Starting phenix.real_space_refine on Wed Feb 14 17:32:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we4_32439/02_2024/7we4_32439_updated.pdb" } resolution = 2.7 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= 0.013 sd= 0.105 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 17 5.49 5 S 63 5.16 5 Cl 1 4.86 5 C 6567 2.51 5 N 1464 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 151": "OD1" <-> "OD2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 356": "OD1" <-> "OD2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ASP 720": "OD1" <-> "OD2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1187": "OE1" <-> "OE2" Residue "A TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1239": "OE1" <-> "OE2" Residue "A ARG 1250": "NH1" <-> "NH2" Residue "A TYR 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1503": "OE1" <-> "OE2" Residue "A ASP 1543": "OD1" <-> "OD2" Residue "A PHE 1624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1717": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9806 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9019 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1122, 9009 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1089} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 1122, 9009 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1089} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 9223 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: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 731 Unusual residues: {'95T': 1, 'CLR': 4, 'LPE': 9, 'NAG': 3, 'PCW': 5} Classifications: {'peptide': 3, 'undetermined': 22} Link IDs: {'TRANS': 2, None: 22} Not linked: pdbres="NAG A2001 " pdbres="NAG A2002 " Not linked: pdbres="NAG A2002 " pdbres="NAG A2003 " Not linked: pdbres="NAG A2003 " pdbres="95T A2004 " Not linked: pdbres="95T A2004 " pdbres="CLR A2005 " Not linked: pdbres="CLR A2005 " pdbres="PCW A2006 " ... (remaining 17 not shown) Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 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: 10.18, per 1000 atoms: 1.04 Number of scatterers: 9806 At special positions: 0 Unit cell: (132.065, 119.075, 99.59, 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 63 16.00 P 17 15.00 O 1694 8.00 N 1464 7.00 C 6567 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=2.02 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 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: 4.51 Conformation dependent library (CDL) restraints added in 3.3 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 2 sheets defined 70.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 130 through 148 Processing helix chain 'A' and resid 157 through 178 removed outlier: 3.896A pdb=" N THR A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.972A pdb=" N LEU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 removed outlier: 4.308A pdb=" N LEU A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.514A pdb=" N THR A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 268 removed outlier: 4.144A pdb=" N ALA A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASP A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 372 through 406 removed outlier: 3.967A pdb=" N PHE A 382 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A 383 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLY A 384 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 385 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR A 387 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 388 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 392 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 393 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A 398 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 405 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 665 through 684 removed outlier: 3.916A pdb=" N MET A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 718 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 745 removed outlier: 3.741A pdb=" N PHE A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 removed outlier: 3.582A pdb=" N LYS A 768 " --> pdb=" O LYS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 782 Processing helix chain 'A' and resid 788 through 815 removed outlier: 5.629A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 