Starting phenix.real_space_refine on Mon Jun 23 01:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y0h_33542/06_2025/7y0h_33542_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y0h_33542/06_2025/7y0h_33542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y0h_33542/06_2025/7y0h_33542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y0h_33542/06_2025/7y0h_33542.map" model { file = "/net/cci-nas-00/data/ceres_data/7y0h_33542/06_2025/7y0h_33542_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y0h_33542/06_2025/7y0h_33542_neut.cif" } resolution = 3.56 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= 0.002 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 16706 2.51 5 N 4468 2.21 5 O 5148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26470 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1786 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 212} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 18, 'TRANS': 209} Chain: "C" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1737 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain breaks: 1 Chain: "J" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 851 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain breaks: 1 Chain: "K" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1737 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain breaks: 1 Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "M" Number of atoms: 7919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7919 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 946} Chain breaks: 17 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "I" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.36, per 1000 atoms: 0.66 Number of scatterers: 26470 At special positions: 0 Unit cell: (165.85, 147.66, 192.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 5148 8.00 N 4468 7.00 C 16706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.03 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.05 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Simple disulfide: pdb=" SG CYS M1149 " - pdb=" SG CYS M1180 " distance=2.03 Simple disulfide: pdb=" SG CYS M1230 " - pdb=" SG CYS M1273 " distance=2.03 Simple disulfide: pdb=" SG CYS M1251 " - pdb=" SG CYS M1264 " distance=2.03 Simple disulfide: pdb=" SG CYS M1344 " - pdb=" SG CYS M1437 " distance=2.04 Simple disulfide: pdb=" SG CYS M1462 " - pdb=" SG CYS M1546 " distance=2.03 Simple disulfide: pdb=" SG CYS M1476 " - pdb=" SG CYS M1501 " distance=2.03 Simple disulfide: pdb=" SG CYS M1505 " - pdb=" SG CYS M1574 " distance=2.03 Simple disulfide: pdb=" SG CYS M1688 " - pdb=" SG CYS M1782 " distance=2.03 Simple disulfide: pdb=" SG CYS M1689 " - pdb=" SG CYS M1906 " distance=2.03 Simple disulfide: pdb=" SG CYS M1807 " - pdb=" SG CYS M1909 " distance=2.03 Simple disulfide: pdb=" SG CYS M1821 " - pdb=" SG CYS M1838 " distance=2.03 Simple disulfide: pdb=" SG CYS M1896 " - pdb=" SG CYS M1907 " distance=2.03 Simple disulfide: pdb=" SG CYS M2001 " - pdb=" SG CYS M2156 " distance=2.03 Simple disulfide: pdb=" SG CYS M2010 " - pdb=" SG CYS M2047 " distance=2.03 Simple disulfide: pdb=" SG CYS M2274 " - pdb=" SG CYS M2277 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG I 1 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 6.78 Conformation dependent library (CDL) restraints added in 3.3 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6376 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 61 sheets defined 28.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 460 through 467 removed outlier: 3.854A pdb=" N ARG A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.565A pdb=" N GLY A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.572A pdb=" N LEU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 529 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.765A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.606A pdb=" N LEU C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.732A pdb=" N THR C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 524 through 531 removed outlier: 3.619A pdb=" N THR D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.528A pdb=" N LEU E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'E' and resid 460 through 466 Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 460 through 465 Processing helix chain 'F' and resid 525 through 530 Processing helix chain 'G' and resid 353 through 361 removed outlier: 3.682A pdb=" N THR G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 420 Processing helix chain 'G' and resid 460 through 467 Processing helix chain 'G' and resid 524 through 530 Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.965A pdb=" N TRP H 418 " --> pdb=" O CYS H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 467 Processing helix chain 'H' and resid 524 through 531 removed outlier: 3.592A pdb=" N THR H 530 " --> pdb=" O GLU H 526 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY H 531 " --> pdb=" O GLU H 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 69 Processing helix chain 'J' and resid 129 through 133 Processing helix chain 'K' and resid 353 through 361 removed outlier: 3.772A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.787A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 466 removed outlier: 4.070A pdb=" N LEU K 466 " --> pdb=" O GLU K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 525 through 529 Processing helix chain 'K' and resid 553 through 557 removed outlier: 4.422A pdb=" N GLY K 557 " --> pdb=" O LYS K 554 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 361 removed outlier: 3.604A pdb=" N ILE L 357 " --> pdb=" O SER L 353 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU L 359 " --> pdb=" O ALA L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 421 removed outlier: 3.912A pdb=" N TRP L 418 " --> pdb=" O CYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 467 removed outlier: 3.588A pdb=" N LEU L 464 " --> pdb=" O ALA L 460 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG L 467 " --> pdb=" O GLN L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 530 Processing helix chain 'L' and resid 553 through 557 Processing helix chain 'M' and resid 1027 through 1050 removed outlier: 3.940A pdb=" N PHE M1031 " --> pdb=" O ASN M1027 " (cutoff:3.500A) Processing helix chain 'M' and resid 1098 through 1122 Processing helix chain 'M' and resid 1140 through 1157 removed outlier: 3.591A pdb=" N PHE M1146 " --> pdb=" O SER M1142 " (cutoff:3.500A) Processing helix chain 'M' and resid 1158 through 1162 removed outlier: 4.167A pdb=" N ASP M1161 " --> pdb=" O PHE M1158 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TRP M1162 " --> pdb=" O ASN M1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1158 through 1162' Processing helix chain 'M' and resid 1169 through 1181 removed outlier: 3.513A pdb=" N PHE M1173 " --> pdb=" O GLY M1169 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE M1175 " --> pdb=" O ASP M1171 " (cutoff:3.500A) Processing helix chain 'M' and resid 1186 through 1200 Processing helix chain 'M' and resid 1266 through 1271 Processing helix chain 'M' and resid 1274 through 1276 No H-bonds generated for 'chain 'M' and resid 1274 through 1276' Processing helix chain 'M' and resid 1292 through 1317 removed outlier: 3.593A pdb=" N THR M1317 " --> pdb=" O GLU M1313 " (cutoff:3.500A) Processing helix chain 'M' and resid 1342 through 1360 Processing helix chain 'M' and resid 1366 through 1381 removed outlier: 4.373A pdb=" N LYS M1371 " --> pdb=" O GLU M1367 " (cutoff:3.500A) Processing helix chain 'M' and resid 1401 through 1423 removed outlier: 5.819A pdb=" N ARG M1410 " --> pdb=" O LYS M1406 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU M1411 " --> pdb=" O GLY M1407 " (cutoff:3.500A) Processing helix chain 'M' and resid 1424 through 1426 No H-bonds generated for 'chain 'M' and resid 1424 through 1426' Processing helix chain 'M' and resid 1444 through 1447 Processing helix chain 'M' and resid 1448 through 1477 Processing helix chain 'M' and resid 1499 through 1530 removed outlier: 4.427A pdb=" N GLN M1517 " --> pdb=" O SER M1513 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU M1518 " --> pdb=" O GLU M1514 " (cutoff:3.500A) Processing helix chain 'M' and resid 1534 through 1543 Processing helix chain 'M' and resid 1544 through 1547 Processing helix chain 'M' and resid 1550 through 1555 Processing helix chain 'M' and resid 1558 through 1565 removed outlier: 3.818A pdb=" N LYS M1562 " --> pdb=" O ASN M1558 