Starting phenix.real_space_refine on Wed Feb 14 05:28:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfw_32476/02_2024/7wfw_32476_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 58 5.16 5 C 5828 2.51 5 N 1300 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 248": "OD1" <-> "OD2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 664": "OD1" <-> "OD2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 817": "NH1" <-> "NH2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A ASP 834": "OD1" <-> "OD2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1136": "OD1" <-> "OD2" Residue "A TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1177": "OD1" <-> "OD2" Residue "A ASP 1190": "OD1" <-> "OD2" Residue "A ARG 1191": "NH1" <-> "NH2" Residue "A PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1222": "OD1" <-> "OD2" Residue "A GLU 1242": "OE1" <-> "OE2" Residue "A ARG 1250": "NH1" <-> "NH2" Residue "A ARG 1256": "NH1" <-> "NH2" Residue "A PHE 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1315": "OD1" <-> "OD2" Residue "A PHE 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1331": "OD1" <-> "OD2" Residue "A PHE 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1378": "OD1" <-> "OD2" Residue "A GLU 1381": "OE1" <-> "OE2" Residue "A GLU 1389": "OE1" <-> "OE2" Residue "A ASP 1390": "OD1" <-> "OD2" Residue "A PHE 1407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1419": "OD1" <-> "OD2" Residue "A PHE 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1432": "OD1" <-> "OD2" Residue "A GLU 1438": "OE1" <-> "OE2" Residue "A ARG 1460": "NH1" <-> "NH2" Residue "A PHE 1468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1496": "OE1" <-> "OE2" Residue "A ASP 1498": "OD1" <-> "OD2" Residue "A GLU 1503": "OE1" <-> "OE2" Residue "A GLU 1522": "OE1" <-> "OE2" Residue "A PHE 1542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1579": "NH1" <-> "NH2" Residue "A ARG 1588": "NH1" <-> "NH2" Residue "A PHE 1598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1633": "NH1" <-> "NH2" Residue "A GLU 1635": "OE1" <-> "OE2" Residue "A ASP 1639": "OD1" <-> "OD2" Residue "A ASP 1640": "OD1" <-> "OD2" Residue "A PHE 1642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1679": "OD1" <-> "OD2" Residue "A ASP 1691": "OD1" <-> "OD2" Residue "A PHE 1701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1723": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8689 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 998, 8054 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 968} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 998, 8054 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 968} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 8246 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 597 Unusual residues: {'CLR': 4, 'LPE': 8, 'NAG': 4, 'PCW': 3} Classifications: {'peptide': 2, 'undetermined': 19} Link IDs: {'TRANS': 1, None: 19} Not linked: pdbres="NAG A2001 " pdbres="NAG A2002 " Not linked: pdbres="NAG A2002 " pdbres="NAG A2003 " Not linked: pdbres="NAG A2003 " pdbres="NAG A2004 " Not linked: pdbres="NAG A2004 " pdbres="CLR A2005 " Not linked: pdbres="CLR A2005 " pdbres="PCW A2006 " ... (remaining 14 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1631 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A1631 " occ=0.50 Time building chain proxies: 8.84, per 1000 atoms: 1.02 Number of scatterers: 8689 At special positions: 0 Unit cell: (129.9, 101.755, 100.672, 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 58 16.00 P 13 15.00 O 1490 8.00 N 1300 7.00 C 5828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 857 " - pdb=" SG CYS A 866 " distance=2.02 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1332 " distance=2.00 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " distance=2.02 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A2001 " - " ASN A 819 " " NAG A2002 " - " ASN A 312 " " NAG A2003 " - " ASN A1328 " " NAG A2004 " - " ASN A1312 " " NAG B 1 " - " ASN A1336 " Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 2.9 seconds 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 2 sheets defined 69.