17), residues: 857 sheet: -0.80 (0.45), residues: 138 loop : -1.25 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 PHE 0.025 0.001 PHE A 183 TYR 0.032 0.001 TYR A1573 ARG 0.002 0.000 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2737.10 seconds wall clock time: 49 minutes 21.17 seconds (2961.17 seconds total)