835 through 846 Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 863 through 893 removed outlier: 3.578A pdb=" N VAL A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1152 through 1171 removed outlier: 3.677A pdb=" N LEU A1169 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE A1171 " --> pdb=" O GLY A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1178 No H-bonds generated for 'chain 'A' and resid 1176 through 1178' Processing helix chain 'A' and resid 1180 through 1207 removed outlier: 3.949A pdb=" N ALA A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1214 Processing helix chain 'A' and resid 1220 through 1237 removed outlier: 3.785A pdb=" N ILE A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1260 removed outlier: 3.638A pdb=" N LEU A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA A1254 " --> pdb=" O ARG A1250 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU A1255 " --> pdb=" O THR A1251 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Proline residue: A1257 - end of helix removed outlier: 4.950A pdb=" N ALA A1260 " --> pdb=" O ARG A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1303 Proline residue: A1279 - end of helix removed outlier: 3.625A pdb=" N ASN A1283 " --> pdb=" O PRO A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1334 removed outlier: 3.514A pdb=" N ILE A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1364 removed outlier: 3.725A pdb=" N LEU A1358 " --> pdb=" O ALA A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1378 Processing helix chain 'A' and resid 1392 through 1404 removed outlier: 3.596A pdb=" N LEU A1396 " --> pdb=" O TYR A1393 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A1401 " --> pdb=" O PHE A1398 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A1402 " --> pdb=" O VAL A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1428 removed outlier: 3.656A pdb=" N LEU A1412 " --> pdb=" O PHE A1408 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A1413 " --> pdb=" O THR A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1451 removed outlier: 3.902A pdb=" N SER A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1474 Processing helix chain 'A' and resid 1476 through 1495 removed outlier: 3.665A pdb=" N VAL A1495 " --> pdb=" O ILE A1491 " (cutoff:3.500A) 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 1538 through 1559 removed outlier: 3.643A pdb=" N PHE A1542 " --> pdb=" O GLY A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1569 through 1588 removed outlier: 4.191A pdb=" N LEU A1577 " --> pdb=" O ARG A1573 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA A1578 " --> pdb=" O VAL A1574 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG A1579 " --> pdb=" O ILE A1575 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE A1580 " --> pdb=" O ARG A1576 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY A1581 " --> pdb=" O LEU A1577 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG A1582 " --> pdb=" O ALA A1578 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A1583 " --> pdb=" O ARG A1579 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A1586 " --> pdb=" O ARG A1582 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A1587 " --> pdb=" O ILE A1583 " (cutoff:3.500A) removed outlier: 4.908A 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 removed outlier: 3.715A pdb=" N ASN A1609 " --> pdb=" O PRO A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1659 removed outlier: 4.220A pdb=" N THR A1659 " --> pdb=" O PHE A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1671 Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1695 through 1727 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 1341 through 1345 536 hydrogen bonds defined for protein. 