Starting phenix.real_space_refine on Sun Dec 10 00:51:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/12_2023/8gz1_34387.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/12_2023/8gz1_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_34387/12_2023/8gz1_34387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/12_2023/8gz1_34387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/12_2023/8gz1_34387.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz1_34387/12_2023/8gz1_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 6 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: 6.83, per 1000 atoms: 0.57 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: 5.42 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: 1.22 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: 3.95 Time building geometry restraints manager: 5.64 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 - 17.88: 6505 17.88 - 35.77: 630 35.77 - 53.65: 114 53.65 - 71.54: 27 71.54 - 89.42: 8 Dihedral angle restraints: 7284 sinusoidal: 3054 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 7281 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: 1.630 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: 4.150 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.130 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- 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 : 14.387 89.423 4520 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 : 1.443 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2225 time to fit residues: 68.8693 Evaluate side-chains 153 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8455 ------------------------------------------------------------------------------- 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: 0.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 66 ASN C 74 ASN C 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12200 Z= 0.191 Angle : 0.611 9.109 16531 Z= 0.315 Chirality : 0.041 0.189 1921 Planarity : 0.004 0.060 2019 Dihedral : 6.811 57.846 1799 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.80 % Allowed : 9.91 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1435 helix: 1.68 (0.18), residues: 834 sheet: 0.09 (0.54), residues: 97 loop : -1.12 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1415 HIS 0.005 0.001 HIS B 131 PHE 0.028 0.001 PHE C 63 TYR 0.021 0.002 TYR B1489 ARG 0.003 0.000 ARG B1296 *********************** 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 194 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 180 average time/residue: 0.2130 time to fit residues: 58.3291 Evaluate side-chains 177 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1134 time to fit residues: 5.0990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.0050 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 347 ASN B 374 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1485 GLN B1653 ASN C 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1612 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= 0.233 Angle : 0.598 9.553 16531 Z= 0.307 Chirality : 0.041 0.207 1921 Planarity : 0.004 0.058 2019 Dihedral : 6.357 54.725 1799 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.09 % Allowed : 13.58 % Favored : 85.32 % 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: 0.88 (0.23), residues: 1435 helix: 1.61 (0.18), residues: 843 sheet: -0.32 (0.52), residues: 109 loop : -1.03 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1415 HIS 0.004 0.001 HIS B 131 PHE 0.027 0.001 PHE C 63 TYR 0.021 0.002 TYR B1580 ARG 0.009 0.000 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 183 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 1.457 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 175 average time/residue: 0.2589 time to fit residues: 69.1721 Evaluate side-chains 164 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1445 time to fit residues: 4.1377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 338 GLN B 347 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: 0.7600 moved from start: 0.1923 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= 0.246 Angle : 0.602 9.266 16531 Z= 0.307 Chirality : 0.041 0.201 1921 Planarity : 0.004 0.057 2019 Dihedral : 5.937 53.804 1799 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.42 % Allowed : 14.68 % Favored : 82.90 % 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: 0.88 (0.23), residues: 1435 helix: 1.62 (0.18), residues: 843 sheet: -0.23 (0.52), residues: 109 loop : -1.07 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.017 0.001 PHE B1616 TYR 0.025 0.002 TYR B1579 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 194 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.384 Fit side-chains outliers start: 31 outliers final: 10 residues processed: 184 average time/residue: 0.2172 time to fit residues: 60.3475 Evaluate side-chains 163 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1206 time to fit residues: 4.0998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12200 Z= 0.170 Angle : 0.585 11.990 16531 Z= 0.294 Chirality : 0.041 0.244 1921 Planarity : 0.004 0.056 2019 Dihedral : 5.570 53.245 1799 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.95 % Allowed : 15.93 % Favored : 82.12 % 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: 1.73 (0.18), residues: 843 sheet: 0.13 (0.54), residues: 99 loop : -1.06 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1185 HIS 0.003 0.001 HIS B1727 PHE 0.019 0.001 PHE B1616 TYR 0.027 0.001 TYR B1580 ARG 0.006 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 187 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.270 Fit side-chains outliers start: 25 outliers final: 7 residues processed: 178 average time/residue: 0.2099 time to fit residues: 57.0319 Evaluate side-chains 158 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1071 time to fit residues: 3.1374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 0.0040 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- 