Starting phenix.real_space_refine on Thu Jan 18 23:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wfr_32475/01_2024/7wfr_32475_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 62 5.16 5 Cl 1 4.86 5 C 6545 2.51 5 N 1438 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 817": "NH1" <-> "NH2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 834": "OD1" <-> "OD2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 893": "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 ASP 1173": "OD1" <-> "OD2" Residue "A ASP 1190": "OD1" <-> "OD2" Residue "A ARG 1191": "NH1" <-> "NH2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1200": "OE1" <-> "OE2" Residue "A TYR 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 1265": "OE1" <-> "OE2" Residue "A ASP 1272": "OD1" <-> "OD2" Residue "A PHE 1295": "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 GLU 1317": "OE1" <-> "OE2" Residue "A PHE 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1351": "OD1" <-> "OD2" Residue "A ASP 1371": "OD1" <-> "OD2" Residue "A TYR 1374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1378": "OD1" <-> "OD2" Residue "A GLU 1381": "OE1" <-> "OE2" Residue "A GLU 1389": "OE1" <-> "OE2" Residue "A TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1419": "OD1" <-> "OD2" Residue "A PHE 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1438": "OE1" <-> "OE2" Residue "A TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1460": "NH1" <-> "NH2" Residue "A PHE 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1479": "OD1" <-> "OD2" Residue "A GLU 1496": "OE1" <-> "OE2" Residue "A GLU 1502": "OE1" <-> "OE2" Residue "A GLU 1503": "OE1" <-> "OE2" Residue "A PHE 1514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1522": "OE1" <-> "OE2" Residue "A PHE 1528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1579": "NH1" <-> "NH2" Residue "A PHE 1608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1633": "NH1" <-> "NH2" Residue "A ASP 1639": "OD1" <-> "OD2" Residue "A ASP 1640": "OD1" <-> "OD2" Residue "A PHE 1642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1664": "OD1" <-> "OD2" Residue "A TYR 1705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1723": "OE1" <-> "OE2" Residue "A PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9748 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1100, 8851 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1067} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 1100, 8851 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1067} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 9060 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: "C" 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: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 831 Unusual residues: {'95T': 1, 'CLR': 5, 'LPE': 12, 'NAG': 3, 'PCW': 7} Classifications: {'peptide': 1, 'undetermined': 28} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 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: 9.98, per 1000 atoms: 1.02 Number of scatterers: 9748 At special positions: 0 Unit cell: (129.9, 124.487, 101.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 62 16.00 P 20 15.00 O 1682 8.00 N 1438 7.00 C 6545 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=2.03 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2001 " - " ASN A 819 " " NAG A2002 " - " ASN A 312 " " NAG A2003 " - " ASN A1312 " " NAG B 1 " - " ASN A1328 " " NAG C 1 " - " ASN A1336 " Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 3.0 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 2 sheets defined 69.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.773A pdb=" N LEU A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 174 removed outlier: 3.647A pdb=" N LEU A 169 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 170 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 172 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 174 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.551A pdb=" N THR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.660A pdb=" N PHE A 217 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 220 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 268 removed outlier: 4.678A pdb=" N VAL A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.649A pdb=" N ILE A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 383 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 406 removed outlier: 3.684A pdb=" N GLN A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 404 " --> pdb=" O TYR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 665 through 684 removed outlier: 4.192A pdb=" N LEU A 669 