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR M1563 " --> pdb=" O ILE M1559 " (cutoff:3.500A) Processing helix chain 'M' and resid 1625 through 1631 Processing helix chain 'M' and resid 1635 through 1643 removed outlier: 4.300A pdb=" N ILE M1639 " --> pdb=" O GLU M1635 " (cutoff:3.500A) Processing helix chain 'M' and resid 1646 through 1674 Processing helix chain 'M' and resid 1683 through 1704 removed outlier: 3.544A pdb=" N CYS M1689 " --> pdb=" O LYS M1685 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP M1700 " --> pdb=" O TYR M1696 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE M1701 " --> pdb=" O ASP M1697 " (cutoff:3.500A) Processing helix chain 'M' and resid 1710 through 1724 removed outlier: 3.920A pdb=" N GLU M1722 " --> pdb=" O SER M1718 " (cutoff:3.500A) Processing helix chain 'M' and resid 1733 through 1744 Processing helix chain 'M' and resid 1756 through 1776 Processing helix chain 'M' and resid 1781 through 1785 Processing helix chain 'M' and resid 1793 through 1821 Processing helix chain 'M' and resid 1837 through 1866 Proline residue: M1851 - end of helix removed outlier: 3.906A pdb=" N ILE M1854 " --> pdb=" O ASN M1850 " (cutoff:3.500A) Processing helix chain 'M' and resid 1887 through 1893 Processing helix chain 'M' and resid 1915 through 1921 removed outlier: 3.602A pdb=" N THR M1921 " --> pdb=" O THR M1917 " (cutoff:3.500A) Processing helix chain 'M' and resid 1930 through 1938 removed outlier: 3.570A pdb=" N GLU M1934 " --> pdb=" O GLU M1930 " (cutoff:3.500A) Processing helix chain 'M' and resid 1939 through 1944 removed outlier: 3.990A pdb=" N MET M1943 " --> pdb=" O PRO M1939 " (cutoff:3.500A) Processing helix chain 'M' and resid 1999 through 2004 removed outlier: 4.256A pdb=" N LEU M2003 " --> pdb=" O LYS M1999 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE M2004 " --> pdb=" O VAL M2000 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1999 through 2004' Processing helix chain 'M' and resid 2041 through 2046 removed outlier: 3.660A pdb=" N LEU M2046 " --> pdb=" O ARG M2042 " (cutoff:3.500A) Processing helix chain 'M' and resid 2049 through 2054 Processing helix chain 'M' and resid 2064 through 2070 removed outlier: 3.551A pdb=" N LYS M2070 " --> pdb=" O GLU M2066 " (cutoff:3.500A) Processing helix chain 'M' and resid 2071 through 2075 removed outlier: 3.948A pdb=" N SER M2074 " --> pdb=" O GLY M2071 " (cutoff:3.500A) Processing helix chain 'M' and resid 2076 through 2081 Processing helix chain 'M' and resid 2088 through 2108 removed outlier: 3.729A pdb=" N ALA M2092 " --> pdb=" O ASP M2088 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU M2093 " --> pdb=" O LYS M2089 " (cutoff:3.500A) Processing helix chain 'M' and resid 2121 through 2133 Processing helix chain 'M' and resid 2154 through 2162 removed outlier: 3.545A pdb=" N SER M2161 " --> pdb=" O GLY M2157 " (cutoff:3.500A) Processing helix chain 'M' and resid 2187 through 2195 removed outlier: 3.954A pdb=" N VAL M2193 " --> pdb=" O TRP M2189 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS M2194 " --> pdb=" O GLY M2190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE M2195 " --> pdb=" O THR M2191 " (cutoff:3.500A) Processing helix chain 'M' and resid 2197 through 2206 Processing helix chain 'M' and resid 2225 through 2230 Processing helix chain 'M' and resid 2232 through 2247 removed outlier: 3.897A pdb=" N SER M2239 " --> pdb=" O SER M2235 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE M2240 " --> pdb=" O ARG M2236 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG M2241 " --> pdb=" O LYS M2237 " (cutoff:3.500A) Processing helix chain 'M' and resid 2265 through 2273 removed outlier: 3.904A pdb=" N TYR M2269 " --> pdb=" O ASP M2265 " (cutoff:3.500A) Processing helix chain 'M' and resid 2276 through 2280 Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 350 removed outlier: 4.177A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 392 removed outlier: 4.328A pdb=" N LYS A 391 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 381 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 427 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 428 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 437 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.545A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.545A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 563 removed outlier: 6.220A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 567 through 568 removed outlier: 7.546A pdb=" N VAL A 567 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.881A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.594A pdb=" N THR B 477 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.594A pdb=" N THR B 477 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG B 514 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB4, first strand: chain 'B' and resid 493 through 494 Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 349 Processing sheet with id=AB6, first strand: chain 'C' and resid 363 through 364 removed outlier: 4.342A pdb=" N THR C 363 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 413 " --> pdb=" O THR C 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 379 through 383 removed outlier: 4.023A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 429 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 453 through 457 Processing sheet with id=AB9, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.567A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AC2, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.509A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 368 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 380 through 384 Processing sheet with id=AC4, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.532A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.532A pdb=" N THR D 473 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'D' and resid 565 through 567 removed outlier: 6.538A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.563A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR E 370 " --> pdb=" O ALA E 407 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA E 407 " --> pdb=" O THR E 370 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.563A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR E 363 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 365 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 411 " --> pdb=" O LEU E 365 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 379 through 383 Processing sheet with id=AD2, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.624A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.624A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AD5, first strand: chain 'F' and resid 346 through 350 removed outlier: 3.747A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR F 363 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE F 413 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS F 367 " --> pdb=" O GLY F 409 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY F 409 " --> pdb=" O CYS F 367 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 379 through 383 Processing sheet with id=AD7, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.794A pdb=" N SER F 519 " --> pdb=" O CYS F 474 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.794A pdb=" N SER F 519 " --> pdb=" O CYS F 474 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AE1, first strand: chain 'F' and resid 565 through 567 removed outlier: 6.191A pdb=" N SER F 565 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.755A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR G 363 " --> pdb=" O ILE G 413 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 381 through 383 removed outlier: 5.365A pdb=" N HIS G 430 " --> pdb=" O SER G 435 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER G 435 " --> pdb=" O HIS G 430 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.623A pdb=" N THR G 477 " --> pdb=" O ASP G 453 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 472 " --> pdb=" O LEU G 521 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER G 519 " --> pdb=" O CYS G 474 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 453 through 457 removed outlier: 3.623A pdb=" N THR G 477 " --> pdb=" O ASP G 453 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE7, first strand: chain 'H' and resid 346 through 347 removed outlier: 3.605A pdb=" N ARG H 346 " --> pdb=" O THR H 370 