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 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12200 Z= 0.261 Angle : 0.635 10.421 16531 Z= 0.318 Chirality : 0.042 0.201 1921 Planarity : 0.004 0.053 2019 Dihedral : 5.493 54.169 1799 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.95 % Allowed : 17.02 % Favored : 81.03 % 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: 0.92 (0.23), residues: 1435 helix: 1.68 (0.18), residues: 836 sheet: 0.17 (0.55), residues: 99 loop : -1.16 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.019 0.001 PHE B 391 TYR 0.038 0.002 TYR B1580 ARG 0.004 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 184 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.346 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 176 average time/residue: 0.2106 time to fit residues: 55.9955 Evaluate side-chains 162 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1064 time to fit residues: 4.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 138 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12200 Z= 0.169 Angle : 0.600 11.000 16531 Z= 0.299 Chirality : 0.041 0.227 1921 Planarity : 0.004 0.054 2019 Dihedral : 5.220 53.291 1799 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.86 % Allowed : 18.58 % Favored : 80.56 % 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: 1.80 (0.18), residues: 837 sheet: 0.22 (0.55), residues: 99 loop : -1.10 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.021 0.001 PHE C 95 TYR 0.043 0.002 TYR B1580 ARG 0.009 0.000 ARG C 137 *********************** 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 171 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 1.262 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 166 average time/residue: 0.2052 time to fit residues: 52.2148 Evaluate side-chains 154 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1170 time to fit residues: 3.2140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 0.0980 chunk 126 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12200 Z= 0.162 Angle : 0.607 10.564 16531 Z= 0.298 Chirality : 0.041 0.220 1921 Planarity : 0.004 0.053 2019 Dihedral : 5.027 53.295 1799 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.62 % Allowed : 18.74 % Favored : 80.64 % 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: 1.15 (0.23), residues: 1435 helix: 1.86 (0.18), residues: 837 sheet: 0.34 (0.55), residues: 99 loop : -1.07 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.013 0.001 PHE B1459 TYR 0.041 0.001 TYR B1580 ARG 0.004 0.000 ARG C 137 *********************** 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 173 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 169 average time/residue: 0.2154 time to fit residues: 55.5537 Evaluate side-chains 158 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1156 time to fit residues: 3.2394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.0870 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1759 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2650 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= 0.194 Angle : 0.626 13.229 16531 Z= 0.307 Chirality : 0.041 0.304 1921 Planarity : 0.004 0.053 2019 Dihedral : 4.981 53.669 1799 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.70 % Allowed : 19.20 % Favored : 80.09 % 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: 1.12 (0.23), residues: 1435 helix: 1.82 (0.18), residues: 838 sheet: 0.45 (0.55), residues: 99 loop : -1.08 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1185 HIS 0.004 0.001 HIS B1727 PHE 0.013 0.001 PHE B1459 TYR 0.041 0.002 TYR B1580 ARG 0.004 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 169 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 167 average time/residue: 0.2131 time to fit residues: 54.6117 Evaluate side-chains 155 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1193 time to fit residues: 2.6986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN B 215 ASN B 404 ASN B 417 GLN B 747 ASN B1759 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12200 Z= 0.341 Angle : 0.716 11.707 16531 Z= 0.352 Chirality : 0.044 0.287 1921 Planarity : 0.004 0.053 2019 Dihedral : 5.349 54.721 1799 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.62 % Allowed : 19.28 % Favored : 80.09 % 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: 0.89 (0.23), residues: 1435 helix: 1.62 (0.18), residues: 832 sheet: 0.46 (0.55), residues: 99 loop : -1.14 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B1185 HIS 0.007 0.001 HIS B1727 PHE 0.019 0.002 PHE B1480 TYR 0.042 0.002 TYR B1580 ARG 0.005 0.001 ARG C 137 ********************** 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 163 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.412 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 158 average time/residue: 0.2030 time to fit residues: 49.7729 Evaluate side-chains 154 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1284 time to fit residues: 3.0310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.142006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.100445 restraints weight = 23663.537| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.67 r_work: 0.3417 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2857 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= 0.241 Angle : 0.668 10.491 16531 Z= 0.329 Chirality : 0.043 0.260 1921 Planarity : 0.004 0.053 2019 Dihedral : 5.230 53.861 1799 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.39 % Allowed : 19.67 % Favored : 79.94 % 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: 0.91 (0.23), residues: 1435 helix: 1.63 (0.18), residues: 833 sheet: 0.14 (0.54), residues: 111 loop : -1.07 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B1185 HIS 0.005 0.001 HIS B1727 PHE 0.015 0.001 PHE B1459 TYR 0.041 0.002 TYR B1580 ARG 0.003 0.000 ARG C 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.54 seconds wall clock time: 44 minutes 55.48 seconds (2695.48 seconds total)