Starting phenix.real_space_refine on Thu Feb 15 17:01:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/02_2024/8gz1_34387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/02_2024/8gz1_34387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/02_2024/8gz1_34387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/02_2024/8gz1_34387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/02_2024/8gz1_34387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/02_2024/8gz1_34387.pdb" } resolution = 3.4 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= 0.029 sd= 0.101 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 957 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 101 5.16 5 Na 2 4.78 5 C 7818 2.51 5 N 1869 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B ASP 821": "OD1" <-> "OD2" Residue "B PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1417": "OD1" <-> "OD2" Residue "B TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1484": "OE1" <-> "OE2" Residue "B PHE 1516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11912 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1409 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 172} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 9307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9307 Classifications: {'peptide': 1152} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 32, 'TRANS': 1119} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 971 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' NA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.68, per 1000 atoms: 0.56 Number of scatterers: 11912 At special positions: 0 Unit cell: (133.12, 141.44, 116.48, 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 101 16.00 Na 2 11.00 O 2122 8.00 N 1869 7.00 C 7818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS C 55 " distance=1.18 Simple disulfide: pdb=" SG CYS B 906 " - pdb=" SG CYS B 912 " distance=2.03 Simple disulfide: pdb=" SG CYS B 944 " - pdb=" SG CYS B 953 " distance=2.03 Simple disulfide: pdb=" SG CYS B1356 " - pdb=" SG CYS B1376 " distance=2.04 Simple disulfide: pdb=" SG CYS B1721 " - pdb=" SG CYS B1736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 1 " - " ASN B 295 " " NAG B2001 " - " ASN B 289 " " NAG D 301 " - " ASN D 135 " " NAG E 1 " - " ASN B 308 " " NAG F 1 " - " ASN B 326 " " NAG G 1 " - " ASN B1358 " " NAG H 1 " - " ASN B1372 " Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2734 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 66.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'D' and resid 153 through 190 removed outlier: 3.557A pdb=" N ILE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.668A pdb=" N SER B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 158 through 179 Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.742A pdb=" N TRP B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 223 through 234 removed outlier: 4.154A pdb=" N ALA B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 251 removed outlier: 3.618A pdb=" N ILE B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.661A pdb=" N SER B 291 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.602A pdb=" N PHE B 312 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 355 through 369 Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.034A pdb=" N LEU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.695A pdb=" N PHE B 391 " --> pdb=" O TYR B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 426 removed outlier: 3.540A pdb=" N GLU B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 731 removed outlier: 3.654A pdb=" N PHE B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 751 removed outlier: 4.397A pdb=" N MET B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 772 removed outlier: 4.019A pdb=" N MET B 772 " --> pdb=" O LEU B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 807 Processing helix chain 'B' and resid 808 through 814 Processing helix chain 'B' and resid 815 through 834 removed outlier: 3.955A pdb=" N LEU B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 833 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 857 removed outlier: 3.971A pdb=" N ARG B 847 " --> pdb=" O ARG B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 873 removed outlier: 3.521A pdb=" N VAL B 872 " --> pdb=" O ILE B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 904 removed outlier: 5.580A pdb=" N LYS