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 670 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.873A pdb=" N GLN A 726 " --> pdb=" O TYR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 745 removed outlier: 3.973A pdb=" N PHE A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 765 removed outlier: 3.516A pdb=" N PHE A 758 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 763 " --> pdb=" O ARG A 759 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 4.559A 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 815 removed outlier: 5.799A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 851 through 860 Processing helix chain 'A' and resid 863 through 893 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1152 through 1171 removed outlier: 3.700A pdb=" N LEU A1169 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1208 removed outlier: 3.628A pdb=" N ALA A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1215 Processing helix chain 'A' and resid 1219 through 1237 Processing helix chain 'A' and resid 1244 through 1259 removed outlier: 3.763A pdb=" N THR A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA A1254 " --> pdb=" O ARG A1250 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A1255 " --> pdb=" O THR A1251 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1265 through 1303 Proline residue: A1279 - end of helix Processing helix chain 'A' and resid 1329 through 1334 Processing helix chain 'A' and resid 1353 through 1365 Processing helix chain 'A' and resid 1369 through 1377 Processing helix chain 'A' and resid 1392 through 1405 removed outlier: 3.546A pdb=" N PHE A1404 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A1405 " --> pdb=" O ILE A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1427 Processing helix chain 'A' and resid 1437 through 1451 removed outlier: 3.835A pdb=" N SER A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1473 removed outlier: 3.979A pdb=" N VAL A1469 " --> pdb=" O PHE A1465 " (cutoff:3.500A) removed outlier: 3.566A 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 1538 through 1560 Processing helix chain 'A' and resid 1569 through 1588 removed outlier: 3.542A pdb=" N ARG A1573 " --> pdb=" O PRO A1569 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A1577 " --> pdb=" O ARG A1573 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A1578 " --> pdb=" O VAL A1574 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG A1579 " --> pdb=" O ILE A1575 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE A1580 " --> pdb=" O ARG A1576 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY A1581 " --> pdb=" O LEU A1577 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG A1582 " --> pdb=" O ALA A1578 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A1583 " --> pdb=" O ARG A1579 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A1586 " --> pdb=" O ARG A1582 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE A1587 " --> pdb=" O ILE A1583 " (cutoff:3.500A) removed outlier: 4.940A 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 1659 removed outlier: 4.216A pdb=" N THR A1659 " --> pdb=" O PHE A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1670 Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1695 through 1727 removed outlier: 3.615A pdb=" N ILE A1707 " --> pdb=" O THR A1703 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1723 " --> pdb=" O ALA A1719 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 274 through 278 Processing sheet with id= B, first strand: chain 'A' and resid 1309 through 1312 535 hydrogen bonds defined for protein. 1452 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: 2.91 Time building geometry restraints manager: 4.59 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: 1569 1.33 - 1.45: 2599 1.45 - 1.57: 5656 1.57 - 1.70: 41 1.70 - 1.82: 103 Bond restraints: 9968 Sorted by residual: bond pdb=" C11 PCW A2007 " pdb=" O3 PCW A2007 " ideal model delta sigma weight residual 1.326 1.459 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C11 PCW A2019 " pdb=" O3 PCW A2019 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C11 PCW A2013 " pdb=" O3 PCW A2013 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C11 PCW A2016 " pdb=" O3 PCW A2016 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 PCW A2007 " pdb=" O2 PCW A2007 " ideal model delta sigma weight residual 1.333 1.457 -0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 9963 not shown) Histogram of bond angle deviations from ideal: 86.48 - 96.10: 3 96.10 - 105.73: 195 105.73 - 115.36: 6310 115.36 - 124.99: 6793 124.99 - 134.62: 160 Bond angle restraints: 13461 