Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 03:40:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b75_12073/05_2023/7b75_12073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b75_12073/05_2023/7b75_12073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b75_12073/05_2023/7b75_12073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b75_12073/05_2023/7b75_12073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b75_12073/05_2023/7b75_12073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b75_12073/05_2023/7b75_12073.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 1.034 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 306 5.16 5 C 24482 2.51 5 N 6728 2.21 5 O 7606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1054": "OE1" <-> "OE2" Residue "A GLU 2054": "OE1" <-> "OE2" Residue "A TYR 2157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2702": "OE1" <-> "OE2" Residue "A PHE 2717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1054": "OE1" <-> "OE2" Residue "B PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2054": "OE1" <-> "OE2" Residue "B TYR 2157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2717": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39122 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 19204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2483, 19204 Classifications: {'peptide': 2483} Link IDs: {'PTRANS': 161, 'TRANS': 2321} Chain breaks: 10 Chain: "B" Number of atoms: 19204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2483, 19204 Classifications: {'peptide': 2483} Link IDs: {'PTRANS': 161, 'TRANS': 2321} Chain breaks: 10 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" 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 chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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 chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N ALA A2293 " occ=0.99 ... (3 atoms not shown) pdb=" CB ALA A2293 " occ=0.99 residue: pdb=" N ALA A2316 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA A2316 " occ=0.94 residue: pdb=" N LEU A2343 " occ=0.98 ... (6 atoms not shown) pdb=" CD2 LEU A2343 " occ=0.98 residue: pdb=" N GLY A2348 " occ=0.97 ... (2 atoms not shown) pdb=" O GLY A2348 " occ=0.97 residue: pdb=" N LEU A2396 " occ=0.96 ... (6 atoms not shown) pdb=" CD2 LEU A2396 " occ=0.94 residue: pdb=" N ALA A2435 " occ=0.98 ... (3 atoms not shown) pdb=" CB ALA A2435 " occ=0.98 residue: pdb=" N ALA A2493 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA A2493 " occ=0.97 residue: pdb=" N LEU A2547 " occ=0.98 ... (6 atoms not shown) pdb=" CD2 LEU A2547 " occ=0.96 residue: pdb=" N ALA A2599 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA A2599 " occ=0.97 residue: pdb=" N GLY A2693 " occ=0.97 ... (2 atoms not shown) pdb=" O GLY A2693 " occ=0.97 residue: pdb=" N ALA B2293 " occ=0.99 ... (3 atoms not shown) pdb=" CB ALA B2293 " occ=0.99 residue: pdb=" N ALA B2316 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA B2316 " occ=0.94 ... (remaining 8 not shown) Time building chain proxies: 19.08, per 1000 atoms: 0.49 Number of scatterers: 39122 At special positions: 0 Unit cell: (188.16, 259.84, 130.56, 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 306 16.00 O 7606 8.00 N 6728 7.00 C 24482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=114, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 120 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS A 408 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 658 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS A 730 " - pdb=" SG CYS A 763 " distance=2.03 Simple disulfide: pdb=" SG CYS A 774 " - pdb=" SG CYS A 898 " distance=2.03 Simple disulfide: pdb=" SG CYS A 900 " - pdb=" SG CYS A 921 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1031 " distance=2.03 Simple disulfide: pdb=" SG CYS A1042 " - pdb=" SG CYS A1049 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1073 " distance=2.02 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1145 " distance=2.04 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1169 " distance=2.03 Simple disulfide: pdb=" SG CYS A1181 " - pdb=" SG CYS A1188 " distance=2.04 Simple disulfide: pdb=" SG CYS A1190 " - pdb=" SG CYS A1210 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1249 " - pdb=" SG CYS A1281 " distance=2.04 Simple disulfide: pdb=" SG CYS A1331 " - pdb=" SG CYS A1347 " distance=2.03 Simple disulfide: pdb=" SG CYS A1440 " - pdb=" SG CYS A1459 " distance=2.03 Simple disulfide: pdb=" SG CYS A1462 " - pdb=" SG CYS A1473 " distance=2.03 Simple disulfide: pdb=" SG CYS A1476 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1493 " - pdb=" SG CYS A1510 " distance=2.04 Simple disulfide: pdb=" SG CYS A1514 " - pdb=" SG CYS A1523 " distance=2.04 Simple disulfide: pdb=" SG CYS A1543 " - pdb=" SG CYS A1565 " distance=2.03 Simple disulfide: pdb=" SG CYS A1603 " - pdb=" SG CYS A1627 " distance=2.03 Simple disulfide: pdb=" SG CYS A1607 " - pdb=" SG CYS A1613 " distance=2.03 Simple disulfide: pdb=" SG CYS A1724 " - pdb=" SG CYS A1749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1734 " distance=2.03 Simple disulfide: pdb=" SG CYS A1760 " - pdb=" SG CYS A1777 " distance=2.04 Simple disulfide: pdb=" SG CYS A1893 " - pdb=" SG CYS A1919 " distance=2.03 Simple disulfide: pdb=" SG CYS A1897 " - pdb=" SG CYS A1904 " distance=2.02 Simple disulfide: pdb=" SG CYS A1928 " - pdb=" SG CYS A1939 " distance=2.03 Simple disulfide: pdb=" SG CYS A1996 " - pdb=" SG CYS A2024 " distance=2.02 Simple disulfide: pdb=" SG CYS A2000 " - pdb=" SG CYS A2006 " distance=2.03 Simple disulfide: pdb=" SG CYS A2005 " - pdb=" SG CYS A2076 " distance=2.04 Simple disulfide: pdb=" SG CYS A2035 " - pdb=" SG CYS A2048 " distance=2.03 Simple disulfide: pdb=" SG CYS A2130 " - pdb=" SG CYS A2154 " distance=2.03 Simple disulfide: pdb=" SG CYS A2134 " - pdb=" SG CYS A2140 " distance=2.04 Simple disulfide: pdb=" SG CYS A2163 " - pdb=" SG CYS A2172 " distance=2.03 Simple disulfide: pdb=" SG CYS A2264 " - pdb=" SG CYS A2281 " distance=2.03 Simple disulfide: pdb=" SG CYS A2442 " - pdb=" SG CYS A2453 " distance=2.03 Simple disulfide: pdb=" SG CYS A2591 " - pdb=" SG CYS A2715 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 92 " distance=2.02 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 297 " distance=2.04 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 620 " distance=2.03 Simple disulfide: pdb=" SG CYS B 408 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 658 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 703 " distance=2.03 Simple disulfide: pdb=" SG CYS B 705 " - pdb=" SG CYS B 726 " distance=2.02 Simple disulfide: pdb=" SG CYS B 730 " - pdb=" SG CYS B 763 " distance=2.03 Simple disulfide: pdb=" SG CYS B 774 " - pdb=" SG CYS B 898 " distance=2.03 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 921 