B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER B 900 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 902 " --> pdb=" O GLY B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 909 removed outlier: 4.062A pdb=" N ILE B 908 " --> pdb=" O CYS B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 Processing helix chain 'B' and resid 937 through 949 removed outlier: 3.981A pdb=" N ASP B 943 " --> pdb=" O GLU B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 981 removed outlier: 3.981A pdb=" N CYS B 953 " --> pdb=" O GLY B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1183 through 1197 Processing helix chain 'B' and resid 1197 through 1214 Processing helix chain 'B' and resid 1225 through 1255 removed outlier: 3.751A pdb=" N LYS B1237 " --> pdb=" O GLU B1233 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B1238 " --> pdb=" O TYR B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1261 Processing helix chain 'B' and resid 1262 through 1284 Processing helix chain 'B' and resid 1289 through 1297 removed outlier: 3.784A pdb=" N THR B1297 " --> pdb=" O LYS B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1298 through 1303 Proline residue: B1303 - end of helix Processing helix chain 'B' and resid 1304 through 1310 removed outlier: 3.880A pdb=" N SER B1308 " --> pdb=" O LEU B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1310 through 1324 Processing helix chain 'B' and resid 1324 through 1350 removed outlier: 4.659A pdb=" N ASN B1329 " --> pdb=" O PRO B1325 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL B1330 " --> pdb=" O SER B1326 " (cutoff:3.500A) Processing helix chain 'B' and resid 1372 through 1383 removed outlier: 3.693A pdb=" N CYS B1376 " --> pdb=" O ASN B1372 " (cutoff:3.500A) Processing helix chain 'B' and resid 1398 through 1411 Processing helix chain 'B' and resid 1414 through 1424 removed outlier: 3.649A pdb=" N ILE B1418 " --> pdb=" O GLY B1414 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1439 No H-bonds generated for 'chain 'B' and resid 1437 through 1439' Processing helix chain 'B' and resid 1440 through 1452 removed outlier: 3.676A pdb=" N PHE B1444 " --> pdb=" O MET B1440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B1452 " --> pdb=" O ILE B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1453 through 1474 Processing helix chain 'B' and resid 1482 through 1496 Processing helix chain 'B' and resid 1509 through 1521 Processing helix chain 'B' and resid 1521 through 1541 removed outlier: 3.787A pdb=" N ASP B1525 " --> pdb=" O GLN B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1547 through 1581 removed outlier: 7.984A pdb=" N HIS B1578 " --> pdb=" O PHE B1574 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR B1579 " --> pdb=" O ALA B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1583 through 1605 Processing helix chain 'B' and resid 1612 through 1622 Processing helix chain 'B' and resid 1623 through 1634 Processing helix chain 'B' and resid 1635 through 1674 Proline residue: B1649 - end of helix removed outlier: 3.902A pdb=" N ALA B1674 " --> pdb=" O MET B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1703 removed outlier: 3.910A pdb=" N THR B1703 " --> pdb=" O PHE B1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 1706 through 1712 Processing helix chain 'B' and resid 1738 through 1772 removed outlier: 3.652A pdb=" N ASN B1759 " --> pdb=" O LEU B1755 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B1767 " --> pdb=" O ALA B1763 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.103A pdb=" N ALA D 30 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN D 50 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR D 55 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG D 72 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP D 57 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 36 through 40 Processing sheet with id=AA3, first strand: chain 'B' and resid 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.503A pdb=" N THR C 33 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.856A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.856A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 129 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 138 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 48 738 hydrogen bonds defined for protein. 