1500 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: 2.79 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1401 1.29 - 1.42: 2633 1.42 - 1.55: 5849 1.55 - 1.68: 44 1.68 - 1.81: 104 Bond restraints: 10031 Sorted by residual: bond pdb=" C ALA A 168 " pdb=" N LEU A 169 " ideal model delta sigma weight residual 1.335 1.234 0.101 1.31e-02 5.83e+03 5.90e+01 bond pdb=" C11 PCW A2007 " pdb=" O3 PCW A2007 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" C38 P5S A2024 " pdb=" O37 P5S A2024 " ideal model delta sigma weight residual 1.331 1.463 -0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C38 P5S A2023 " pdb=" O37 P5S A2023 " ideal model delta sigma weight residual 1.331 1.461 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C17 P5S A2024 " pdb=" O19 P5S A2024 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.18e+01 ... (remaining 10026 not shown) Histogram of bond angle deviations from ideal: 93.54 - 103.24: 115 103.24 - 112.93: 5555 112.93 - 122.62: 7130 122.62 - 132.32: 723 132.32 - 142.01: 29 Bond angle restraints: 13552 Sorted by residual: angle pdb=" N GLU A 157 " pdb=" CA GLU A 157 " pdb=" C GLU A 157 " ideal model delta sigma weight residual 111.28 100.51 10.77 1.09e+00 8.42e-01 9.76e+01 angle pdb=" N GLY A1690 " pdb=" CA GLY A1690 " pdb=" C GLY A1690 " ideal model delta sigma weight residual 110.55 122.52 -11.97 1.64e+00 3.72e-01 5.32e+01 angle pdb=" N TRP A1218 " pdb=" CA TRP A1218 " pdb=" C TRP A1218 " ideal model delta sigma weight residual 114.12 104.09 10.03 1.39e+00 5.18e-01 5.20e+01 angle pdb=" N GLU A 811 " pdb=" CA GLU A 811 " pdb=" C GLU A 811 " ideal model delta sigma weight residual 111.71 119.56 -7.85 1.15e+00 7.56e-01 4.66e+01 angle pdb=" C09 95T A2004 " pdb=" C13 95T A2004 " pdb=" N06 95T A2004 " ideal model delta sigma weight residual 119.48 139.89 -20.41 3.00e+00 1.11e-01 4.63e+01 ... (remaining 13547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.50: 5935 32.50 - 65.01: 229 65.01 - 97.51: 35 97.51 - 130.02: 11 130.02 - 162.52: 4 Dihedral angle restraints: 6214 sinusoidal: 2927 harmonic: 3287 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 93.00 176.58 -83.58 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS A 310 " pdb=" SG CYS A 310 " pdb=" SG CYS A 325 " pdb=" CB CYS A 325 " ideal model delta sinusoidal sigma weight residual -86.00 -162.39 76.39 1 1.00e+01 1.00e-02 7.34e+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 -86.00 -144.64 58.64 1 1.00e+01 1.00e-02 4.60e+01 ... (remaining 6211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.312: 1524 0.312 - 0.624: 12 0.624 - 0.936: 1 0.936 - 1.248: 0 1.248 - 1.560: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" C1 NAG A2003 " pdb=" ND2 ASN A1312 " pdb=" C2 NAG A2003 " pdb=" O5 NAG A2003 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-01 2.50e+01 6.09e+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 -2.27 -0.13 2.00e-02 2.50e+03 4.02e+01 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 1.58e+01 ... (remaining 1535 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.338 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG B 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2003 " 0.298 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C7 NAG A2003 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG A2003 " 0.145 2.00e-02 2.50e+03 pdb=" N2 NAG A2003 " -0.464 2.00e-02 2.50e+03 pdb=" O7 NAG A2003 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " -0.300 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C7 NAG A2001 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " -0.073 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1937 2.77 - 3.30: 9656 3.30 - 3.84: 15792 3.84 - 4.37: 19354 4.37 - 4.90: 31851 Nonbonded interactions: 78590 Sorted by model distance: nonbonded pdb=" O ILE A1699 " pdb=" OG1 THR A1703 " model vdw 2.238 2.440 nonbonded pdb=" O LEU A 220 " pdb=" N LEU A 223 " model vdw 2.257 2.520 nonbonded pdb=" O ILE A1700 " pdb=" OG1 THR A1704 " model vdw 2.295 2.440 nonbonded pdb=" O GLY A1405 " pdb=" OG1 THR A1409 " model vdw 2.304 2.440 nonbonded pdb=" OD1 ASN A 390 " pdb=" CD1 TYR A1717 " model vdw 2.309 3.340 ... (remaining 78585 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: 0.880 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: 3.510 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 37.040 Find NCS groups from input model: 0.280 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:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.012 0.132 10031 Z= 0.747 Angle : 1.593 20.411 13552 Z= 0.870 Chirality : 0.089 1.560 1538 Planarity : 0.016 0.292 1571 Dihedral : 18.128 162.522 4069 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.30 % Favored : 94.17 % Rotamer: Outliers : 0.31 % Allowed : 2.44 % Favored : 97.25 % Cbeta Deviations : 0.38 % 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: -0.28 (0.26), residues: 1117 helix: 0.81 (0.19), residues: 776 sheet: -2.35 (0.95), residues: 22 loop : -2.53 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP A1369 HIS 0.003 0.001 HIS A 129 PHE 0.046 0.002 PHE A 177 TYR 0.085 0.003 TYR A1374 ARG 0.012 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.018 Fit side-chains REVERT: A 182 PHE cc_start: 0.5153 (t80) cc_final: 0.4855 (m-80) outliers start: 3 outliers final: 0 residues processed: 171 average time/residue: 1.1216 time to fit residues: 206.9792 Evaluate side-chains 126 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 271 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN A1420 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10031 Z= 0.207 Angle : 0.722 16.282 13552 Z= 0.350 Chirality : 0.043 0.244 1538 Planarity : 0.005 0.057 1571 Dihedral : 18.356 170.086 2006 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.83 % Allowed : 9.77 % Favored : 88.40 % 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: 0.48 (0.26), residues: 1117 helix: 1.29 (0.19), residues: 769 sheet: -2.29 (0.86), residues: 24 loop : -1.85 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1369 HIS 0.003 0.001 HIS A 129 PHE 0.036 0.002 PHE A 693 TYR 0.036 0.002 TYR A1374 ARG 0.009 0.001 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.066 Fit side-chains REVERT: A 156 ILE cc_start: 0.5024 (OUTLIER) cc_final: 0.4788 (mp) REVERT: A 1147 ARG cc_start: 0.6376 (mtp180) cc_final: 0.6056 (mtm-85) REVERT: A 1315 ASP cc_start: 0.6355 (p0) cc_final: 0.6143 (p0) REVERT: A 1384 MET cc_start: 0.8132 (mtm) cc_final: 0.7894 (mtm) REVERT: A 1722 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8174 (mm) outliers start: 18 outliers final: 6 residues processed: 140 average time/residue: 1.1106 time to fit residues: 168.4182 Evaluate side-chains 132 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1722 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.0670 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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** A 807 GLN ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10031 Z= 0.157 Angle : 0.593 14.590 13552 Z= 0.293 Chirality : 0.039 0.186 1538 Planarity : 0.004 0.049 1571 Dihedral : 16.419 170.863 2006 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.53 % Allowed : 12.11 % Favored : 86.37 % 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: 1.01 (0.26), residues: 1117 helix: 1.55 (0.19), residues: 770 sheet: -2.28 (0.86), residues: 24 loop : -1.21 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1369 HIS 0.002 0.001 HIS A 837 PHE 0.028 0.001 PHE A 693 TYR 0.024 0.001 TYR A1374 ARG 0.006 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.139 Fit side-chains REVERT: A 165 THR cc_start: 0.7737 (m) cc_final: 0.7439 (p) REVERT: A 1147 ARG cc_start: 0.6381 (mtp180) cc_final: 0.6114 (mtm-85) REVERT: A 1315 ASP cc_start: 0.6378 (p0) cc_final: 0.6060 (p0) REVERT: A 1384 MET cc_start: 0.8120 (mtm) cc_final: 0.7912 (mtm) outliers start: 15 outliers final: 6 residues processed: 141 average time/residue: 1.0762 time to fit residues: 164.8435 Evaluate side-chains 127 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1601 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 0.0980 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN A1178 GLN A1301 ASN A1345 ASN ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10031 Z= 0.163 Angle : 0.583 13.546 13552 Z= 0.290 Chirality : 0.039 0.171 1538 Planarity : 0.004 0.047 1571 Dihedral : 15.377 169.739 2006 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.42 % Allowed : 13.53 % Favored : 85.05 % 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: 1.28 (0.26), residues: 1117 helix: 1.66 (0.19), residues: 769 sheet: -1.66 (0.96), residues: 20 loop : -0.92 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1369 HIS 0.002 0.001 HIS A 687 PHE 0.034 0.001 PHE A 386 TYR 0.020 0.002 TYR A1374 ARG 0.004 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.213 Fit side-chains REVERT: A 1315 ASP cc_start: 0.6271 (p0) cc_final: 0.6023 (p0) REVERT: A 1384 MET cc_start: 0.8123 (mtm) cc_final: 0.7878 (mtm) outliers start: 14 outliers final: 8 residues processed: 133 average time/residue: 1.0680 time to fit residues: 154.6121 Evaluate side-chains 130 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1601 