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 233 through 268 removed outlier: 3.514A pdb=" N ALA A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.835A pdb=" N VAL A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 382 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 406 removed outlier: 3.853A pdb=" N ILE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 394 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 658 Processing helix chain 'A' and resid 667 through 684 removed outlier: 3.826A pdb=" N MET A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 728 through 745 removed outlier: 4.072A pdb=" N PHE A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 765 removed outlier: 5.096A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL A 763 " --> pdb=" O ARG A 759 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 783 Processing helix chain 'A' and resid 788 through 819 removed outlier: 5.254A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 817 " --> pdb=" O TYR A 813 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASN A 819 " --> pdb=" O ASN A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 847 Processing helix chain 'A' and resid 852 through 860 removed outlier: 4.002A pdb=" N ALA A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 893 removed outlier: 4.080A pdb=" N LEU A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.847A pdb=" N GLU A1150 " --> pdb=" O TYR A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1169 removed outlier: 3.785A pdb=" N LEU A1169 " --> pdb=" O SER A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 removed outlier: 4.114A pdb=" N ASP A1177 " --> pdb=" O TYR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1208 Processing helix chain 'A' and resid 1210 through 1216 removed outlier: 4.098A pdb=" N PHE A1214 " --> pdb=" O PHE A1210 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR A1215 " --> pdb=" O LYS A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1237 removed outlier: 3.896A pdb=" N THR A1234 " --> pdb=" O LEU A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1263 removed outlier: 3.735A pdb=" N THR A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA A1254 " --> pdb=" O ARG A1250 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU A1255 " --> pdb=" O THR A1251 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Proline residue: A1257 - end of helix removed outlier: 4.771A pdb=" N ALA A1260 " --> pdb=" O ARG A1256 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A1261 " --> pdb=" O PRO A1257 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG A1263 " --> pdb=" O ARG A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1275 Processing helix chain 'A' and resid 1278 through 1303 removed outlier: 3.516A pdb=" N PHE A1295 " --> pdb=" O PHE A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1332 No H-bonds generated for 'chain 'A' and resid 1329 through 1332' Processing helix chain 'A' and resid 1353 through 1364 Processing helix chain 'A' and resid 1369 through 1377 removed outlier: 3.713A pdb=" N ALA A1375 " --> pdb=" O ASP A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1428 removed outlier: 3.765A pdb=" N TYR A1395 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A1400 " --> pdb=" O TYR A1397 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A1405 " --> pdb=" O ILE A1402 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A1406 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A1407 " --> pdb=" O PHE A1404 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A1408 " --> pdb=" O GLY A1405 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A1409 " --> pdb=" O GLY A1406 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1410 " --> pdb=" O PHE A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1451 removed outlier: 3.639A pdb=" N LYS A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1473 removed outlier: 3.871A pdb=" N PHE A1470 " --> pdb=" O GLN A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1494 Processing helix chain 'A' and resid 1502 through 1529 Processing helix chain 'A' and resid 1533 through 1536 No H-bonds generated for 'chain 'A' and resid 1533 through 1536' Processing helix chain 'A' and resid 1539 through 1560 Processing helix chain 'A' and resid 1569 through 1578 removed outlier: 3.600A pdb=" N ALA A1578 " --> pdb=" O ILE A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1588 removed outlier: 4.179A pdb=" N LEU A1586 " --> pdb=" O ARG A1582 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ILE A1587 " --> pdb=" O ILE A1583 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG A1588 " --> pdb=" O LEU A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1628 Proline residue: A1605 - end of helix Processing helix chain 'A' and resid 1647 through 1658 Processing helix