Sorted by residual: angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 111.14 123.54 -12.40 1.08e+00 8.57e-01 1.32e+02 angle pdb=" N VAL A1632 " pdb=" CA VAL A1632 " pdb=" C VAL A1632 " ideal model delta sigma weight residual 110.05 121.50 -11.45 1.09e+00 8.42e-01 1.10e+02 angle pdb=" C5 PCW A2019 " pdb=" N PCW A2019 " pdb=" C8 PCW A2019 " ideal model delta sigma weight residual 111.64 86.50 25.14 3.00e+00 1.11e-01 7.02e+01 angle pdb=" N SER A1685 " pdb=" CA SER A1685 " pdb=" C SER A1685 " ideal model delta sigma weight residual 110.28 121.54 -11.26 1.48e+00 4.57e-01 5.78e+01 angle pdb=" C6 PCW A2019 " pdb=" N PCW A2019 " pdb=" C8 PCW A2019 " ideal model delta sigma weight residual 109.11 86.48 22.63 3.00e+00 1.11e-01 5.69e+01 ... (remaining 13456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 5815 32.51 - 65.02: 353 65.02 - 97.53: 36 97.53 - 130.04: 8 130.04 - 162.55: 8 Dihedral angle restraints: 6220 sinusoidal: 3005 harmonic: 3215 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 93.00 176.85 -83.85 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA ASP A1691 " pdb=" C ASP A1691 " pdb=" N CYS A1692 " pdb=" CA CYS A1692 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" N PCW A2006 " pdb=" C4 PCW A2006 " pdb=" C5 PCW A2006 " pdb=" O4P PCW A2006 " ideal model delta sinusoidal sigma weight residual 293.34 130.79 162.55 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1272 0.073 - 0.146: 197 0.146 - 0.219: 34 0.219 - 0.292: 17 0.292 - 0.365: 1 Chirality restraints: 1521 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.62e+01 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 1.52e+01 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1518 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.229 2.00e-02 2.50e+03 1.94e-01 4.73e+02 pdb=" C7 NAG B 2 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.320 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 95T A2004 " 0.205 2.00e-02 2.50e+03 1.73e-01 3.73e+02 pdb=" C09 95T A2004 " 0.139 2.00e-02 2.50e+03 pdb=" C13 95T A2004 " -0.053 2.00e-02 2.50e+03 pdb=" N06 95T A2004 " -0.291 2.00e-02 2.50e+03 pdb=" O05 95T A2004 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.042 2.00e-02 2.50e+03 3.43e-02 1.47e+01 pdb=" C7 NAG B 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.054 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.008 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 46 2.54 - 3.13: 8008 3.13 - 3.72: 14569 3.72 - 4.31: 20551 4.31 - 4.90: 33701 Nonbonded interactions: 76875 Sorted by model distance: nonbonded pdb=" O3 NAG A2001 " pdb=" O7 NAG A2001 " model vdw 1.953 2.440 nonbonded pdb=" N GLU A1503 " pdb=" OE1 GLU A1503 " model vdw 2.269 2.520 nonbonded pdb=" O THR A1659 " pdb=" OG SER A1660 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASP A1664 " pdb=" N GLY A1665 " model vdw 2.343 2.520 nonbonded pdb=" O SER A 357 " pdb=" OG SER A 357 " model vdw 2.359 2.440 ... (remaining 76870 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 'B' selection = chain 'C' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.430 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 36.070 Find NCS groups from input model: 0.300 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.009 0.133 9968 Z= 0.534 Angle : 1.354 25.139 13461 Z= 0.658 Chirality : 0.060 0.365 1521 Planarity : 0.008 0.194 1541 Dihedral : 20.374 162.547 4123 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 0.51 % Allowed : 1.13 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1093 helix: 1.15 (0.19), residues: 753 sheet: -3.27 (0.84), residues: 22 loop : -1.82 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 729 HIS 0.002 0.001 HIS A 824 PHE 0.041 0.002 PHE A 194 TYR 0.044 0.003 TYR A1717 ARG 0.010 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.054 Fit side-chains REVERT: A 1556 PHE cc_start: 0.8519 (t80) cc_final: 0.7954 (t80) outliers start: 5 outliers final: 0 residues processed: 116 average time/residue: 1.0350 time to fit residues: 130.7168 Evaluate side-chains 78 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 271 ASN A 390 ASN ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 ASN A1631 HIS A Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9968 Z= 0.199 Angle : 0.738 9.878 13461 Z= 0.359 Chirality : 0.044 0.303 1521 Planarity : 0.005 0.039 1541 Dihedral : 19.383 164.356 2084 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.13 % Allowed : 11.33 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.64 (0.26), residues: 1093 helix: 1.34 (0.19), residues: 748 sheet: -3.15 (0.85), residues: 22 loop : -1.49 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1369 