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 380 through 384 removed outlier: 3.513A pdb=" N CYS H 426 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 399 through 400 removed outlier: 3.655A pdb=" N THR H 404 " --> pdb=" O HIS H 400 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 455 through 457 Processing sheet with id=AF2, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AF3, first strand: chain 'H' and resid 500 through 507 removed outlier: 6.009A pdb=" N THR H 502 " --> pdb=" O ILE H 520 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE H 520 " --> pdb=" O THR H 502 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA H 504 " --> pdb=" O HIS H 518 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N HIS H 518 " --> pdb=" O ALA H 504 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 21 through 22 Processing sheet with id=AF5, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AF6, first strand: chain 'J' and resid 112 through 116 removed outlier: 3.524A pdb=" N VAL J 124 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 379 through 382 Processing sheet with id=AF8, first strand: chain 'K' and resid 455 through 457 removed outlier: 3.711A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 455 through 457 removed outlier: 3.711A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET K 506 " --> pdb=" O PHE K 516 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.595A pdb=" N GLN K 493 " --> pdb=" O GLN K 490 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE K 485 " --> pdb=" O ALA K 539 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN K 487 " --> pdb=" O VAL K 537 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 381 through 382 removed outlier: 3.655A pdb=" N SER L 381 " --> pdb=" O THR L 427 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR L 427 " --> pdb=" O SER L 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'L' and resid 450 through 454 removed outlier: 5.580A pdb=" N ARG L 451 " --> pdb=" O SER L 480 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER L 480 " --> pdb=" O ARG L 451 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY L 478 " --> pdb=" O ASP L 453 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR L 477 " --> pdb=" O ALA L 517 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA L 517 " --> pdb=" O THR L 477 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 469 through 473 Processing sheet with id=AG5, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AG6, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AG7, first strand: chain 'M' and resid 1278 through 1279 removed outlier: 3.612A pdb=" N ASP M1279 " --> pdb=" O ARG M1285 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2733 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: 10.67 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8558 1.35 - 1.47: 6771 1.47 - 1.60: 11571 1.60 - 1.72: 0 1.72 - 1.85: 198 Bond restraints: 27098 Sorted by residual: bond pdb=" C1 NAG H 601 " pdb=" O5 NAG H 601 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" CA ASN H 563 " pdb=" CB ASN H 563 " ideal model delta sigma weight residual 1.524 1.572 -0.048 1.62e-02 3.81e+03 8.77e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG F 601 " pdb=" O5 NAG F 601 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 27093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 36192 1.85 - 3.69: 552 3.69 - 5.54: 133 5.54 - 7.39: 8 7.39 - 9.24: 1 Bond angle restraints: 36886 Sorted by residual: angle pdb=" CA CYS M2047 " pdb=" CB CYS M2047 " pdb=" SG CYS M2047 " ideal model delta sigma weight residual 114.40 123.64 -9.24 2.30e+00 1.89e-01 1.61e+01 angle pdb=" N THR E 533 " pdb=" CA THR E 533 " pdb=" CB THR E 533 " ideal model delta sigma weight residual 114.17 109.67 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" C LEU M2019 " pdb=" N ASP M2020 " pdb=" CA ASP M2020 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" CA LYS G 391 " pdb=" CB LYS G 391 " pdb=" CG LYS G 391 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.02e+00 angle pdb=" C SER M1955 " pdb=" CA SER M1955 " pdb=" CB SER M1955 " ideal model delta sigma weight residual 110.42 115.74 -5.32 1.99e+00 2.53e-01 7.15e+00 ... (remaining 36881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.00: 15618 24.00 - 48.00: 853 48.00 - 72.01: 107 72.01 - 96.01: 26 96.01 - 120.01: 11 Dihedral angle restraints: 16615 sinusoidal: 6816 harmonic: 9799 Sorted by residual: dihedral pdb=" CB CYS L 367 " pdb=" SG CYS L 367 " pdb=" SG CYS L 426 " pdb=" CB CYS L 426 " ideal model delta sinusoidal sigma weight residual 93.00 19.88 73.12 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS J 108 " pdb=" SG CYS J 108 " pdb=" SG CYS J 133 " pdb=" CB CYS J 133 " ideal model delta sinusoidal sigma weight residual -86.00 -140.33 54.33 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS G 367 " pdb=" SG CYS G 367 " pdb=" SG CYS G 426 " pdb=" CB CYS G 426 " ideal model delta sinusoidal sigma weight residual 93.00 146.99 -53.99 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 16612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3896 0.089 - 0.179: 306 0.179 - 0.268: 3 0.268 - 0.357: 0 0.357 - 0.447: 1 Chirality restraints: 4206 Sorted by residual: chirality pdb=" C1 NAG K 601 " pdb=" ND2 ASN K 563 " pdb=" C2 NAG K 601 " pdb=" O5 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" C1 NAG F 601 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG F 601 " pdb=" O5 NAG F 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG G 601 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG G 601 " pdb=" O5 NAG G 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 4203 not shown) Planarity restraints: 4715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M2189 " 0.015 2.00e-02 2.50e+03 1.65e-02 6.79e+00 pdb=" CG TRP M2189 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP M2189 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP M2189 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP M2189 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP M2189 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M2189 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP M2189 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M2189 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP M2189 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU M2019 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C LEU M2019 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU M2019 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP M2020 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M2040 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO M2041 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO M2041 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO M2041 " -0.029 5.00e-02 4.00e+02 ... (remaining 4712 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 238 2.56 - 3.15: 22784 3.15 - 3.73: 40923 3.73 - 4.32: 56253 4.32 - 4.90: 93112 Nonbonded interactions: 213310 Sorted by model distance: nonbonded pdb=" OG1 THR F 373 " pdb=" OD2 ASP F 432 " model vdw 1.981 3.040 nonbonded pdb=" O MET K 489 " pdb=" OG1 THR K 535 " model vdw 2.045 3.040 nonbonded pdb=" OG SER F 381 " pdb=" OG1 THR F 427 " model vdw 2.086 3.040 nonbonded pdb=" OG1 THR G 363 " pdb=" O ILE G 413 " model vdw 2.102 3.040 nonbonded pdb=" OD2 ASP M2105 " pdb=" NH1 ARG M2184 " model vdw 2.138 3.120 ... (remaining 213305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.600 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: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 61.540 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.003 0.074 27146 Z= 0.151 Angle : 0.618 10.232 36994 Z= 0.317 Chirality : 0.043 0.447 4206 Planarity : 0.004 0.069 4704 Dihedral : 14.662 120.009 10131 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.21 (0.15), residues: 3270 helix: 0.54 (0.19), residues: 804 sheet: -0.24 (0.19), residues: 747 loop : -0.32 (0.16), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP M2189 HIS 0.008 0.001 HIS K 540 PHE 0.026 0.001 PHE M1795 TYR 0.031 0.001 TYR D 455 ARG 0.010 0.001 ARG M1797 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 11) link_NAG-ASN : angle 3.87518 ( 33) link_BETA1-4 : bond 0.01393 ( 1) link_BETA1-4 : angle 3.17792 ( 3) hydrogen bonds : bond 0.23428 ( 918) hydrogen bonds : angle 9.24510 ( 2733) SS BOND : bond 0.00360 ( 36) SS BOND : angle 1.58484 ( 72) covalent geometry : bond 0.00336 (27098) covalent geometry : angle 0.60351 (36886) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 TRP cc_start: 0.5587 (m100) cc_final: 0.5343 (m100) REVERT: A 455 TYR cc_start: 0.8164 (m-80) cc_final: 0.7946 (m-10) REVERT: A 502 THR cc_start: 0.9058 (t) cc_final: 0.8799 (m) REVERT: A 519 SER cc_start: 0.8926 (m) cc_final: 0.8504 (m) REVERT: A 554 LYS cc_start: 0.8257 (tttp) cc_final: 0.7987 (tttm) REVERT: C 345 ILE cc_start: 0.5050 (mt) cc_final: 0.4745 (tt) REVERT: D 413 ILE cc_start: 0.6907 (mt) cc_final: 0.6703 (mt) REVERT: F 443 ARG cc_start: 0.7406 (ptm160) cc_final: 0.7138 (mtp180) REVERT: G 553 ASP cc_start: 0.7131 (p0) cc_final: 0.6707 (p0) REVERT: K 364 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8510 (mmmm) REVERT: K 455 TYR cc_start: 0.6770 (m-80) cc_final: 0.6559 (m-80) REVERT: K 483 ASP cc_start: 0.6225 (t0) cc_final: 0.5394 (t0) REVERT: K 518 HIS cc_start: 0.6580 (m-70) cc_final: 0.5878 (m170) REVERT: M 1042 ILE cc_start: 0.8821 (mt) cc_final: 0.8587 (mt) REVERT: M 1639 ILE cc_start: 0.9199 (mp) cc_final: 0.8976 (mp) REVERT: M 1668 TYR cc_start: 0.6435 (t80) cc_final: 0.6078 (t80) REVERT: M 1670 TRP cc_start: 0.8616 (t-100) cc_final: 0.8307 (t-100) REVERT: M 1758 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8615 (pp30) REVERT: M 1759 LEU cc_start: 0.9313 (tp) cc_final: 0.9089 (tp) REVERT: M 1787 HIS cc_start: 0.7387 (t70) cc_final: 0.7081 (t70) REVERT: M 2039 ILE cc_start: 0.8844 (mm) cc_final: 0.8530 (mm) REVERT: M 2194 CYS cc_start: 0.8839 (m) cc_final: 0.8572 (m) outliers start: 2 outliers final: 0 residues processed: 481 average time/residue: 0.3946 time to fit residues: 298.2165 Evaluate side-chains 358 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 257 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 191 optimal weight: 30.0000 chunk 297 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 545 ASN ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN H 490 GLN ** K 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN K 545 ASN L 393 HIS L 395 ASN L 463 GLN M1271 ASN ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1864 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.188896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123270 restraints weight = 43442.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124973 restraints weight = 27974.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124547 restraints weight = 19680.685| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27146 Z= 0.166 Angle : 0.649 11.896 36994 Z= 0.337 Chirality : 0.046 0.408 4206 Planarity : 0.005 0.058 4704 Dihedral : 7.704 102.733 3827 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.08 % Allowed : 8.64 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3270 helix: 0.40 (0.17), residues: 874 sheet: -0.13 (0.19), residues: 737 loop : -0.46 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 418 HIS 0.009 0.001 HIS C 430 PHE 0.025 0.002 PHE L 358 TYR 0.027 0.002 TYR M1867 ARG 0.007 0.001 ARG M1797 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 11) link_NAG-ASN : angle 4.27616 ( 33) link_BETA1-4 : bond 0.00799 ( 1) link_BETA1-4 : angle 3.15299 ( 3) hydrogen bonds : bond 0.04835 ( 918) hydrogen bonds : angle 6.51180 ( 2733) SS BOND : bond 0.00501 ( 36) SS BOND : angle 1.33863 ( 72) covalent geometry : bond 0.00377 (27098) covalent geometry : angle 0.63346 (36886) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 423 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 TRP cc_start: 0.5959 (m100) cc_final: 0.5304 (m100) REVERT: A 554 LYS cc_start: 0.8677 (tttp) cc_final: 0.8317 (tttm) REVERT: B 423 ARG cc_start: 0.8762 (ttt-90) cc_final: 0.8545 (tmm-80) REVERT: F 354 PHE cc_start: 0.8571 (t80) cc_final: 0.8348 (t80) REVERT: F 371 ASP cc_start: 0.6213 (t0) cc_final: 0.5999 (t0) REVERT: F 443 ARG cc_start: 0.7505 (ptm160) cc_final: 0.7255 (mtp-110) REVERT: F 465 ASN cc_start: 0.8476 (m-40) cc_final: 0.8220 (m-40) REVERT: H 416 ASP cc_start: 0.8613 (p0) cc_final: 0.8317 (p0) REVERT: H 488 TRP cc_start: 0.8393 (m100) cc_final: 0.8141 (m100) REVERT: H 530 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8155 (t) REVERT: J 125 GLU cc_start: 0.6424 (tp30) cc_final: 0.6195 (tp30) REVERT: K 419 ASN cc_start: 0.9208 (t0) cc_final: 0.8960 (m110) REVERT: K 455 TYR cc_start: 0.7131 (m-80) cc_final: 0.6694 (m-80) REVERT: K 483 ASP cc_start: 0.6180 (t0) cc_final: 0.5835 (t0) REVERT: K 554 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8204 (mmtp) REVERT: L 354 PHE cc_start: 0.8609 (m-80) cc_final: 0.8249 (m-80) REVERT: L 493 GLN cc_start: 0.7497 (pp30) cc_final: 0.7239 (pp30) REVERT: M 1639 ILE cc_start: 0.9114 (mp) cc_final: 0.8812 (mp) REVERT: M 1700 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6625 (t0) REVERT: M 1758 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8747 (pp30) REVERT: M 1759 LEU cc_start: 0.9408 (tp) cc_final: 0.9111 (tp) REVERT: M 1764 MET cc_start: 0.8927 (tpp) cc_final: 0.8475 (tpp) REVERT: M 1773 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8711 (pt0) REVERT: M 1787 HIS cc_start: 0.7513 (t70) cc_final: 0.7243 (t70) REVERT: M 2194 CYS cc_start: 0.8995 (m) cc_final: 0.8491 (m) outliers start: 32 outliers final: 18 residues processed: 437 average time/residue: 0.4485 time to fit residues: 308.8194 Evaluate side-chains 378 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 357 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain G residue 414 CYS Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 554 LYS Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1604 THR Chi-restraints excluded: chain M residue 1700 ASP Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 167 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 316 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS L 419 ASN L 490 GLN L 529 ASN ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1944 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.187404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118192 restraints weight = 43261.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121411 restraints weight = 27897.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122283 restraints weight = 17772.318| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27146 Z= 0.187 Angle : 0.630 12.040 36994 Z= 0.324 Chirality : 0.046 0.392 4206 Planarity : 0.005 0.061 4704 Dihedral : 7.326 102.003 3827 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.93 % Allowed : 11.73 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.34 (0.15), residues: 3270 helix: 0.42 (0.17), residues: 874 sheet: -0.17 (0.18), residues: 740 loop : -0.50 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M1761 HIS 0.016 0.001 HIS L 393 PHE 0.033 0.002 PHE A 354 TYR 0.023 0.002 TYR M1867 ARG 0.011 0.001 ARG M1797 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 11) link_NAG-ASN : angle 4.26239 ( 33) link_BETA1-4 : bond 0.01255 ( 1) link_BETA1-4 : angle 3.74597 ( 3) hydrogen bonds : bond 0.04318 ( 918) hydrogen bonds : angle 6.05101 ( 2733) SS BOND : bond 0.00425 ( 36) SS BOND : angle 1.04783 ( 72) covalent geometry : bond 0.00436 (27098) covalent geometry : angle 0.61482 (36886) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 393 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.6936 (mt) REVERT: A 418 TRP cc_start: 0.6020 (m100) cc_final: 0.5296 (m100) REVERT: A 502 THR cc_start: 0.9093 (t) cc_final: 0.8892 (m) REVERT: A 506 MET cc_start: 0.7547 (mmm) cc_final: 0.7198 (mmm) REVERT: A 554 LYS cc_start: 0.8702 (tttp) cc_final: 0.8399 (tttm) REVERT: B 423 ARG cc_start: 0.8783 (ttt-90) cc_final: 0.8496 (tmm-80) REVERT: F 465 ASN cc_start: 0.8488 (m-40) cc_final: 0.8241 (m-40) REVERT: F 493 GLN cc_start: 0.7633 (mp10) cc_final: 0.7425 (mp10) REVERT: H 488 TRP cc_start: 0.8415 (m100) cc_final: 0.8132 (m100) REVERT: H 530 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8163 (t) REVERT: J 125 GLU cc_start: 0.6487 (tp30) cc_final: 0.6156 (tp30) REVERT: K 453 ASP cc_start: 0.8169 (p0) cc_final: 0.7843 (p0) REVERT: K 483 ASP cc_start: 0.6304 (t0) cc_final: 0.5940 (t0) REVERT: K 490 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7728 (tm-30) REVERT: K 554 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8046 (mmtp) REVERT: L 354 PHE cc_start: 0.8276 (m-80) cc_final: 0.8025 (m-80) REVERT: L 493 GLN cc_start: 0.7431 (pp30) cc_final: 0.7059 (pp30) REVERT: M 1506 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: M 1639 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8956 (mt) REVERT: M 1670 TRP cc_start: 0.8872 (t-100) cc_final: 0.8658 (t-100) REVERT: M 1696 