chain 'A' and resid 1663 through 1670 Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1695 through 1724 removed outlier: 3.869A pdb=" N ILE A1700 " --> pdb=" O ALA A1696 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1703 " --> pdb=" O ILE A1699 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A1706 " --> pdb=" O PHE A1702 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A1719 " --> pdb=" O ASN A1715 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1720 " --> pdb=" O MET A1716 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 274 through 278 removed outlier: 3.677A pdb=" N LEU A 326 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 277 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 324 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1341 through 1344 459 hydrogen bonds defined for protein. 1257 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: 2.89 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1562 1.33 - 1.45: 2264 1.45 - 1.58: 4944 1.58 - 1.70: 28 1.70 - 1.82: 96 Bond restraints: 8894 Sorted by residual: bond pdb=" C PRO A1630 " pdb=" N AHIS A1631 " ideal model delta sigma weight residual 1.332 1.471 -0.139 1.52e-02 4.33e+03 8.34e+01 bond pdb=" C38 P5S A2020 " pdb=" O37 P5S A2020 " ideal model delta sigma weight residual 1.331 1.463 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C17 P5S A2020 " pdb=" O19 P5S A2020 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C11 PCW A2011 " pdb=" O3 PCW A2011 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C11 PCW A2007 " pdb=" O3 PCW A2007 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.02e+01 ... (remaining 8889 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.16: 158 105.16 - 112.46: 4780 112.46 - 119.77: 3074 119.77 - 127.08: 3910 127.08 - 134.39: 92 Bond angle restraints: 12014 Sorted by residual: angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 111.81 102.26 9.55 8.60e-01 1.35e+00 1.23e+02 angle pdb=" N GLY A 810 " pdb=" CA GLY A 810 " pdb=" C GLY A 810 " ideal model delta sigma weight residual 112.73 124.35 -11.62 1.20e+00 6.94e-01 9.38e+01 angle pdb=" N ARG A 817 " pdb=" CA ARG A 817 " pdb=" C ARG A 817 " ideal model delta sigma weight residual 112.38 124.01 -11.63 1.22e+00 6.72e-01 9.09e+01 angle pdb=" N LYS A1329 " pdb=" CA LYS A1329 " pdb=" C LYS A1329 " ideal model delta sigma weight residual 112.23 103.25 8.98 1.26e+00 6.30e-01 5.08e+01 angle pdb=" N LEU A 809 " pdb=" CA LEU A 809 " pdb=" C LEU A 809 " ideal model delta sigma weight residual 111.36 118.96 -7.60 1.09e+00 8.42e-01 4.86e+01 ... (remaining 12009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 5206 32.50 - 65.00: 285 65.00 - 97.50: 25 97.50 - 129.99: 6 129.99 - 162.49: 3 Dihedral angle restraints: 5525 sinusoidal: 2606 harmonic: 2919 Sorted by residual: dihedral pdb=" CB CYS A 857 " pdb=" SG CYS A 857 " pdb=" SG CYS A 866 " pdb=" CB CYS A 866 " ideal model delta sinusoidal sigma weight residual -86.00 -173.35 87.35 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS A1310 " pdb=" SG CYS A1310 " pdb=" SG CYS A1332 " pdb=" CB CYS A1332 " ideal model delta sinusoidal sigma weight residual 93.00 173.16 -80.16 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CA PRO A 332 " pdb=" C PRO A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta harmonic sigma weight residual -180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1309 0.145 - 0.290: 48 0.290 - 0.434: 3 0.434 - 0.579: 1 0.579 - 0.724: 2 Chirality restraints: 1363 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.66e+01 chirality pdb=" C1 NAG A2001 " pdb=" ND2 ASN A 819 " pdb=" C2 NAG A2001 " pdb=" O5 NAG A2001 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C1 NAG A2004 " pdb=" ND2 ASN A1312 " pdb=" C2 NAG A2004 " pdb=" O5 NAG A2004 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 1360 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " 0.313 2.00e-02 2.50e+03 2.75e-01 9.48e+02 pdb=" C7 NAG A2001 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " 0.082 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " -0.492 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2004 " -0.282 2.00e-02 2.50e+03 2.38e-01 7.08e+02 pdb=" C7 NAG A2004 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A2004 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG A2004 " 0.404 2.00e-02 2.50e+03 pdb=" O7 NAG A2004 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.272 2.00e-02 2.50e+03 2.28e-01 6.48e+02 pdb=" C7 NAG B 