2088 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: 3.98 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3607 1.34 - 1.46: 3169 1.46 - 1.59: 5260 1.59 - 1.71: 0 1.71 - 1.83: 164 Bond restraints: 12200 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.34e+00 ... (remaining 12195 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.96: 169 104.96 - 112.24: 6138 112.24 - 119.52: 4000 119.52 - 126.80: 6072 126.80 - 134.08: 152 Bond angle restraints: 16531 Sorted by residual: angle pdb=" C GLU B1366 " pdb=" N ILE B1367 " pdb=" CA ILE B1367 " ideal model delta sigma weight residual 121.65 118.44 3.21 9.40e-01 1.13e+00 1.16e+01 angle pdb=" N SER B1452 " pdb=" CA SER B1452 " pdb=" C SER B1452 " ideal model delta sigma weight residual 114.56 110.67 3.89 1.27e+00 6.20e-01 9.39e+00 angle pdb=" N PRO B1718 " pdb=" CA PRO B1718 " pdb=" C PRO B1718 " ideal model delta sigma weight residual 110.70 114.21 -3.51 1.22e+00 6.72e-01 8.28e+00 angle pdb=" N TRP B 284 " pdb=" CA TRP B 284 " pdb=" C TRP B 284 " ideal model delta sigma weight residual 109.81 116.08 -6.27 2.21e+00 2.05e-01 8.04e+00 angle pdb=" N GLN B 246 " pdb=" CA GLN B 246 " pdb=" CB GLN B 246 " ideal model delta sigma weight residual 110.16 114.31 -4.15 1.48e+00 4.57e-01 7.85e+00 ... (remaining 16526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 6737 22.10 - 44.20: 521 44.20 - 66.30: 59 66.30 - 88.41: 41 88.41 - 110.51: 21 Dihedral angle restraints: 7379 sinusoidal: 3149 harmonic: 4230 Sorted by residual: dihedral pdb=" CB CYS B 944 " pdb=" SG CYS B 944 " pdb=" SG CYS B 953 " pdb=" CB CYS B 953 " ideal model delta sinusoidal sigma weight residual -86.00 -166.62 80.62 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS B1356 " pdb=" SG CYS B1356 " pdb=" SG CYS B1376 " pdb=" CB CYS B1376 " ideal model delta sinusoidal sigma weight residual -86.00 -148.42 62.42 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CA TYR B1580 " pdb=" C TYR B1580 " pdb=" N PHE B1581 " pdb=" CA PHE B1581 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 7376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1588 0.056 - 0.111: 287 0.111 - 0.167: 34 0.167 - 0.223: 3 0.223 - 0.278: 9 Chirality restraints: 1921 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B1358 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1918 not shown) Planarity restraints: 2026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 736 " 0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO B 737 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 737 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 737 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1718 " -0.039 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO B1719 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B1719 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1719 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1415 " -0.014 2.00e-02 2.50e+03 1.45e-02 5.27e+00 pdb=" CG TRP B1415 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B1415 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B1415 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1415 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1415 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1415 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1415 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1415 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B1415 " -0.001 2.00e-02 2.50e+03 ... (remaining 2023 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 70 2.53 - 3.12: 9506 3.12 - 3.72: 18693 3.72 - 4.31: 24804 4.31 - 4.90: 41070 Nonbonded interactions: 94143 Sorted by model distance: nonbonded pdb=" SG CYS B 912 " pdb=" CD ARG C 135 " model vdw 1.940 3.800 nonbonded pdb=" SG CYS B 912 " pdb=" NE ARG C 135 " model vdw 2.024 2.880 nonbonded pdb=" N LYS B 907 " pdb=" OH TYR C 56 " model vdw 2.030 2.520 nonbonded pdb=" CA LYS B 907 " pdb=" OH TYR C 56 " model vdw 2.101 3.470 nonbonded pdb=" O ILE B 868 " pdb=" OG SER B 871 " model vdw 2.217 2.440 ... (remaining 94138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 4.170 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 34.550 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12200 Z= 0.229 Angle : 0.681 7.938 16531 Z= 0.356 Chirality : 0.046 0.278 1921 Planarity : 0.004 0.070 2019 Dihedral : 17.164 110.508 4615 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1435 helix: 1.49 (0.18), residues: 827 sheet: -0.04 (0.54), residues: 97 loop : -1.25 