TYR cc_start: 0.7977 (m-10) cc_final: 0.7482 (m-80) REVERT: M 1700 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6611 (t0) REVERT: M 1758 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8733 (pp30) REVERT: M 1759 LEU cc_start: 0.9383 (tp) cc_final: 0.8883 (tp) REVERT: M 1764 MET cc_start: 0.8962 (tpp) cc_final: 0.8515 (tpp) REVERT: M 1773 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8702 (pt0) REVERT: M 1797 ARG cc_start: 0.8749 (mtm180) cc_final: 0.7516 (mtm-85) REVERT: M 1798 TRP cc_start: 0.9028 (m-10) cc_final: 0.8652 (m-10) REVERT: M 1927 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7424 (mm-40) REVERT: M 2194 CYS cc_start: 0.8954 (m) cc_final: 0.8464 (m) outliers start: 57 outliers final: 36 residues processed: 424 average time/residue: 0.3974 time to fit residues: 266.4750 Evaluate side-chains 396 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 354 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 554 LYS Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 556 THR Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1506 GLU Chi-restraints excluded: chain M residue 1604 THR Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1700 ASP Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1888 VAL Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 2123 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 15 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 274 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 193 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 HIS E 419 ASN ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 419 ASN ** M1721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1944 ASN ** M2232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.181826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111474 restraints weight = 43713.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114534 restraints weight = 28603.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114243 restraints weight = 18418.660| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 27146 Z= 0.393 Angle : 0.792 14.002 36994 Z= 0.410 Chirality : 0.051 0.407 4206 Planarity : 0.006 0.070 4704 Dihedral : 7.418 102.727 3827 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.15 % Allowed : 14.47 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.73 (0.15), residues: 3270 helix: 0.10 (0.17), residues: 874 sheet: -0.48 (0.18), residues: 768 loop : -0.72 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M1761 HIS 0.042 0.002 HIS L 393 PHE 0.026 0.003 PHE E 479 TYR 0.039 0.003 TYR A 455 ARG 0.010 0.001 ARG M1797 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 11) link_NAG-ASN : angle 4.91574 ( 33) link_BETA1-4 : bond 0.01489 ( 1) link_BETA1-4 : angle 4.15461 ( 3) hydrogen bonds : bond 0.04613 ( 918) hydrogen bonds : angle 6.23103 ( 2733) SS BOND : bond 0.00810 ( 36) SS BOND : angle 1.48989 ( 72) covalent geometry : bond 0.00930 (27098) covalent geometry : angle 0.77595 (36886) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 354 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 TRP cc_start: 0.6031 (m100) cc_final: 0.5313 (m100) REVERT: B 391 LYS cc_start: 0.7349 (mppt) cc_final: 0.6624 (mmtt) REVERT: E 566 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8644 (mp) REVERT: F 456 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8466 (mp) REVERT: F 493 GLN cc_start: 0.7920 (mp10) cc_final: 0.7714 (mp10) REVERT: J 125 GLU cc_start: 0.6684 (tp30) cc_final: 0.6431 (tp30) REVERT: K 419 ASN cc_start: 0.9257 (t0) cc_final: 0.8964 (m110) REVERT: K 453 ASP cc_start: 0.8214 (p0) cc_final: 0.7968 (p0) REVERT: K 490 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7838 (tp40) REVERT: L 493 GLN cc_start: 0.7418 (pp30) cc_final: 0.6977 (pp30) REVERT: M 1147 PHE cc_start: 0.8441 (t80) cc_final: 0.8238 (t80) REVERT: M 1506 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: M 1639 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8983 (mt) REVERT: M 1670 TRP cc_start: 0.8892 (t-100) cc_final: 0.8661 (t-100) REVERT: M 1700 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7083 (t0) REVERT: M 1758 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8751 (pp30) REVERT: M 1764 MET cc_start: 0.9008 (tpp) cc_final: 0.8513 (tpp) REVERT: M 1773 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8664 (pt0) REVERT: M 1884 MET cc_start: 0.6215 (mmt) cc_final: 0.5929 (mmt) REVERT: M 1927 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7551 (mm-40) REVERT: M 2143 TRP cc_start: 0.7637 (t-100) cc_final: 0.7354 (t-100) REVERT: M 2194 CYS cc_start: 0.9051 (m) cc_final: 0.8756 (m) REVERT: M 2272 GLU cc_start: 0.8568 (pp20) cc_final: 0.7975 (pp20) outliers start: 93 outliers final: 55 residues processed: 421 average time/residue: 0.3808 time to fit residues: 254.5296 Evaluate side-chains 383 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 323 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 493 GLN Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 413 ILE Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain L residue 556 THR Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1339 LEU Chi-restraints excluded: chain M residue 1506 GLU Chi-restraints excluded: chain M residue 1604 THR Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1700 ASP Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1867 TYR Chi-restraints excluded: chain M residue 1888 VAL Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 2052 VAL Chi-restraints excluded: chain M residue 2176 THR Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 138 optimal weight: 5.9990 chunk 303 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 chunk 327 optimal weight: 0.7980 chunk 283 optimal weight: 0.0670 chunk 67 optimal weight: 20.0000 chunk 309 optimal weight: 0.8980 chunk 282 optimal weight: 0.1980 chunk 298 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 chunk 222 optimal weight: 4.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 GLN ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS L 490 GLN M1231 GLN ** M1721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1944 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.188392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121061 restraints weight = 43386.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122066 restraints weight = 28296.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122472 restraints weight = 20615.881| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27146 Z= 0.127 Angle : 0.620 11.884 36994 Z= 0.315 Chirality : 0.045 0.337 4206 Planarity : 0.004 0.066 4704 Dihedral : 6.643 102.916 3827 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.24 % Allowed : 16.61 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.47 (0.15), residues: 3270 helix: 0.36 (0.17), residues: 867 sheet: -0.26 (0.18), residues: 778 loop : -0.62 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP M1761 HIS 0.009 0.001 HIS C 430 PHE 0.017 0.002 PHE K 516 TYR 0.028 0.002 TYR A 455 ARG 0.011 0.001 ARG G 443 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 11) link_NAG-ASN : angle 4.31908 ( 33) link_BETA1-4 : bond 0.01486 ( 1) link_BETA1-4 : angle 3.63496 ( 3) hydrogen bonds : bond 0.03747 ( 918) hydrogen bonds : angle 5.61277 ( 2733) SS BOND : bond 0.00450 ( 36) SS BOND : angle 1.09622 ( 72) covalent geometry : bond 0.00279 (27098) covalent geometry : angle 0.60469 (36886) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 393 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7077 (mt) REVERT: A 418 TRP cc_start: 0.6203 (m100) cc_final: 0.5597 (m100) REVERT: A 506 MET cc_start: 0.7548 (mmm) cc_final: 0.7158 (mmm) REVERT: A 554 LYS cc_start: 0.8692 (tttp) cc_final: 0.8434 (tttm) REVERT: B 361 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8675 (tppt) REVERT: B 423 ARG cc_start: 0.8778 (ttt-90) cc_final: 0.8459 (tmm-80) REVERT: C 364 LYS cc_start: 0.7957 (mmmm) cc_final: 0.7723 (mmmm) REVERT: E 566 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8591 (mp) REVERT: F 418 TRP cc_start: 0.8028 (t-100) cc_final: 0.7766 (t-100) REVERT: F 443 ARG cc_start: 0.7448 (ptm160) cc_final: 0.7104 (ptm160) REVERT: F 465 ASN cc_start: 0.8401 (m-40) cc_final: 0.8123 (m-40) REVERT: J 120 GLU cc_start: 0.6973 (pm20) cc_final: 0.6664 (pm20) REVERT: J 125 GLU cc_start: 0.6536 (tp30) cc_final: 0.6278 (tp30) REVERT: K 419 ASN cc_start: 0.9252 (t0) cc_final: 0.8979 (m110) REVERT: K 453 ASP cc_start: 0.8080 (p0) cc_final: 0.7827 (p0) REVERT: K 489 MET cc_start: 