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.383 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.002 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1015 2.73 - 3.28: 8990 3.28 - 3.82: 13490 3.82 - 4.36: 16922 4.36 - 4.90: 28529 Nonbonded interactions: 68946 Sorted by model distance: nonbonded pdb=" OD1 ASN A1537 " pdb=" N GLY A1538 " model vdw 2.192 2.520 nonbonded pdb=" N GLU A1502 " pdb=" OE1 GLU A1502 " model vdw 2.270 2.520 nonbonded pdb=" O THR A1659 " pdb=" OG SER A1660 " model vdw 2.346 2.440 nonbonded pdb=" OH TYR A1443 " pdb=" OE2 GLU A1723 " model vdw 2.397 2.440 nonbonded pdb=" OD2 ASP A1543 " pdb=" NH2 ARG A1588 " model vdw 2.407 2.520 ... (remaining 68941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 33.310 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 : 0.013 0.139 8894 Z= 0.775 Angle : 1.387 12.067 12014 Z= 0.726 Chirality : 0.073 0.724 1363 Planarity : 0.015 0.275 1394 Dihedral : 19.229 162.492 3620 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.38 % Favored : 91.52 % Rotamer: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.57 % 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: -2.32 (0.24), residues: 993 helix: -0.93 (0.18), residues: 685 sheet: -2.91 (1.00), residues: 22 loop : -2.65 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.005 TRP A1369 HIS 0.018 0.003 HIS A 833 PHE 0.027 0.004 PHE A 659 TYR 0.023 0.003 TYR A 362 ARG 0.012 0.002 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 689 MET cc_start: 0.7771 (mtt) cc_final: 0.7510 (mtt) REVERT: A 1397 TYR cc_start: 0.7246 (t80) cc_final: 0.6163 (t80) REVERT: A 1579 ARG cc_start: 0.6253 (mtt180) cc_final: 0.5808 (mtt180) REVERT: A 1705 TYR cc_start: 0.7089 (t80) cc_final: 0.6532 (t80) REVERT: A 1712 ILE cc_start: 0.6777 (mm) cc_final: 0.6564 (mm) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.2118 time to fit residues: 39.9443 Evaluate side-chains 121 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN A 831 HIS ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 8894 Z= 0.252 Angle : 0.736 10.137 12014 Z= 0.368 Chirality : 0.045 0.481 1363 Planarity : 0.005 0.050 1394 Dihedral : 16.428 164.595 1751 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.68 % Allowed : 11.06 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.05 (0.26), residues: 993 helix: 0.03 (0.19), residues: 691 sheet: None (None), residues: 0 loop : -2.31 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 850 HIS 0.010 0.002 HIS A 833 PHE 0.026 0.002 PHE A1514 TYR 0.025 0.002 TYR A1717 ARG 0.006 0.001 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 1393 TYR cc_start: 0.7492 (m-80) cc_final: 0.7164 (m-80) REVERT: A 1397 TYR cc_start: 0.7059 (t80) cc_final: 0.6532 (t80) REVERT: A 1527 MET cc_start: 0.6626 (mtm) cc_final: 0.6204 (mtm) REVERT: A 1579 ARG cc_start: 0.6122 (mtt180) cc_final: 0.5692 (mtt180) outliers start: 6 outliers final: 2 residues processed: 128 average time/residue: 0.2112 time to fit residues: 37.8837 Evaluate side-chains 119 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 1492 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8894 Z= 0.213 Angle : 0.658 10.952 12014 Z= 0.328 Chirality : 0.042 0.405 1363 Planarity : 0.005 0.048 1394 Dihedral : 15.316 173.948 1751 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.90 % Allowed : 14.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.56 (0.27), residues: 993 helix: 0.41 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -2.10 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1369 HIS 0.007 0.001 HIS A 833 PHE 0.021 0.001 PHE A1514 TYR 0.028 0.002 TYR A1705 ARG 0.006 0.001 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1393 TYR cc_start: 0.7504 (m-80) cc_final: 0.7212 (m-80) REVERT: A 1397 TYR cc_start: 0.7090 (t80) cc_final: 0.6742 (t80) REVERT: A 1527 MET cc_start: 0.6581 (mtm) cc_final: 0.6310 (mtm) REVERT: A 1579 ARG cc_start: 0.6003 (mtt180) cc_final: 0.5600 (mtt180) outliers start: 8 outliers final: 4 residues processed: 132 average time/residue: 0.2094 time to fit residues: 39.0744 Evaluate side-chains 123 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 1157 PHE Chi-restraints excluded: chain A residue 1492 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 0.0170 chunk 95 optimal weight: 0.0770 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 ASN ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8894 Z= 0.182 Angle : 0.607 10.960 12014 Z= 0.300 Chirality : 0.040 0.385 1363 Planarity : 0.004 0.044 1394 Dihedral : 14.134 166.456 1751 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.79 % Allowed : 15.