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 ASN A 878 ASN ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10031 Z= 0.322 Angle : 0.667 13.424 13552 Z= 0.338 Chirality : 0.043 0.181 1538 Planarity : 0.005 0.045 1571 Dihedral : 15.065 167.874 2006 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.34 % Allowed : 13.63 % Favored : 84.03 % 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: 0.94 (0.26), residues: 1117 helix: 1.43 (0.19), residues: 768 sheet: -2.03 (0.90), residues: 24 loop : -1.08 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1369 HIS 0.005 0.001 HIS A 687 PHE 0.032 0.002 PHE A 386 TYR 0.024 0.002 TYR A1374 ARG 0.006 0.001 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.134 Fit side-chains REVERT: A 281 MET cc_start: 0.5184 (mpt) cc_final: 0.4953 (mpp) REVERT: A 817 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8141 (ptt90) REVERT: A 1315 ASP cc_start: 0.6548 (p0) cc_final: 0.6300 (p0) REVERT: A 1384 MET cc_start: 0.8192 (mtm) cc_final: 0.7897 (mtm) outliers start: 23 outliers final: 11 residues processed: 146 average time/residue: 1.0555 time to fit residues: 167.4104 Evaluate side-chains 136 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 817 ARG Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1392 VAL Chi-restraints excluded: chain A residue 1681 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 789 ASN A1301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10031 Z= 0.167 Angle : 0.580 13.629 13552 Z= 0.289 Chirality : 0.039 0.176 1538 Planarity : 0.004 0.044 1571 Dihedral : 14.355 167.593 2006 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.22 % Allowed : 15.06 % Favored : 83.72 % 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: 1.30 (0.26), residues: 1117 helix: 1.66 (0.19), residues: 769 sheet: -1.53 (0.90), residues: 22 loop : -0.85 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 191 HIS 0.011 0.001 HIS A 129 PHE 0.017 0.001 PHE A 693 TYR 0.022 0.001 TYR A 164 ARG 0.005 0.001 ARG A1250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.151 Fit side-chains REVERT: A 281 MET cc_start: 0.5283 (mpt) cc_final: 0.5063 (mpp) REVERT: A 1315 ASP cc_start: 0.6345 (p0) cc_final: 0.6138 (p0) REVERT: A 1317 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: A 1384 MET cc_start: 0.8152 (mtm) cc_final: 0.7911 (mtm) outliers start: 12 outliers final: 7 residues processed: 133 average time/residue: 1.0692 time to fit residues: 155.1045 Evaluate side-chains 125 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1317 GLU Chi-restraints excluded: chain A residue 1392 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS A 789 ASN A 878 ASN A1178 GLN A1301 ASN ** A1466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10031 Z= 0.209 Angle : 0.597 13.247 13552 Z= 0.300 Chirality : 0.040 0.240 1538 Planarity : 0.004 0.045 1571 Dihedral : 14.105 167.720 2006 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.73 % Allowed : 14.85 % Favored : 83.42 % 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: 1.24 (0.26), residues: 1117 helix: 1.64 (0.19), residues: 769 sheet: -2.01 (0.88), residues: 24 loop : -0.89 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.010 0.001 HIS A 129 PHE 0.018 0.001 PHE A 693 TYR 0.026 0.002 TYR A 164 ARG 0.005 0.001 ARG A1250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.118 Fit side-chains REVERT: A 281 MET cc_start: 0.5301 (mpt) cc_final: 0.5095 (mpp) REVERT: A 758 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7124 (t80) REVERT: A 1315 ASP cc_start: 0.6506 (p0) cc_final: 0.6260 (p0) REVERT: A 1317 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: A 1384 MET cc_start: 0.8155 (mtm) cc_final: 0.7914 (mtm) outliers start: 17 outliers final: 7 residues processed: 128 average time/residue: 1.2496 time to fit residues: 172.9500 Evaluate side-chains 126 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1317 GLU Chi-restraints excluded: chain A residue 1392 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A 878 ASN A1178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10031 Z= 0.159 Angle : 0.559 12.761 13552 Z= 0.279 Chirality : 0.038 0.232 1538 Planarity : 0.004 0.048 1571 Dihedral : 13.500 168.066 2006 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.83 % Allowed : 15.36 % Favored : 82.81 % 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: 1.49 (0.26), residues: 1117 helix: 1.76 (0.19), residues: 771 sheet: -1.74 (0.87), residues: 22 loop : -0.67 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 191 HIS 0.010 0.001 HIS A 129 PHE 0.036 0.001 PHE A 386 TYR 0.020 0.001 TYR A 164 ARG 0.005 0.000 ARG A1250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.123 Fit side-chains REVERT: A 147 MET cc_start: 0.7010 (ptm) cc_final: 0.6786 (ptt) REVERT: A 281 MET cc_start: 0.5271 (mpt) cc_final: 0.5046 (mpp) REVERT: A 758 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7079 (t80) REVERT: A 1315 ASP cc_start: 0.6399 (p0) cc_final: 0.6176 (p0) REVERT: A 1317 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: A 1384 MET cc_start: 0.8138 (mtm) cc_final: 0.7903 (mtm) outliers start: 18 outliers final: 8 residues processed: 131 average time/residue: 1.0645 time to fit residues: 151.8409 Evaluate side-chains 128 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1317 GLU Chi-restraints excluded: chain A residue 1355 MET Chi-restraints excluded: chain A residue 1392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** A 789 ASN A 878 ASN ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10031 Z= 0.193 Angle : 0.576 12.483 13552 Z= 0.289 Chirality : 0.039 0.220 1538 Planarity : 0.004 0.050 1571 Dihedral : 13.382 169.090 2006 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.42 % Allowed : 15.97 % Favored : 82.60 % 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: 1.46 (0.26), residues: 1117 helix: 1.76 (0.19), residues: 770 sheet: -1.67 (0.90), residues: 22 loop : -0.74 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 191 HIS 0.002 0.001 HIS A 687 PHE 0.031 0.002 PHE A 386 TYR 0.022 0.002 TYR A 164 ARG 0.003 0.000 ARG A1259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.210 Fit side-chains REVERT: A 281 MET cc_start: 0.5298 (mpt) cc_final: 0.5089 (mpp) REVERT: A 1384 MET cc_start: 0.8146 (mtm) cc_final: 0.7907 (mtm) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 1.0442 time to fit residues: 145.3908 Evaluate side-chains 128 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** A 789 ASN A 878 ASN ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10031 Z= 0.177 Angle : 0.576 12.463 13552 Z= 0.289 Chirality : 0.039 0.222 1538 Planarity : 0.004 0.050 1571 Dihedral : 13.243 169.965 2006 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.12 % Allowed : 16.28 % Favored : 82.60 % 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: 1.54 (0.26), residues: 1117 helix: 1.81 (0.19), residues: 772 sheet: -1.68 (0.90), residues: 22 loop : -0.68 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.002 0.001 HIS A 687 PHE 0.038 0.002 PHE A 386 TYR 0.021 0.001 TYR A 164 ARG 0.003 0.000 ARG A1460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.030 Fit side-chains REVERT: A 147 MET cc_start: 0.7004 (ptm) cc_final: 0.6798 (ptt) REVERT: A 758 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7182 (t80) REVERT: A 1384 MET cc_start: 0.8148 (mtm) cc_final: 0.7901 (mtm) outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 1.1514 time to fit residues: 160.3273 Evaluate side-chains 127 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1211 LYS Chi-restraints excluded: chain A residue 1291 PHE Chi-restraints excluded: chain A residue 1392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A 789 ASN ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110856 restraints weight = 13917.849| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.98 r_work: 0.3250 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10031 Z= 0.170 Angle : 0.567 12.236 13552 Z= 0.285 Chirality : 0.039 0.220 1538 Planarity : 0.004 0.054 1571 Dihedral : 13.077 171.085 2006 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.02 % Allowed : 16.58 % Favored : 82.40 % 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: 1.58 (0.26), residues: 1117 helix: 1.84 (0.19), residues: 772 sheet: -1.71 (0.90), residues: 22 loop : -0.65 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 191 HIS 0.002 0.001 HIS A 687 PHE 0.038 0.001 PHE A 386 TYR 0.020 0.001 TYR A 164 ARG 0.003 0.000 ARG A1460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.14 seconds wall clock time: 64 minutes 32.34 seconds (3872.34 seconds total)