0.8614 (mpp) cc_final: 0.8345 (mpp) REVERT: K 537 VAL cc_start: 0.7567 (OUTLIER) cc_final: 0.7246 (m) REVERT: K 554 LYS cc_start: 0.8619 (mttp) cc_final: 0.8210 (mttp) REVERT: L 493 GLN cc_start: 0.7466 (pp30) cc_final: 0.7075 (pp30) REVERT: M 1116 ASP cc_start: 0.8831 (m-30) cc_final: 0.8599 (t0) REVERT: M 1178 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8782 (tttt) REVERT: M 1639 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8935 (mt) REVERT: M 1670 TRP cc_start: 0.8872 (t-100) cc_final: 0.8639 (t-100) REVERT: M 1700 ASP cc_start: 0.7390 (m-30) cc_final: 0.6701 (t0) REVERT: M 1758 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8753 (pp30) REVERT: M 1773 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8664 (pt0) REVERT: M 1797 ARG cc_start: 0.8708 (mtm180) cc_final: 0.7466 (mtm-85) REVERT: M 1884 MET cc_start: 0.6196 (mmt) cc_final: 0.5905 (mmt) REVERT: M 1927 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7517 (mm-40) REVERT: M 2194 CYS cc_start: 0.8924 (m) cc_final: 0.8367 (m) outliers start: 66 outliers final: 35 residues processed: 441 average time/residue: 0.3981 time to fit residues: 279.0937 Evaluate side-chains 383 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 344 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 413 ILE Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 426 CYS Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain M residue 1173 PHE Chi-restraints excluded: chain M residue 1176 LEU Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1867 TYR Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 2038 LEU Chi-restraints excluded: chain M residue 2125 LEU Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 324 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 HIS ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS ** K 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 465 ASN L 490 GLN ** M1721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1944 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.184551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113873 restraints weight = 43416.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116476 restraints weight = 29749.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117736 restraints weight = 20535.749| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27146 Z= 0.253 Angle : 0.679 12.567 36994 Z= 0.345 Chirality : 0.047 0.390 4206 Planarity : 0.005 0.070 4704 Dihedral : 6.486 99.980 3827 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 2.61 % Allowed : 17.80 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.50 (0.15), residues: 3270 helix: 0.30 (0.17), residues: 865 sheet: -0.33 (0.18), residues: 776 loop : -0.58 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP M1761 HIS 0.012 0.001 HIS C 430 PHE 0.022 0.002 PHE G 405 TYR 0.027 0.002 TYR A 455 ARG 0.005 0.000 ARG M1797 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 11) link_NAG-ASN : angle 4.52411 ( 33) link_BETA1-4 : bond 0.01479 ( 1) link_BETA1-4 : angle 3.93826 ( 3) hydrogen bonds : bond 0.03923 ( 918) hydrogen bonds : angle 5.71874 ( 2733) SS BOND : bond 0.00540 ( 36) SS BOND : angle 1.47552 ( 72) covalent geometry : bond 0.00605 (27098) covalent geometry : angle 0.66192 (36886) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 352 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 TRP cc_start: 0.6114 (m100) cc_final: 0.5419 (m100) REVERT: A 521 LEU cc_start: 0.8571 (tt) cc_final: 0.8059 (tp) REVERT: A 554 LYS cc_start: 0.8685 (tttp) cc_final: 0.8375 (tttm) REVERT: B 361 LYS cc_start: 0.9144 (mmmt) cc_final: 0.8733 (tppt) REVERT: B 423 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8469 (tmm-80) REVERT: D 391 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8470 (mmmt) REVERT: D 473 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8568 (p) REVERT: E 566 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8580 (mp) REVERT: E 568 MET cc_start: 0.7546 (mmm) cc_final: 0.7128 (mmm) REVERT: J 120 GLU cc_start: 0.6995 (pm20) cc_final: 0.6661 (pm20) REVERT: J 125 GLU cc_start: 0.6768 (tp30) cc_final: 0.6395 (tp30) REVERT: K 419 ASN cc_start: 0.9254 (t0) cc_final: 0.8999 (m110) REVERT: K 453 ASP cc_start: 0.8108 (p0) cc_final: 0.7789 (p0) REVERT: K 483 ASP cc_start: 0.6376 (t0) cc_final: 0.5901 (t0) REVERT: K 537 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7363 (m) REVERT: K 554 LYS cc_start: 0.8657 (mttp) cc_final: 0.8434 (mttp) REVERT: L 490 GLN cc_start: 0.7555 (tt0) cc_final: 0.7318 (tt0) REVERT: L 493 GLN cc_start: 0.7438 (pp30) cc_final: 0.7187 (pp30) REVERT: M 1178 LYS cc_start: 0.9150 (ttmm) cc_final: 0.8789 (tttt) REVERT: M 1639 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8946 (mt) REVERT: M 1670 TRP cc_start: 0.8870 (t-100) cc_final: 0.8651 (t-100) REVERT: M 1700 ASP cc_start: 0.7412 (m-30) cc_final: 0.6793 (t0) REVERT: M 1758 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8700 (pp30) REVERT: M 1764 MET cc_start: 0.9033 (tpp) cc_final: 0.8488 (tpp) REVERT: M 1773 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8629 (pt0) REVERT: M 1797 ARG cc_start: 0.8837 (mtm180) cc_final: 0.7542 (mtm-85) REVERT: M 1884 MET cc_start: 0.6137 (mmt) cc_final: 0.5839 (mmt) REVERT: M 1927 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7563 (mm-40) REVERT: M 2122 LYS cc_start: 0.7203 (ttpp) cc_final: 0.6654 (mtpp) outliers start: 77 outliers final: 53 residues processed: 409 average time/residue: 0.3944 time to fit residues: 259.3889 Evaluate side-chains 386 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 329 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 524 SER Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain G residue 418 TRP Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 426 CYS Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1604 THR Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1641 ILE Chi-restraints excluded: chain M residue 1688 CYS Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1867 TYR Chi-restraints excluded: chain M residue 1888 VAL Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 2052 VAL Chi-restraints excluded: chain M residue 2106 ILE Chi-restraints excluded: chain M residue 2125 LEU Chi-restraints excluded: chain M residue 2176 THR Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 132 optimal weight: 0.6980 chunk 206 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 300 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** M1721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1847 ASN ** 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 = 0.4367 r_free = 0.4367 target = 0.186249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118094 restraints weight = 43382.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120672 restraints weight = 27753.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120424 restraints weight = 18536.087| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27146 Z= 0.167 Angle : 0.636 12.529 36994 Z= 0.320 Chirality : 0.045 0.343 4206 Planarity : 0.004 0.071 4704 Dihedral : 6.194 99.149 3827 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 2.47 % Allowed : 18.47 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.44 (0.15), residues: 3270 helix: 0.39 (0.17), residues: 859 sheet: -0.24 (0.18), residues: 776 loop : -0.60 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP M1761 HIS 0.010 0.001 HIS C 430 PHE 0.019 0.002 PHE L 358 TYR 0.047 0.002 TYR A 455 ARG 0.009 0.000 ARG L 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 11) link_NAG-ASN : angle 4.30362 ( 33) link_BETA1-4 : bond 0.01540 ( 1) link_BETA1-4 : angle 3.83886 ( 3) hydrogen bonds : bond 0.03654 ( 918) hydrogen bonds : angle 5.49863 ( 2733) SS BOND : bond 0.00415 ( 36) SS BOND : angle 1.27386 ( 72) covalent geometry : bond 0.00393 (27098) covalent geometry : angle 0.62047 (36886) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 354 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 TRP cc_start: 0.6305 (m100) cc_final: 0.5565 (m100) REVERT: A 521 LEU cc_start: 0.8590 (tt) cc_final: 0.8161 (tp) REVERT: B 361 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8740 (tppt) REVERT: B 423 ARG cc_start: 0.8765 (ttt-90) cc_final: 0.8469 (tmm-80) REVERT: D 391 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8490 (mmmt) REVERT: D 473 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8517 (p) REVERT: E 566 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8580 (mp) REVERT: E 568 MET cc_start: 0.7529 (mmm) cc_final: 0.7202 (mmm) REVERT: J 120 GLU cc_start: 0.7073 (pm20) cc_final: 0.6705 (pm20) REVERT: J 125 GLU cc_start: 0.6730 (tp30) cc_final: 0.6352 (tp30) REVERT: K 419 ASN cc_start: 0.9246 (t0) cc_final: 0.9015 (m110) REVERT: K 455 TYR cc_start: 0.7167 (m-80) cc_final: 0.6629 (m-80) REVERT: K 554 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8310 (mttp) REVERT: L 489 MET cc_start: 0.7295 (mmt) cc_final: 0.7050 (tpp) REVERT: L 493 GLN cc_start: 0.7522 (pp30) cc_final: 0.7211 (pp30) REVERT: M 1178 LYS cc_start: 0.9139 (ttmm) cc_final: 0.8787 (tttt) REVERT: M 1639 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8947 (mt) REVERT: M 1670 TRP cc_start: 0.8860 (t-100) cc_final: 0.8640 (t-100) REVERT: M 1700 ASP cc_start: 0.7396 (m-30) cc_final: 0.6924 (t0) REVERT: M 1758 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8693 (pp30) REVERT: M 1764 MET cc_start: 0.8999 (tpp) cc_final: 0.8452 (tpp) REVERT: M 1773 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8700 (pt0) REVERT: M 1927 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7526 (mm-40) REVERT: M 2122 LYS cc_start: 0.7079 (ttpp) cc_final: 0.6695 (mtpp) outliers start: 73 outliers final: 57 residues processed: 409 average time/residue: 0.3975 time to fit residues: 260.8251 Evaluate side-chains 396 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 335 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 554 LYS Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 426 CYS Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain M residue 1173 PHE Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1339 LEU Chi-restraints excluded: chain M residue 1604 THR Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1641 ILE Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1717 ASP Chi-restraints excluded: chain M residue 1867 TYR Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 2038 LEU Chi-restraints excluded: chain M residue 2052 VAL Chi-restraints excluded: chain M residue 2106 ILE Chi-restraints excluded: chain M residue 2125 LEU Chi-restraints excluded: chain M residue 2136 THR Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 204 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 116 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 487 GLN L 393 HIS L 490 GLN M1721 ASN ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.186360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119541 restraints weight = 43260.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121123 restraints weight = 26865.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120882 restraints weight = 19091.813| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27146 Z= 0.171 Angle : 0.640 12.105 36994 Z= 0.323 Chirality : 0.045 0.347 4206 Planarity : 0.005 0.070 4704 Dihedral : 6.049 97.319 3827 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 2.85 % Allowed : 18.27 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3270 helix: 0.41 (0.17), residues: 862 sheet: -0.20 (0.18), residues: 780 loop : -0.59 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M1761 HIS 0.010 0.001 HIS C 430 PHE 0.023 0.002 PHE G 405 TYR 0.042 0.002 TYR A 455 ARG 0.007 0.000 ARG L 491 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 11) link_NAG-ASN : angle 4.27942 ( 33) link_BETA1-4 : bond 0.01532 ( 1) link_BETA1-4 : angle 3.72369 ( 3) hydrogen bonds : bond 0.03708 ( 918) hydrogen bonds : angle 5.42743 ( 2733) SS BOND : bond 0.00505 ( 36) SS BOND : angle 1.47910 ( 72) covalent geometry : bond 0.00402 (27098) covalent geometry : angle 0.62343 (36886) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 343 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 LEU cc_start: 0.8565 (tt) cc_final: 0.8176 (tp) REVERT: B 361 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8734 (tppt) REVERT: B 423 ARG cc_start: 0.8768 (ttt-90) cc_final: 0.8491 (tmm-80) REVERT: D 391 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8538 (mmmt) REVERT: D 473 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8010 (p) REVERT: E 566 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8579 (mp) REVERT: E 568 MET cc_start: 0.7434 (mmm) cc_final: 0.7161 (mmm) REVERT: J 120 GLU cc_start: 0.7096 (pm20) cc_final: 0.6735 (pm20) REVERT: J 125 GLU cc_start: 0.6767 (tp30) cc_final: 0.6377 (tp30) REVERT: K 416 ASP cc_start: 0.9091 (t0) cc_final: 0.8723 (p0) REVERT: K 419 ASN cc_start: 0.9225 (t0) cc_final: 0.9011 (m110) REVERT: K 518 HIS cc_start: 0.6964 (m170) cc_final: 0.6647 (m170) REVERT: K 554 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8266 (mttp) REVERT: L 489 MET cc_start: 0.7017 (mmt) cc_final: 0.6815 (tpp) REVERT: L 493 GLN cc_start: 0.7426 (pp30) cc_final: 0.7117 (pp30) REVERT: M 1173 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8020 (t80) REVERT: M 1178 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8855 (ttmt) REVERT: M 1639 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8973 (mt) REVERT: M 1758 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8671 (pp30) REVERT: M 1764 MET cc_start: 0.8989 (tpp) cc_final: 0.8435 (tpp) REVERT: M 1773 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8714 (pt0) REVERT: M 1786 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7961 (mm-30) REVERT: M 1927 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7529 (mm-40) REVERT: M 2069 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8340 (mm) REVERT: M 2122 LYS cc_start: 0.7193 (ttpp) cc_final: 0.6837 (mtpp) outliers start: 84 outliers final: 68 residues processed: 404 average time/residue: 0.3734 time to fit residues: 244.4085 Evaluate side-chains 404 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 330 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 487 GLN Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 554 LYS Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 426 CYS Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain M residue 1173 PHE Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1339 LEU Chi-restraints excluded: chain M residue 1604 THR Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1641 ILE Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1717 ASP Chi-restraints excluded: chain M residue 1867 TYR Chi-restraints excluded: chain M residue 1888 VAL Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 2038 LEU Chi-restraints excluded: chain M residue 2052 VAL Chi-restraints excluded: chain M residue 2069 LEU Chi-restraints excluded: chain M residue 2125 LEU Chi-restraints excluded: chain M residue 2136 THR Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 225 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 78 optimal weight: 0.0870 chunk 194 optimal weight: 30.0000 chunk 151 optimal weight: 0.5980 chunk 237 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 269 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 HIS L 393 HIS L 395 ASN L 465 ASN L 490 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.188503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124736 restraints weight = 43303.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123850 restraints weight = 27489.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123637 restraints weight = 21257.481| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27146 Z= 0.129 Angle : 0.628 12.203 36994 Z= 0.317 Chirality : 0.045 0.332 4206 Planarity : 0.004 0.069 4704 Dihedral : 5.847 95.440 3827 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.98 % Rotamer: Outliers : 2.47 % Allowed : 19.19 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.42 (0.15), residues: 3270 helix: 0.37 (0.17), residues: 871 sheet: -0.09 (0.18), residues: 791 loop : -0.65 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP M1670 HIS 0.009 0.001 HIS L 393 PHE 0.021 0.001 PHE L 358 TYR 0.036 0.001 TYR A 455 ARG 0.008 0.000 ARG M1769 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 11) link_NAG-ASN : angle 4.15413 ( 33) link_BETA1-4 : bond 0.01452 ( 1) link_BETA1-4 : angle 3.52777 ( 3) hydrogen bonds : bond 0.03516 ( 918) hydrogen bonds : angle 5.28496 ( 2733) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.37971 ( 72) covalent geometry : bond 0.00299 (27098) covalent geometry : angle 0.61242 (36886) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 368 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 LEU cc_start: 0.8448 (tt) cc_final: 0.8109 (tp) REVERT: B 361 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8671 (tppt) REVERT: B 423 ARG cc_start: 0.8754 (ttt-90) cc_final: 0.8441 (tmm-80) REVERT: C 480 SER