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.19 (0.27), residues: 993 helix: 0.70 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1369 HIS 0.005 0.001 HIS A 833 PHE 0.024 0.001 PHE A 707 TYR 0.030 0.002 TYR A1705 ARG 0.004 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.6888 (ttp) cc_final: 0.6551 (ttt) REVERT: A 1393 TYR cc_start: 0.7481 (m-80) cc_final: 0.7259 (m-80) REVERT: A 1579 ARG cc_start: 0.6108 (mtt180) cc_final: 0.5698 (mtt180) outliers start: 7 outliers final: 4 residues processed: 136 average time/residue: 0.2206 time to fit residues: 41.7571 Evaluate side-chains 130 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 729 TRP Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 1157 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 0.0670 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 HIS ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8894 Z= 0.175 Angle : 0.594 10.701 12014 Z= 0.293 Chirality : 0.040 0.387 1363 Planarity : 0.004 0.043 1394 Dihedral : 13.490 156.066 1751 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.68 % Allowed : 16.70 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.07 (0.27), residues: 993 helix: 0.80 (0.20), residues: 692 sheet: -3.55 (0.94), residues: 10 loop : -1.93 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 850 HIS 0.004 0.001 HIS A 833 PHE 0.025 0.001 PHE A 707 TYR 0.024 0.002 TYR A1705 ARG 0.003 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 374 MET cc_start: 0.6932 (ttp) cc_final: 0.6508 (ttt) REVERT: A 1393 TYR cc_start: 0.7474 (m-80) cc_final: 0.7264 (m-80) REVERT: A 1579 ARG cc_start: 0.6057 (mtt180) cc_final: 0.5657 (mtt180) outliers start: 6 outliers final: 4 residues processed: 138 average time/residue: 0.2049 time to fit residues: 39.6186 Evaluate side-chains 131 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 729 TRP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 1157 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.0010 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 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 : 0.003 0.055 8894 Z= 0.176 Angle : 0.584 11.537 12014 Z= 0.292 Chirality : 0.039 0.378 1363 Planarity : 0.004 0.039 1394 Dihedral : 12.961 150.800 1751 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.68 % Allowed : 17.27 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.05 (0.27), residues: 993 helix: 0.90 (0.20), residues: 693 sheet: -3.70 (0.98), residues: 10 loop : -1.91 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 850 HIS 0.004 0.001 HIS A 833 PHE 0.025 0.001 PHE A 707 TYR 0.023 0.001 TYR A1705 ARG 0.004 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 240 ILE cc_start: 0.8242 (mm) cc_final: 0.8027 (mm) REVERT: A 374 MET cc_start: 0.6824 (ttp) cc_final: 0.6421 (ttt) REVERT: A 376 PHE cc_start: 0.7036 (t80) cc_final: 0.6506 (t80) REVERT: A 1393 TYR cc_start: 0.7519 (m-80) cc_final: 0.7302 (m-80) REVERT: A 1579 ARG cc_start: 0.6086 (mtt180) cc_final: 0.5648 (mtt180) outliers start: 6 outliers final: 4 residues processed: 130 average time/residue: 0.2062 time to fit residues: 37.9719 Evaluate side-chains 129 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 729 TRP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 1157 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 0.0030 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 0.0050 chunk 59 optimal weight: 0.0270 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8894 Z= 0.148 Angle : 0.571 11.657 12014 Z= 0.279 Chirality : 0.038 0.336 1363 Planarity : 0.004 0.038 1394 Dihedral : 12.345 145.273 1751 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.45 % Allowed : 17.27 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.27 (0.27), residues: 993 helix: 1.05 (0.20), residues: 695 sheet: -3.45 (1.05), residues: 10 loop : -1.80 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 850 HIS 0.003 0.001 HIS A 833 PHE 0.035 0.001 PHE A1514 TYR 0.018 0.001 TYR A1705 ARG 0.003 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 376 PHE cc_start: 0.6981 (t80) cc_final: 0.6541 (t80) REVERT: A 1579 ARG cc_start: 0.5901 (mtt180) cc_final: 0.5438 (mtt180) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.1995 time to fit residues: 38.4116 Evaluate side-chains 128 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 TRP Chi-restraints excluded: chain A residue 1157 