Starting phenix.real_space_refine on Thu Mar 14 21:44:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wel_32451/03_2024/7wel_32451_updated.pdb" } resolution = 3.2 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 21 5.49 5 S 62 5.16 5 Cl 1 4.86 5 C 6594 2.51 5 N 1443 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 GLU 154": "OE1" <-> "OE2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1177": "OD1" <-> "OD2" Residue "A GLU 1187": "OE1" <-> "OE2" Residue "A ASP 1190": "OD1" <-> "OD2" Residue "A PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1222": "OD1" <-> "OD2" Residue "A GLU 1242": "OE1" <-> "OE2" Residue "A PHE 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1371": "OD1" <-> "OD2" Residue "A GLU 1389": "OE1" <-> "OE2" Residue "A PHE 1407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1419": "OD1" <-> "OD2" Residue "A ASP 1432": "OD1" <-> "OD2" Residue "A GLU 1437": "OE1" <-> "OE2" Residue "A TYR 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1503": "OE1" <-> "OE2" Residue "A PHE 1556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1639": "OD1" <-> "OD2" Residue "A TYR 1717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1723": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9815 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8882 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1102, 8872 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1069} 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: 1102, 8872 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1069} 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: 9083 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: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 877 Unusual residues: {'95T': 1, 'CLR': 5, 'LPE': 12, 'NAG': 3, 'PCW': 7} Classifications: {'peptide': 2, 'undetermined': 28} Link IDs: {'TRANS': 1, None: 28} 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="CLR A2006 " ... (remaining 23 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 7 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: 9.71, per 1000 atoms: 0.99 Number of scatterers: 9815 At special positions: 0 Unit cell: (130.982, 121.24, 100.672, 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 21 15.00 O 1694 8.00 N 1443 7.00 C 6594 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=2.22 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: 4.21 Conformation dependent library (CDL) restraints added in 3.1 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 2 sheets defined 71.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 130 through 148 Processing helix chain 'A' and resid 156 through 176 removed outlier: 3.584A pdb=" N ILE A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 213 through 227 removed outlier: 3.686A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 268 removed outlier: 3.671A pdb=" N HIS A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 255 " --> pdb=" O ILE A 251 " (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: 3.870A pdb=" N VAL A 380 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 382 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE A 386 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR A 387 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 393 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET A 398 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 665 through 684 removed outlier: 3.777A pdb=" N THR A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.560A pdb=" N GLN A 726 " --> pdb=" O TYR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 745 Processing helix chain 'A' and resid 753 through 757 Processing helix chain 'A' and resid 759 through 765 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 788 through 809 Processing helix chain 'A' and resid 812 through 815 No H-bonds generated for 'chain 'A' and resid 812 through 815' 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 892 Processing helix chain 'A' and resid 1137 through 1150 Processing helix chain 'A' and resid 1152 through 1171 removed outlier: 3.556A pdb=" N LEU A1169 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.120A 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 1208 Processing helix chain 'A' and resid 1210 through 1213 No H-bonds generated for 'chain 'A' and resid 1210 through 1213' Processing helix chain 'A' and resid 1219 through 1237 Processing helix chain 'A' and resid 1244 through 1263 removed outlier: 3.979A pdb=" N THR A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A1252 " --> pdb=" O ALA A1248 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A1253 " --> pdb=" O LEU A1249 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA A1254 " --> pdb=" O ARG A1250 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU A1255 " --> pdb=" O THR A1251 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Proline residue: A1257 - end of helix removed outlier: 4.347A 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: 3.558A pdb=" N ASN A1283 " --> pdb=" O PRO A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1334 removed outlier: 3.754A pdb=" N LYS A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1365 removed outlier: 3.537A pdb=" N LEU A1358 " --> pdb=" O ALA A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1377 Processing helix chain 'A' and resid 1392 through 1428 removed outlier: 3.712A pdb=" N TYR A1395 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A1396 " --> pdb=" O TYR A1393 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY A1405 " --> pdb=" O ILE A1402 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLY A1406 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE A1407 " --> pdb=" O PHE A1404 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1410 " --> pdb=" O PHE A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1451 removed outlier: 3.509A pdb=" N GLY A1450 " --> pdb=" O MET A1446 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.655A 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 1563 removed outlier: 3.558A pdb=" N ALA A1558 " --> pdb=" O LEU A1554 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1561 " --> pdb=" O SER A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1569 through 1578 removed outlier: 3.523A pdb=" N VAL A1574 " --> pdb=" O THR A1570 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A1577 " --> pdb=" O ARG A1573 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA A1578 " --> pdb=" O VAL A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1588 removed outlier: 4.222A pdb=" N LEU A1586 " --> pdb=" O ARG A1582 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE A1587 " --> pdb=" O ILE A1583 " (cutoff:3.500A) removed outlier: 4.784A 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: 3.569A pdb=" N ASN A1609 " --> pdb=" O PRO A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1658 Processing helix chain 'A' and resid 1663 through 1670 Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1695 through 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 553 hydrogen bonds defined for protein. 1482 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: 2.80 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1374 1.30 - 1.43: 2605 1.43 - 1.56: 5900 1.56 - 1.68: 54 1.68 - 1.81: 103 Bond restraints: 10036 Sorted by residual: bond pdb=" C38 P5S A2029 " pdb=" O37 P5S A2029 " ideal model delta sigma weight residual 1.331 1.465 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C11 PCW A2008 " pdb=" O3 PCW A2008 " ideal model delta sigma weight residual 1.326 1.456 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C17 P5S A2029 " pdb=" O19 P5S A2029 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C11 PCW A2012 " pdb=" O3 PCW A2012 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C31 PCW A2008 " pdb=" O2 PCW A2008 " ideal model delta sigma weight residual 1.333 1.459 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 10031 not shown) Histogram of bond angle deviations from ideal: 98.73 - 107.40: 371 107.40 - 116.06: 6382 116.06 - 124.73: 6629 124.73 - 133.39: 133 133.39 - 142.06: 29 Bond angle restraints: 13544 Sorted by residual: angle pdb=" N GLY A1687 " pdb=" CA GLY A1687 " pdb=" C GLY A1687 " ideal model delta sigma weight residual 112.73 124.33 -11.60 1.20e+00 6.94e-01 9.35e+01 angle pdb=" N LYS A 155 " pdb=" CA LYS A 155 " pdb=" C LYS A 155 " ideal model delta sigma weight residual 114.62 104.44 10.18 1.14e+00 7.69e-01 7.98e+01 angle pdb=" N ASP A1691 " pdb=" CA ASP A1691 " pdb=" C ASP A1691 " ideal model delta sigma weight residual 113.15 103.68 9.47 1.19e+00 7.06e-01 6.33e+01 angle pdb=" N ALA A1589 " pdb=" CA ALA A1589 " pdb=" C ALA A1589 " ideal model delta sigma weight residual 111.36 119.65 -8.29 1.09e+00 8.42e-01 5.79e+01 angle pdb=" C09 95T A2004 " pdb=" C13 95T A2004 " pdb=" N06 95T A2004 " ideal model delta sigma weight residual 119.48 139.83 -20.35 3.00e+00 1.11e-01 4.60e+01 ... (remaining 13539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 5928 32.52 - 65.03: 294 65.03 - 97.55: 34 97.55 - 130.06: 9 130.06 - 162.58: 6 Dihedral angle restraints: 6271 sinusoidal: 3048 harmonic: 3223 Sorted by residual: 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 -171.70 85.70 1 1.00e+01 1.00e-02 8.88e+01 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 93.00 176.32 -83.32 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" N PHE A1408 " pdb=" C PHE A1408 " pdb=" CA PHE A1408 " pdb=" CB PHE A1408 " ideal model delta harmonic sigma weight residual 122.80 141.40 -18.60 0 2.50e+00 1.60e-01 5.53e+01 ... (remaining 6268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1450 0.152 - 0.304: 67 0.304 - 0.457: 6 0.457 - 0.609: 1 0.609 - 0.761: 1 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.23e+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 1.55e+01 chirality pdb=" CA PHE A1408 " pdb=" N PHE A1408 " pdb=" C PHE A1408 " pdb=" CB PHE A1408 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 1522 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.300 2.00e-02 2.50e+03 2.64e-01 8.74e+02 pdb=" C7 NAG B 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.276 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" C7 NAG C 1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.390 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.244 2.00e-02 2.50e+03 2.09e-01 5.48e+02 pdb=" C7 NAG B 2 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.350 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.184 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 10 2.46 - 3.07: 6884 3.07 - 3.68: 14174 3.68 - 4.29: 21538 4.29 - 4.90: 34890 Nonbonded interactions: 77496 Sorted by model distance: nonbonded pdb=" CD2 LEU A 214 " pdb=" NH2 ARG A 215 " model vdw 1.853 3.540 nonbonded pdb=" O3 NAG A2001 " pdb=" O7 NAG A2001 " model vdw 2.129 2.440 nonbonded pdb=" CD2 LEU A 889 " pdb=" OD1 ASN A1411 " model vdw 2.279 3.460 nonbonded pdb=" CD1 PHE A1171 " pdb=" C2N LPE A2022 " model vdw 2.383 3.760 nonbonded pdb=" O GLN A1500 " pdb=" O1P PCW A2027 " model vdw 2.383 3.040 ... (remaining 77491 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: 0.790 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: 3.360 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.640 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.010 0.134 10036 Z= 0.567 Angle : 1.416 20.355 13544 Z= 0.722 Chirality : 0.072 0.761 1525 Planarity : 0.013 0.264 1549 Dihedral : 18.796 162.577 4168 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 23.37 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.03 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 2.16 % Favored : 97.43 % 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: 1.04 (0.26), residues: 1095 helix: 1.56 (0.19), residues: 793 sheet: -1.42 (0.97), residues: 12 loop : -1.69 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP A1369 HIS 0.002 0.001 HIS A 833 PHE 0.047 0.002 PHE A 135 TYR 0.056 0.003 TYR A1374 ARG 0.007 0.001 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 202 time to evaluate : 1.024 Fit side-chains REVERT: A 1160 PHE cc_start: 0.8306 (m-80) cc_final: 0.8103 (m-80) REVERT: A 1215 THR cc_start: 0.7703 (m) cc_final: 0.7461 (p) REVERT: A 1446 MET cc_start: 0.6689 (ttp) cc_final: 0.6464 (ttp) outliers start: 4 outliers final: 1 residues processed: 204 average time/residue: 0.2103 time to fit residues: 61.7483 Evaluate side-chains 141 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.0670 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 190 ASN A 833 HIS A1216 ASN ** A1362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 HIS A Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10036 Z= 0.181 Angle : 0.716 15.115 13544 Z= 0.343 Chirality : 0.042 0.278 1525 Planarity : 0.006 0.048 1549 Dihedral : 18.552 168.675 2127 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.66 % Favored : 96.06 % Rotamer: Outliers : 1.03 % Allowed : 8.43 % Favored : 90.54 % 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: 1.15 (0.26), residues: 1095 helix: 1.55 (0.19), residues: 786 sheet: -1.90 (1.08), residues: 12 loop : -1.24 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1369 HIS 0.002 0.000 HIS A 318 PHE 0.043 0.002 PHE A1556 TYR 0.039 0.003 TYR A1374 ARG 0.005 0.001 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 1.035 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 155 average time/residue: 0.1713 time to fit residues: 40.3800 Evaluate side-chains 142 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 HIS A1631 HIS B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10036 Z= 0.195 Angle : 0.636 13.300 13544 Z= 0.310 Chirality : 0.040 0.263 1525 Planarity : 0.005 0.047 1549 Dihedral : 16.309 169.955 2125 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.57 % Favored : 96.06 % Rotamer: Outliers : 1.03 % Allowed : 10.38 % Favored : 88.59 % 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: 1.13 (0.26), residues: 1095 helix: 1.48 (0.19), residues: 787 sheet: -2.78 (1.10), residues: 12 loop : -1.01 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1369 HIS 0.003 0.001 HIS A 831 PHE 0.049 0.002 PHE A1556 TYR 0.027 0.002 TYR A1374 ARG 0.005 0.001 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.153 Fit side-chains REVERT: A 281 MET cc_start: 0.3428 (mpp) cc_final: 0.1900 (mpp) outliers start: 10 outliers final: 7 residues processed: 143 average time/residue: 0.1687 time to fit residues: 37.2917 Evaluate side-chains 141 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1446 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10036 Z= 0.172 Angle : 0.579 12.012 13544 Z= 0.286 Chirality : 0.039 0.248 1525 Planarity : 0.005 0.046 1549 Dihedral : 15.353 168.942 2125 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.48 % Favored : 96.15 % Rotamer: Outliers : 0.92 % Allowed : 11.10 % Favored : 87.98 % 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: 1.18 (0.26), residues: 1095 helix: 1.45 (0.19), residues: 789 sheet: -2.54 (1.14), residues: 12 loop : -0.84 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1369 HIS 0.002 0.001 HIS A 837 PHE 0.024 0.001 PHE A1421 TYR 0.023 0.002 TYR A1374 ARG 0.004 0.000 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.3722 (mpp) cc_final: 0.2063 (mpp) REVERT: A 324 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7367 (tt) REVERT: A 1446 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6304 (mtm) outliers start: 9 outliers final: 6 residues processed: 142 average time/residue: 0.1821 time to fit residues: 39.2286 Evaluate side-chains 139 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN A1151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10036 Z= 0.211 Angle : 0.599 11.427 13544 Z= 0.297 Chirality : 0.039 0.239 1525 Planarity : 0.005 0.047 1549 Dihedral : 14.608 167.264 2125 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.12 % Favored : 95.51 % Rotamer: Outliers : 1.85 % Allowed : 10.79 % Favored : 87.36 % 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: 1.14 (0.27), residues: 1095 helix: 1.43 (0.19), residues: 782 sheet: -3.30 (1.09), residues: 14 loop : -0.77 (0.40), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1369 HIS 0.003 0.001 HIS A 837 PHE 0.025 0.002 PHE A 160 TYR 0.019 0.002 TYR A 362 ARG 0.004 0.001 ARG A1309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 281 MET cc_start: 0.3556 (mpp) cc_final: 0.1830 (mpp) REVERT: A 1413 PHE cc_start: 0.7333 (t80) cc_final: 0.7079 (t80) REVERT: A 1446 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6362 (mtm) outliers start: 18 outliers final: 13 residues processed: 148 average time/residue: 0.1681 time to fit residues: 38.4250 Evaluate side-chains 147 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN A1151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10036 Z= 0.163 Angle : 0.566 10.793 13544 Z= 0.281 Chirality : 0.038 0.204 1525 Planarity : 0.005 0.046 1549 Dihedral : 14.094 167.365 2125 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.75 % Favored : 95.97 % Rotamer: Outliers : 1.44 % Allowed : 12.02 % Favored : 86.54 % 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: 1.24 (0.27), residues: 1095 helix: 1.50 (0.19), residues: 780 sheet: -2.63 (1.16), residues: 12 loop : -0.76 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1369 HIS 0.001 0.000 HIS A 831 PHE 0.025 0.001 PHE A1421 TYR 0.018 0.002 TYR A1374 ARG 0.004 0.000 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.3412 (mpp) cc_final: 0.1706 (mpp) REVERT: A 713 VAL cc_start: 0.8613 (p) cc_final: 0.8403 (p) REVERT: A 1413 PHE cc_start: 0.7362 (t80) cc_final: 0.7116 (t80) REVERT: A 1446 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6351 (mtm) outliers start: 14 outliers final: 10 residues processed: 145 average time/residue: 0.1912 time to fit residues: 42.7218 Evaluate side-chains 144 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 10036 Z= 0.155 Angle : 0.553 10.292 13544 Z= 0.275 Chirality : 0.037 0.204 1525 Planarity : 0.005 0.046 1549 Dihedral : 13.606 168.862 2125 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.94 % Favored : 95.79 % Rotamer: Outliers : 1.13 % Allowed : 12.54 % Favored : 86.33 % 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: 1.33 (0.27), residues: 1095 helix: 1.55 (0.19), residues: 781 sheet: -2.71 (1.13), residues: 12 loop : -0.67 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1369 HIS 0.001 0.001 HIS A 831 PHE 0.027 0.001 PHE A 160 TYR 0.025 