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1415 HIS 0.011 0.001 HIS B 131 PHE 0.030 0.001 PHE B1581 TYR 0.018 0.002 TYR B1488 ARG 0.007 0.001 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: D 154 MET cc_start: 0.7000 (ttm) cc_final: 0.6565 (ttt) REVERT: B 1265 CYS cc_start: 0.7722 (m) cc_final: 0.7204 (m) REVERT: B 1286 TYR cc_start: 0.6252 (m-80) cc_final: 0.6022 (m-80) REVERT: B 1735 ASP cc_start: 0.6243 (t70) cc_final: 0.5902 (t0) REVERT: C 65 LEU cc_start: 0.6511 (pp) cc_final: 0.6041 (pp) REVERT: C 82 GLN cc_start: 0.8539 (mt0) cc_final: 0.7991 (mm110) REVERT: C 84 ARG cc_start: 0.5827 (mpt-90) cc_final: 0.5503 (mmt90) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2404 time to fit residues: 74.4824 Evaluate side-chains 156 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1466 ASN B1521 GLN C 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12200 Z= 0.188 Angle : 0.617 9.156 16531 Z= 0.314 Chirality : 0.042 0.187 1921 Planarity : 0.004 0.060 2019 Dihedral : 11.269 68.566 1894 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.64 % Allowed : 9.68 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1435 helix: 1.69 (0.18), residues: 835 sheet: 0.08 (0.54), residues: 97 loop : -1.12 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1415 HIS 0.006 0.001 HIS B 131 PHE 0.029 0.001 PHE C 63 TYR 0.021 0.002 TYR B1489 ARG 0.003 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 154 MET cc_start: 0.6995 (ttm) cc_final: 0.6606 (ttt) REVERT: D 180 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6003 (t80) REVERT: B 1206 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6737 (t80) REVERT: B 1265 CYS cc_start: 0.7776 (m) cc_final: 0.7214 (m) REVERT: B 1331 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8253 (tt) REVERT: B 1735 ASP cc_start: 0.6111 (t70) cc_final: 0.5738 (t0) REVERT: C 82 GLN cc_start: 0.8178 (mt0) cc_final: 0.7481 (mm-40) REVERT: C 143 HIS cc_start: 0.5993 (t70) cc_final: 0.5790 (t70) outliers start: 21 outliers final: 13 residues processed: 183 average time/residue: 0.2283 time to fit residues: 62.4928 Evaluate side-chains 177 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1331 LEU Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 347 ASN B 374 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12200 Z= 0.280 Angle : 0.630 10.655 16531 Z= 0.321 Chirality : 0.043 0.198 1921 Planarity : 0.004 0.058 2019 Dihedral : 8.511 57.049 1894 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.50 % Allowed : 13.74 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1435 helix: 1.58 (0.18), residues: 842 sheet: -0.32 (0.52), residues: 109 loop : -1.06 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1415 HIS 0.004 0.001 HIS B1727 PHE 0.026 0.002 PHE C 63 TYR 0.022 0.002 TYR B1580 ARG 0.009 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8201 (t80) cc_final: 0.7981 (t80) REVERT: B 388 MET cc_start: 0.7757 (tmm) cc_final: 0.7379 (tmm) REVERT: B 848 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8401 (mm) REVERT: B 858 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.6813 (m-10) REVERT: B 1206 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6967 (t80) REVERT: B 1265 CYS cc_start: 0.7927 (m) cc_final: 0.7639 (m) REVERT: B 1580 TYR cc_start: 0.5765 (m-10) cc_final: 0.5515 (m-10) REVERT: B 1670 MET cc_start: 0.7946 (mtt) cc_final: 0.7738 (mtt) REVERT: C 82 GLN cc_start: 0.8283 (mt0) cc_final: 0.8077 (mm-40) outliers start: 32 outliers final: 20 residues processed: 180 average time/residue: 0.2100 time to fit residues: 57.2571 Evaluate side-chains 181 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN B 347 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12200 Z= 0.168 Angle : 0.568 8.990 16531 Z= 0.288 Chirality : 0.041 0.197 1921 Planarity : 0.004 0.057 2019 Dihedral : 6.350 53.012 1894 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.67 % Allowed : 13.66 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1435 helix: 1.76 (0.18), residues: 842 sheet: -0.25 (0.52), residues: 109 loop : -1.02 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1185 HIS 0.003 0.001 HIS B1727 PHE 0.030 0.001 PHE C 63 TYR 0.017 0.001 TYR B 812 ARG 0.006 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 168 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8213 (t80) cc_final: 0.8007 (t80) REVERT: D 154 MET cc_start: 0.7096 (ttm) cc_final: 0.6705 (ttt) REVERT: D 180 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6156 (t80) REVERT: B 829 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 848 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8562 (mm) REVERT: B 858 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.6735 (m-10) REVERT: B 1206 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6867 (t80) REVERT: B 1220 ILE cc_start: 0.8563 (pt) cc_final: 0.8333 (mm) REVERT: B 1265 CYS cc_start: 0.7942 (m) cc_final: 0.7318 (m) REVERT: B 1304 LEU cc_start: 0.8728 (mt) cc_final: 0.8505 (mt) REVERT: B 1600 MET cc_start: 0.7805 (tmm) cc_final: 0.7195 (tmm) outliers start: 47 outliers final: 24 residues processed: 196 average time/residue: 0.2201 time to fit residues: 65.9245 Evaluate side-chains 186 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1579 TYR Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12200 Z= 0.178 Angle : 0.573 9.069 16531 Z= 0.289 Chirality : 0.041 0.212 1921 Planarity : 0.004 0.056 2019 Dihedral : 5.642 53.468 1894 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.36 % Allowed : 15.07 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1435 helix: 1.84 (0.18), residues: 841 sheet: 0.12 (0.55), residues: 99 loop : -1.06 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1185 HIS 0.003 0.001 HIS B1727 PHE 0.018 0.001 PHE B1616 TYR 0.024 0.001 TYR B1580 ARG 0.005 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8193 (t80) cc_final: 0.7961 (t80) REVERT: D 154 MET cc_start: 0.7124 (ttm) cc_final: 0.6738 (ttt) REVERT: D 184 LYS cc_start: 0.9138 (ttmt) cc_final: 0.8542 (mttt) REVERT: B 388 MET cc_start: 0.7519 (tmm) cc_final: 0.7190 (tmm) REVERT: B 829 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8270 (mm) REVERT: B 848 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8586 (mm) REVERT: B 858 TRP cc_start: 0.7847 (OUTLIER) cc_final: 0.6713 (m-10) REVERT: B 1206 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6988 (t80) REVERT: B 1265 CYS cc_start: 0.8008 (m) cc_final: 0.7371 (m) REVERT: B 1437 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8244 (t0) REVERT: B 1559 LEU cc_start: 0.8390 (mt) cc_final: 0.7967 (pp) REVERT: C 79 MET cc_start: 0.7046 (pmm) cc_final: 0.6610 (tmm) outliers start: 43 outliers final: 27 residues processed: 187 average time/residue: 0.2170 time to fit residues: 60.7657 Evaluate side-chains 189 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 954 LEU Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1327 ILE Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 139 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 ASN B 774 HIS C 62 GLN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12200 Z= 0.232 Angle : 0.607 10.699 16531 Z= 0.304 Chirality : 0.041 0.198 1921 Planarity : 0.004 0.054 2019 Dihedral : 5.463 54.164 1894 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.36 % Allowed : 16.71 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1435 helix: 1.77 (0.18), residues: 842 sheet: 0.18 (0.56), residues: 99 loop : -1.04 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.016 0.001 PHE B1616 TYR 0.024 0.002 TYR B 812 ARG 0.005 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8259 (t80) cc_final: 0.8034 (t80) REVERT: D 154 MET cc_start: 0.7137 (ttm) cc_final: 0.6770 (ttt) REVERT: D 184 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8533 (mttt) REVERT: B 388 MET cc_start: 0.7612 (tmm) cc_final: 0.7279 (tmm) REVERT: B 848 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8602 (mm) REVERT: B 858 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.6858 (m-10) REVERT: B 1206 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6914 (t80) REVERT: B 1265 CYS cc_start: 0.7980 (m) cc_final: 0.7689 (m) REVERT: B 1437 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8294 (t0) REVERT: B 1559 LEU cc_start: 0.8437 (mt) cc_final: 0.8140 (pp) REVERT: C 79 MET cc_start: 0.7282 (pmm) cc_final: 0.6672 (tmm) outliers start: 43 outliers final: 26 residues processed: 190 average time/residue: 0.2099 time to fit residues: 60.0324 Evaluate side-chains 186 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN C 74 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12200 Z= 0.164 Angle : 0.577 10.906 16531 Z= 0.289 Chirality : 0.040 0.197 1921 Planarity : 0.004 0.054 2019 Dihedral : 5.194 53.505 1894 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.04 % Allowed : 17.25 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1435 helix: 1.91 (0.18), residues: 