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8894 Z= 0.164 Angle : 0.588 12.473 12014 Z= 0.289 Chirality : 0.039 0.350 1363 Planarity : 0.004 0.037 1394 Dihedral : 12.057 143.530 1751 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.68 % Allowed : 18.17 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.33 (0.27), residues: 993 helix: 1.05 (0.20), residues: 697 sheet: -3.33 (1.12), residues: 10 loop : -1.68 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 850 HIS 0.003 0.001 HIS A 833 PHE 0.026 0.001 PHE A 707 TYR 0.018 0.001 TYR A1705 ARG 0.003 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 MET cc_start: 0.6772 (ttp) cc_final: 0.6401 (ttt) REVERT: A 376 PHE cc_start: 0.6985 (t80) cc_final: 0.6562 (t80) REVERT: A 758 PHE cc_start: 0.6602 (t80) cc_final: 0.6385 (t80) REVERT: A 1378 ASP cc_start: 0.7331 (m-30) cc_final: 0.6864 (m-30) REVERT: A 1579 ARG cc_start: 0.5772 (mtt180) cc_final: 0.5270 (mtt180) outliers start: 6 outliers final: 3 residues processed: 135 average time/residue: 0.2032 time to fit residues: 38.9657 Evaluate side-chains 132 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 TRP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 888 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8894 Z= 0.180 Angle : 0.604 12.839 12014 Z= 0.296 Chirality : 0.039 0.365 1363 Planarity : 0.004 0.037 1394 Dihedral : 11.800 142.117 1751 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.45 % Allowed : 18.40 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.30 (0.27), residues: 993 helix: 1.02 (0.20), residues: 698 sheet: -3.29 (1.16), residues: 10 loop : -1.70 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 850 HIS 0.003 0.001 HIS A 833 PHE 0.038 0.001 PHE A1514 TYR 0.019 0.001 TYR A1705 ARG 0.003 0.000 ARG A 814 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 374 MET cc_start: 0.6784 (ttp) cc_final: 0.6412 (ttt) REVERT: A 1579 ARG cc_start: 0.5892 (mtt180) cc_final: 0.5232 (mtt180) outliers start: 4 outliers final: 4 residues processed: 131 average time/residue: 0.2002 time to fit residues: 36.8421 Evaluate side-chains 128 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 729 TRP Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 888 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 48 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.0060 chunk 24 optimal weight: 0.9980 overall best weight: 0.2432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8894 Z= 0.145 Angle : 0.591 12.558 12014 Z= 0.292 Chirality : 0.038 0.308 1363 Planarity : 0.004 0.036 1394 Dihedral : 11.354 137.407 1751 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.56 % Allowed : 18.62 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.51 (0.27), residues: 993 helix: 1.18 (0.20), residues: 697 sheet: -3.13 (1.20), residues: 10 loop : -1.60 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 850 HIS 0.005 0.001 HIS A1151 PHE 0.028 0.001 PHE A 707 TYR 0.017 0.001 TYR A1705 ARG 0.004 0.000 ARG A 814 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 376 PHE cc_start: 0.7034 (t80) cc_final: 0.6695 (t80) REVERT: A 758 PHE cc_start: 0.6542 (t80) cc_final: 0.6258 (t80) REVERT: A 1527 MET cc_start: 0.6811 (mtm) cc_final: 0.6603 (mtm) REVERT: A 1579 ARG cc_start: 0.6113 (mtt180) cc_final: 0.5272 (mtt180) outliers start: 5 outliers final: 4 residues processed: 136 average time/residue: 0.2057 time to fit residues: 39.3653 Evaluate side-chains 134 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 729 TRP Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1331 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.207754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.176541 restraints weight = 17048.779| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.97 r_work: 0.4050 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8894 Z= 0.180 Angle : 0.609 13.064 12014 Z= 0.301 Chirality : 0.039 0.352 1363 Planarity : 0.004 0.090 1394 Dihedral : 11.339 136.642 1751 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.56 % Allowed : 18.85 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.41 (0.27), residues: 993 helix: 1.11 (0.20), residues: 696 sheet: -3.13 (1.19), residues: 10 loop : -1.66 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 850 HIS 0.004 0.001 HIS A 833 PHE 0.027 0.001 PHE A 707 TYR 0.018 0.001 TYR A 362 ARG 0.005 0.000 ARG A 762 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.96 seconds wall clock time: 37 minutes 59.93 seconds (2279.93 seconds total)