0.002 TYR A1705 ARG 0.004 0.000 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.3521 (mpp) cc_final: 0.1794 (mpp) REVERT: A 713 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8344 (p) REVERT: A 1446 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6348 (mtm) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 0.1608 time to fit residues: 35.4996 Evaluate side-chains 142 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10036 Z= 0.239 Angle : 0.602 10.543 13544 Z= 0.300 Chirality : 0.039 0.208 1525 Planarity : 0.005 0.048 1549 Dihedral : 13.693 171.799 2125 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.49 % Favored : 95.24 % Rotamer: Outliers : 1.03 % Allowed : 12.95 % Favored : 86.02 % 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: 1.11 (0.26), residues: 1095 helix: 1.40 (0.19), residues: 783 sheet: -3.39 (1.05), residues: 14 loop : -0.73 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1369 HIS 0.003 0.001 HIS A 837 PHE 0.020 0.002 PHE A1421 TYR 0.024 0.002 TYR A1705 ARG 0.003 0.001 ARG A 756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.3995 (mpp) cc_final: 0.2225 (mpp) REVERT: A 1413 PHE cc_start: 0.7295 (t80) cc_final: 0.7065 (t80) REVERT: A 1446 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6313 (mtm) outliers start: 10 outliers final: 7 residues processed: 136 average time/residue: 0.1588 time to fit residues: 33.4748 Evaluate side-chains 139 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN A1489 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10036 Z= 0.166 Angle : 0.552 9.939 13544 Z= 0.276 Chirality : 0.038 0.190 1525 Planarity : 0.005 0.047 1549 Dihedral : 13.352 172.681 2125 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.12 % Favored : 95.60 % Rotamer: Outliers : 1.03 % Allowed : 13.57 % Favored : 85.41 % 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: 1.26 (0.27), residues: 1095 helix: 1.53 (0.19), residues: 780 sheet: -2.55 (1.17), residues: 12 loop : -0.79 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1369 HIS 0.002 0.001 HIS A 831 PHE 0.025 0.001 PHE A1421 TYR 0.024 0.002 TYR A1705 ARG 0.004 0.000 ARG A1582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.3963 (mpp) cc_final: 0.2193 (mpp) REVERT: A 1413 PHE cc_start: 0.7298 (t80) cc_final: 0.7072 (t80) REVERT: A 1446 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6307 (mtm) REVERT: A 1587 ILE cc_start: 0.8905 (pt) cc_final: 0.8466 (mt) outliers start: 10 outliers final: 8 residues processed: 143 average time/residue: 0.1741 time to fit residues: 38.5915 Evaluate side-chains 144 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10036 Z= 0.168 Angle : 0.548 9.695 13544 Z= 0.273 Chirality : 0.037 0.179 1525 Planarity : 0.005 0.047 1549 Dihedral : 13.185 173.599 2125 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.21 % Favored : 95.51 % Rotamer: Outliers : 1.13 % Allowed : 13.87 % Favored : 84.99 % 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 (0.27), residues: 1095 helix: 1.55 (0.19), residues: 781 sheet: -2.43 (1.18), residues: 12 loop : -0.74 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1369 HIS 0.002 0.001 HIS A 831 PHE 0.024 0.001 PHE A1421 TYR 0.032 0.002 TYR A1705 ARG 0.003 0.000 ARG A 756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.3943 (mpp) cc_final: 0.2676 (mpp) REVERT: A 1413 PHE cc_start: 0.7297 (t80) cc_final: 0.7078 (t80) REVERT: A 1446 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6310 (mtm) REVERT: A 1587 ILE cc_start: 0.8871 (pt) cc_final: 0.8451 (mt) outliers start: 11 outliers final: 8 residues processed: 142 average time/residue: 0.1590 time to fit residues: 35.2719 Evaluate side-chains 143 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113366 restraints weight = 33959.330| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.96 r_work: 0.3341 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 10036 Z= 0.159 Angle : 0.544 9.634 13544 Z= 0.272 Chirality : 0.037 0.179 1525 Planarity : 0.005 0.047 1549 Dihedral : 12.932 174.511 2125 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.03 % Favored : 95.70 % Rotamer: Outliers : 1.13 % Allowed : 13.98 % Favored : 84.89 % 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: 1.39 (0.27), residues: 1095 helix: 1.61 (0.19), residues: 779 sheet: -2.35 (1.14), residues: 12 loop : -0.68 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1369 HIS 0.001 0.000 HIS A 318 PHE 0.023 0.001 PHE A1421 TYR 0.030 0.002 TYR A1705 ARG 0.003 0.000 ARG A 756 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.65 seconds wall clock time: 39 minutes 2.93 seconds (2342.93 seconds total)