836 sheet: 0.17 (0.55), residues: 99 loop : -1.07 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1185 HIS 0.003 0.001 HIS B1727 PHE 0.017 0.001 PHE B1616 TYR 0.021 0.001 TYR B 812 ARG 0.005 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8268 (t80) cc_final: 0.8012 (t80) REVERT: D 184 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8523 (mttt) REVERT: B 388 MET cc_start: 0.7476 (tmm) cc_final: 0.7099 (tmm) REVERT: B 845 SER cc_start: 0.8979 (t) cc_final: 0.8463 (t) REVERT: B 848 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8651 (mm) REVERT: B 858 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.6849 (m-10) REVERT: B 1206 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.7010 (t80) REVERT: B 1265 CYS cc_start: 0.7985 (m) cc_final: 0.7355 (m) REVERT: B 1301 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8362 (mm) REVERT: B 1357 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7808 (t80) REVERT: B 1375 GLU cc_start: 0.7090 (tp30) cc_final: 0.6864 (tp30) REVERT: B 1437 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8233 (t0) REVERT: B 1559 LEU cc_start: 0.8507 (mt) cc_final: 0.8262 (pp) REVERT: C 79 MET cc_start: 0.7280 (pmm) cc_final: 0.6679 (tmm) outliers start: 39 outliers final: 28 residues processed: 192 average time/residue: 0.2074 time to fit residues: 60.1499 Evaluate side-chains 191 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1307 LEU Chi-restraints excluded: chain B residue 1357 PHE Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1601 PHE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B 747 ASN ** B1727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 12200 Z= 0.383 Angle : 0.710 11.152 16531 Z= 0.356 Chirality : 0.045 0.232 1921 Planarity : 0.004 0.053 2019 Dihedral : 5.604 54.978 1894 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.83 % Allowed : 16.86 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1435 helix: 1.59 (0.18), residues: 831 sheet: 0.09 (0.54), residues: 99 loop : -1.20 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1185 HIS 0.007 0.001 HIS B1727 PHE 0.021 0.002 PHE C 95 TYR 0.036 0.002 TYR C 69 ARG 0.004 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 152 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8396 (t80) cc_final: 0.8174 (t80) REVERT: D 184 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8526 (mttt) REVERT: B 388 MET cc_start: 0.7807 (tmm) cc_final: 0.7531 (tmm) REVERT: B 812 TYR cc_start: 0.6975 (t80) cc_final: 0.6697 (t80) REVERT: B 848 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8586 (mm) REVERT: B 858 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.6875 (m-10) REVERT: B 1206 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6971 (t80) REVERT: B 1265 CYS cc_start: 0.8077 (m) cc_final: 0.7834 (m) REVERT: B 1301 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8513 (mm) REVERT: B 1437 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8431 (t0) REVERT: B 1670 MET cc_start: 0.7863 (mtt) cc_final: 0.7350 (mtt) REVERT: C 79 MET cc_start: 0.7353 (pmm) cc_final: 0.6737 (tmm) outliers start: 49 outliers final: 33 residues processed: 182 average time/residue: 0.2194 time to fit residues: 59.8968 Evaluate side-chains 187 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1205 ILE Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1307 LEU Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1601 PHE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 84 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12200 Z= 0.170 Angle : 0.615 10.694 16531 Z= 0.304 Chirality : 0.041 0.239 1921 Planarity : 0.004 0.054 2019 Dihedral : 5.213 53.218 1894 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.73 % Allowed : 17.95 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1435 helix: 1.83 (0.18), residues: 836 sheet: 0.22 (0.55), residues: 99 loop : -1.08 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B1185 HIS 0.003 0.001 HIS B1727 PHE 0.017 0.001 PHE B1616 TYR 0.028 0.001 TYR B 812 ARG 0.005 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8335 (t80) cc_final: 0.8130 (t80) REVERT: D 154 MET cc_start: 0.7265 (ttm) cc_final: 0.6924 (ttt) REVERT: D 184 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8457 (mttt) REVERT: B 139 MET cc_start: 0.6301 (tpp) cc_final: 0.5569 (ttm) REVERT: B 388 MET cc_start: 0.7551 (tmm) cc_final: 0.7156 (tmm) REVERT: B 845 SER cc_start: 0.9001 (t) cc_final: 0.8471 (t) REVERT: B 848 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 858 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.6764 (m-10) REVERT: B 1206 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.7030 (t80) REVERT: B 1265 CYS cc_start: 0.7966 (m) cc_final: 0.7320 (m) REVERT: B 1301 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8379 (mm) REVERT: B 1380 MET cc_start: 0.7102 (mmt) cc_final: 0.6790 (mmt) REVERT: B 1437 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8273 (t0) REVERT: B 1536 MET cc_start: 0.8339 (tmm) cc_final: 0.7990 (tmm) REVERT: B 1559 LEU cc_start: 0.8441 (mt) cc_final: 0.8175 (pp) REVERT: C 79 MET cc_start: 0.7362 (pmm) cc_final: 0.6776 (tmm) outliers start: 35 outliers final: 24 residues processed: 183 average time/residue: 0.2253 time to fit residues: 61.8352 Evaluate side-chains 180 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1307 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1601 PHE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 0.0050 chunk 132 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12200 Z= 0.247 Angle : 0.651 10.061 16531 Z= 0.322 Chirality : 0.042 0.230 1921 Planarity : 0.004 0.053 2019 Dihedral : 5.255 53.883 1894 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.73 % Allowed : 18.11 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1435 helix: 1.76 (0.18), residues: 836 sheet: 0.30 (0.56), residues: 99 loop : -1.11 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B1185 HIS 0.006 0.001 HIS B 775 PHE 0.024 0.001 PHE B1616 TYR 0.024 0.002 TYR B 812 ARG 0.004 0.000 ARG C 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 32 TYR cc_start: 0.8359 (t80) cc_final: 0.8150 (t80) REVERT: D 154 MET cc_start: 0.7322 (ttm) cc_final: 0.6982 (ttt) REVERT: D 184 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8513 (mttt) REVERT: B 139 MET cc_start: 0.6364 (tpp) cc_final: 0.5627 (ttm) REVERT: B 388 MET cc_start: 0.7574 (tmm) cc_final: 0.7223 (tmm) REVERT: B 845 SER cc_start: 0.9050 (t) cc_final: 0.8541 (t) REVERT: B 848 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 858 TRP cc_start: 0.8059 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: B 1206 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6923 (t80) REVERT: B 1265 CYS cc_start: 0.7989 (m) cc_final: 0.7327 (m) REVERT: B 1301 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8397 (mm) REVERT: B 1380 MET cc_start: 0.7197 (mmt) cc_final: 0.6921 (mmt) REVERT: B 1437 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8354 (t0) REVERT: B 1559 LEU cc_start: 0.8441 (mt) cc_final: 0.8171 (pp) REVERT: C 79 MET cc_start: 0.7343 (pmm) cc_final: 0.6728 (tmm) outliers start: 35 outliers final: 28 residues processed: 175 average time/residue: 0.2167 time to fit residues: 56.9359 Evaluate side-chains 183 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 1198 ASN Chi-restraints excluded: chain B residue 1206 PHE Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1236 ASP Chi-restraints excluded: chain B residue 1257 VAL Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1307 LEU Chi-restraints excluded: chain B residue 1332 LEU Chi-restraints excluded: chain B residue 1437 ASN Chi-restraints excluded: chain B residue 1601 PHE Chi-restraints excluded: chain B residue 1616 PHE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1759 ASN Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 137 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN ** C 82 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 = 0.4107 r_free = 0.4107 target = 0.141217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102034 restraints weight = 23698.017| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.11 r_work: 0.3384 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12200 Z= 0.274 Angle : 0.655 9.902 16531 Z= 0.325 Chirality : 0.043 0.227 1921 Planarity : 0.004 0.053 2019 Dihedral : 5.291 53.953 1894 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.97 % Allowed : 17.95 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.99 (0.23), residues: 1435 helix: 1.71 (0.18), residues: 837 sheet: 0.31 (0.56), residues: 99 loop : -1.11 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1185 HIS 0.006 0.001 HIS B 775 PHE 0.024 0.001 PHE B1616 TYR 0.023 0.002 TYR B 812 ARG 0.004 0.000 ARG C 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.43 seconds wall clock time: 45 minutes 17.18 seconds (2717.18 seconds total)