cc_start: 0.9025 (t) cc_final: 0.8765 (p) REVERT: D 545 ASN cc_start: 0.8745 (m110) cc_final: 0.8410 (m-40) REVERT: E 566 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8515 (mp) REVERT: E 568 MET cc_start: 0.7503 (mmm) cc_final: 0.7283 (mmm) REVERT: J 120 GLU cc_start: 0.7176 (pm20) cc_final: 0.6872 (pm20) REVERT: J 125 GLU cc_start: 0.6782 (tp30) cc_final: 0.6367 (tp30) REVERT: K 419 ASN cc_start: 0.9198 (t0) cc_final: 0.8948 (m110) REVERT: K 518 HIS cc_start: 0.6756 (m170) cc_final: 0.6506 (m170) REVERT: L 493 GLN cc_start: 0.7341 (pp30) cc_final: 0.7039 (pp30) REVERT: M 1173 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8031 (t80) REVERT: M 1178 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8855 (ttmt) REVERT: M 1639 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8987 (mt) REVERT: M 1758 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8664 (pp30) REVERT: M 1764 MET cc_start: 0.8949 (tpp) cc_final: 0.8402 (tpp) REVERT: M 1773 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8712 (pt0) REVERT: M 1786 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7889 (mm-30) REVERT: M 1927 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7465 (mm-40) REVERT: M 2069 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8305 (mm) REVERT: M 2122 LYS cc_start: 0.7075 (ttpp) cc_final: 0.6754 (mtpp) outliers start: 73 outliers final: 59 residues processed: 422 average time/residue: 0.4942 time to fit residues: 339.7883 Evaluate side-chains 401 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 338 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 426 CYS Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain M residue 1173 PHE Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1339 LEU Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1641 ILE Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1717 ASP Chi-restraints excluded: chain M residue 1867 TYR Chi-restraints excluded: chain M residue 1888 VAL Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 1933 CYS Chi-restraints excluded: chain M residue 2038 LEU Chi-restraints excluded: chain M residue 2052 VAL Chi-restraints excluded: chain M residue 2069 LEU Chi-restraints excluded: chain M residue 2136 THR Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 260 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 5 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 301 optimal weight: 0.0000 chunk 64 optimal weight: 0.5980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 HIS K 487 GLN L 393 HIS L 395 ASN L 490 GLN ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.188138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120488 restraints weight = 42953.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123543 restraints weight = 28053.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123294 restraints weight = 19817.323| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27146 Z= 0.141 Angle : 0.644 11.734 36994 Z= 0.323 Chirality : 0.045 0.347 4206 Planarity : 0.005 0.079 4704 Dihedral : 5.733 93.280 3827 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 2.41 % Allowed : 19.39 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.37 (0.15), residues: 3270 helix: 0.40 (0.17), residues: 871 sheet: -0.02 (0.18), residues: 800 loop : -0.64 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M1670 HIS 0.015 0.001 HIS L 393 PHE 0.024 0.001 PHE G 405 TYR 0.036 0.002 TYR A 455 ARG 0.008 0.000 ARG J 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 11) link_NAG-ASN : angle 4.14667 ( 33) link_BETA1-4 : bond 0.01152 ( 1) link_BETA1-4 : angle 3.33985 ( 3) hydrogen bonds : bond 0.03515 ( 918) hydrogen bonds : angle 5.22387 ( 2733) SS BOND : bond 0.00387 ( 36) SS BOND : angle 1.31174 ( 72) covalent geometry : bond 0.00331 (27098) covalent geometry : angle 0.62932 (36886) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 351 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8665 (tppt) REVERT: B 423 ARG cc_start: 0.8779 (ttt-90) cc_final: 0.8500 (tmm-80) REVERT: B 525 GLU cc_start: 0.7991 (tp30) cc_final: 0.7433 (tm-30) REVERT: C 480 SER cc_start: 0.9021 (t) cc_final: 0.8767 (p) REVERT: D 473 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8227 (p) REVERT: D 545 ASN cc_start: 0.8748 (m110) cc_final: 0.8423 (m-40) REVERT: E 566 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8500 (mp) REVERT: E 568 MET cc_start: 0.7474 (mmm) cc_final: 0.7268 (mmm) REVERT: J 125 GLU cc_start: 0.6646 (tp30) cc_final: 0.6301 (tp30) REVERT: K 415 GLU cc_start: 0.8071 (tt0) cc_final: 0.7868 (tm-30) REVERT: K 506 MET cc_start: 0.8663 (mpp) cc_final: 0.8399 (mpp) REVERT: L 493 GLN cc_start: 0.7600 (pp30) cc_final: 0.7195 (pp30) REVERT: M 1173 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7968 (t80) REVERT: M 1178 LYS cc_start: 0.9137 (ttmm) cc_final: 0.8836 (ttmt) REVERT: M 1639 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8965 (mt) REVERT: M 1758 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8660 (pp30) REVERT: M 1764 MET cc_start: 0.9001 (tpp) cc_final: 0.8454 (tpp) REVERT: M 1773 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8713 (pt0) REVERT: M 1786 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7902 (mm-30) REVERT: M 2069 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8262 (mm) REVERT: M 2122 LYS cc_start: 0.7169 (ttpp) cc_final: 0.6896 (mtpp) outliers start: 71 outliers final: 64 residues processed: 406 average time/residue: 0.4088 time to fit residues: 268.5835 Evaluate side-chains 406 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 518 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 358 PHE Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 370 THR Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 518 HIS Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain H residue 535 THR Chi-restraints excluded: chain H residue 536 CYS Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 400 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 347 VAL Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 426 CYS Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 537 VAL Chi-restraints excluded: chain M residue 1173 PHE Chi-restraints excluded: chain M residue 1304 ILE Chi-restraints excluded: chain M residue 1339 LEU Chi-restraints excluded: chain M residue 1639 ILE Chi-restraints excluded: chain M residue 1641 ILE Chi-restraints excluded: chain M residue 1708 VAL Chi-restraints excluded: chain M residue 1717 ASP Chi-restraints excluded: chain M residue 1867 TYR Chi-restraints excluded: chain M residue 1888 VAL Chi-restraints excluded: chain M residue 1892 LEU Chi-restraints excluded: chain M residue 1933 CYS Chi-restraints excluded: chain M residue 2038 LEU Chi-restraints excluded: chain M residue 2052 VAL Chi-restraints excluded: chain M residue 2069 LEU Chi-restraints excluded: chain M residue 2136 THR Chi-restraints excluded: chain M residue 2189 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 297 optimal weight: 0.1980 chunk 224 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 HIS K 487 GLN L 393 HIS L 395 ASN L 465 ASN L 490 GLN ** M1847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.188526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123735 restraints weight = 43347.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123638 restraints weight = 26555.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123774 restraints weight = 19678.575| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27146 Z= 0.134 Angle : 0.639 11.588 36994 Z= 0.320 Chirality : 0.045 0.345 4206 Planarity : 0.005 0.072 4704 Dihedral : 5.627 91.479 3827 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 2.54 % Allowed : 19.66 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3270 helix: 0.40 (0.17), residues: 873 sheet: 0.05 (0.18), residues: 788 loop : -0.62 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M1670 HIS 0.014 0.001 HIS L 393 PHE 0.022 0.001 PHE L 358 TYR 0.034 0.001 TYR A 455 ARG 0.009 0.000 ARG F 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 11) link_NAG-ASN : angle 4.09547 ( 33) link_BETA1-4 : bond 0.01244 ( 1) link_BETA1-4 : angle 3.28155 ( 3) hydrogen bonds : bond 0.03482 ( 918) hydrogen bonds : angle 5.15133 ( 2733) SS BOND : bond 0.00366 ( 36) SS BOND : angle 1.22655 ( 72) covalent geometry : bond 0.00314 (27098) covalent geometry : angle 0.62455 (36886) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11376.67 seconds wall clock time: 203 minutes 1.08 seconds (12181.08 seconds total)