HIS 0.002 0.001 HIS A 241 PHE 0.030 0.001 PHE A 194 TYR 0.028 0.002 TYR A1717 ARG 0.007 0.001 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.4635 (mmp) cc_final: 0.4333 (ttp) REVERT: A 1446 MET cc_start: 0.8335 (ppp) cc_final: 0.8115 (ptt) REVERT: A 1556 PHE cc_start: 0.8478 (t80) cc_final: 0.7872 (t80) outliers start: 11 outliers final: 2 residues processed: 91 average time/residue: 1.0555 time to fit residues: 105.3871 Evaluate side-chains 80 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 TYR Chi-restraints excluded: chain A residue 744 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 0.0870 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9968 Z= 0.167 Angle : 0.635 9.074 13461 Z= 0.315 Chirality : 0.043 0.345 1521 Planarity : 0.004 0.030 1541 Dihedral : 17.659 165.439 2084 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.93 % Allowed : 13.80 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.80 (0.26), residues: 1093 helix: 1.40 (0.19), residues: 746 sheet: -2.90 (0.89), residues: 22 loop : -1.23 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1369 HIS 0.002 0.001 HIS A 241 PHE 0.025 0.001 PHE A 194 TYR 0.021 0.002 TYR A 400 ARG 0.006 0.000 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.273 Fit side-chains REVERT: A 1556 PHE cc_start: 0.8468 (t80) cc_final: 0.7844 (t80) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.9508 time to fit residues: 92.6749 Evaluate side-chains 80 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN A1444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9968 Z= 0.160 Angle : 0.599 8.982 13461 Z= 0.297 Chirality : 0.041 0.312 1521 Planarity : 0.004 0.031 1541 Dihedral : 16.484 164.219 2084 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.93 % Allowed : 15.24 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1093 helix: 1.49 (0.19), residues: 746 sheet: -2.83 (0.91), residues: 22 loop : -1.18 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1663 HIS 0.001 0.001 HIS A 837 PHE 0.020 0.001 PHE A 194 TYR 0.030 0.002 TYR A1717 ARG 0.004 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 1.095 Fit side-chains REVERT: A 1556 PHE cc_start: 0.8466 (t80) cc_final: 0.7823 (t80) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.9168 time to fit residues: 89.2046 Evaluate side-chains 82 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9736 > 50: distance: 2 - 17: 8.134 distance: 15 - 17: 8.194 distance: 17 - 18: 9.572 distance: 18 - 19: 13.166 distance: 19 - 20: 8.765 distance: 19 - 23: 3.552 distance: 21 - 22: 10.924 distance: 23 - 24: 8.731 distance: 24 - 25: 14.791 distance: 24 - 27: 6.819 distance: 25 - 26: 4.905 distance: 25 - 31: 16.983 distance: 27 - 28: 5.182 distance: 28 - 29: 4.263 distance: 28 - 30: 5.245 distance: 31 - 32: 33.729 distance: 32 - 33: 7.583 distance: 32 - 35: 10.323 distance: 33 - 34: 50.470 distance: 33 - 36: 38.752 distance: 36 - 37: 10.311 distance: 37 - 38: 19.022 distance: 37 - 40: 30.161 distance: 38 - 39: 6.898 distance: 38 - 47: 30.265 distance: 40 - 41: 39.694 distance: 41 - 42: 27.146 distance: 41 - 43: 14.650 distance: 42 - 44: 4.613 distance: 43 - 45: 11.635 distance: 44 - 46: 3.580 distance: 45 - 46: 8.310 distance: 47 - 48: 23.927 distance: 48 - 49: 9.381 distance: 48 - 51: 11.271 distance: 49 - 50: 7.095 distance: 49 - 56: 13.456 distance: 51 - 52: 28.932 distance: 52 - 53: 23.560 distance: 53 - 54: 14.003 distance: 53 - 55: 16.342 distance: 56 - 57: 13.434 distance: 57 - 58: 15.259 distance: 57 - 60: 11.590 distance: 58 - 59: 14.198 distance: 58 - 64: 18.618 distance: 60 - 61: 6.453 distance: 61 - 62: 15.143 distance: 61 - 63: 15.164 distance: 64 - 65: 11.708 distance: 65 - 66: 11.485 distance: 65 - 68: 13.116 distance: 66 - 67: 7.100 distance: 66 - 76: 9.357 distance: 68 - 69: 3.995 distance: 69 - 70: 3.970 distance: 70 - 72: 4.265 distance: 71 - 73: 3.617 distance: 72 - 74: 3.405 distance: 73 - 74: 3.493 distance: 74 - 75: 3.008 distance: 76 - 77: 7.067 distance: 77 - 78: 12.297 distance: 77 - 80: 13.948 distance: 78 - 79: 11.934 distance: 78 - 88: 20.690 distance: 80 - 81: 5.006 distance: 81 - 82: 5.392 distance: 81 - 83: 7.356 distance: 82 - 84: 5.395 distance: 83 - 85: 3.647 distance: 84 - 86: 5.371 distance: 85 - 86: 7.766 distance: 86 - 87: 8.583 distance: 88 - 89: 4.996 distance: 89 - 90: 11.066 distance: 89 - 92: 4.906 distance: 90 - 91: 3.125 distance: 90 - 96: 13.028 distance: 92 - 93: 3.884 distance: 93 - 94: 6.809 distance: 96 - 97: 14.546 distance: 97 - 98: 16.574 distance: 97 - 100: 9.536 distance: 98 - 99: 15.312 distance: 98 - 104: 9.682 distance: 100 - 101: 3.692 distance: 101 - 102: 3.726 distance: 101 - 103: 3.650