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1031 " distance=2.03 Simple disulfide: pdb=" SG CYS B1042 " - pdb=" SG CYS B1049 " distance=2.03 Simple disulfide: pdb=" SG CYS B1051 " - pdb=" SG CYS B1073 " distance=2.02 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1145 " distance=2.04 Simple disulfide: pdb=" SG CYS B1149 " - pdb=" SG CYS B1169 " distance=2.03 Simple disulfide: pdb=" SG CYS B1181 " - pdb=" SG CYS B1188 " distance=2.04 Simple disulfide: pdb=" SG CYS B1190 " - pdb=" SG CYS B1210 " distance=2.03 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1245 " distance=2.03 Simple disulfide: pdb=" SG CYS B1249 " - pdb=" SG CYS B1281 " distance=2.04 Simple disulfide: pdb=" SG CYS B1331 " - pdb=" SG CYS B1347 " distance=2.03 Simple disulfide: pdb=" SG CYS B1440 " - pdb=" SG CYS B1459 " distance=2.03 Simple disulfide: pdb=" SG CYS B1462 " - pdb=" SG CYS B1473 " distance=2.03 Simple disulfide: pdb=" SG CYS B1476 " - pdb=" SG CYS B1490 " distance=2.03 Simple disulfide: pdb=" SG CYS B1493 " - pdb=" SG CYS B1510 " distance=2.04 Simple disulfide: pdb=" SG CYS B1514 " - pdb=" SG CYS B1523 " distance=2.04 Simple disulfide: pdb=" SG CYS B1543 " - pdb=" SG CYS B1565 " distance=2.03 Simple disulfide: pdb=" SG CYS B1603 " - pdb=" SG CYS B1627 " distance=2.03 Simple disulfide: pdb=" SG CYS B1607 " - pdb=" SG CYS B1613 " distance=2.03 Simple disulfide: pdb=" SG CYS B1724 " - pdb=" SG CYS B1749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1728 " - pdb=" SG CYS B1734 " distance=2.03 Simple disulfide: pdb=" SG CYS B1760 " - pdb=" SG CYS B1777 " distance=2.04 Simple disulfide: pdb=" SG CYS B1893 " - pdb=" SG CYS B1919 " distance=2.03 Simple disulfide: pdb=" SG CYS B1897 " - pdb=" SG CYS B1904 " distance=2.02 Simple disulfide: pdb=" SG CYS B1928 " - pdb=" SG CYS B1939 " distance=2.03 Simple disulfide: pdb=" SG CYS B1996 " - pdb=" SG CYS B2024 " distance=2.02 Simple disulfide: pdb=" SG CYS B2000 " - pdb=" SG CYS B2006 " distance=2.03 Simple disulfide: pdb=" SG CYS B2005 " - pdb=" SG CYS B2076 " distance=2.03 Simple disulfide: pdb=" SG CYS B2035 " - pdb=" SG CYS B2048 " distance=2.03 Simple disulfide: pdb=" SG CYS B2130 " - pdb=" SG CYS B2154 " distance=2.03 Simple disulfide: pdb=" SG CYS B2134 " - pdb=" SG CYS B2140 " distance=2.04 Simple disulfide: pdb=" SG CYS B2163 " - pdb=" SG CYS B2172 " distance=2.03 Simple disulfide: pdb=" SG CYS B2264 " - pdb=" SG CYS B2281 " distance=2.03 Simple disulfide: pdb=" SG CYS B2442 " - pdb=" SG CYS B2453 " distance=2.03 Simple disulfide: pdb=" SG CYS B2591 " - pdb=" SG CYS B2715 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM38665 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM38760 O5 NAG L 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " MAN H 4 " - " MAN H 5 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " ALPHA1-6 " BMA H 3 " - " MAN H 6 " " BMA N 3 " - " MAN N 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A2801 " - " ASN A 76 " " NAG A2802 " - " ASN A 748 " " NAG A2803 " - " ASN A 947 " " NAG A2804 " - " ASN A1220 " " NAG A2805 " - " ASN A1349 " " NAG A2806 " - " ASN A1365 " " NAG A2807 " - " ASN A1774 " " NAG A2808 " - " ASN A2250 " " NAG B2801 " - " ASN B 76 " " NAG B2802 " - " ASN B 748 " " NAG B2803 " - " ASN B 947 " " NAG B2804 " - " ASN B1220 " " NAG B2805 " - " ASN B1349 " " NAG B2806 " - " ASN B1365 " " NAG B2807 " - " ASN B1774 " " NAG B2808 " - " ASN B2250 " " NAG C 1 " - " ASN A 484 " " NAG D 1 " - " ASN A1716 " " NAG E 1 " - " ASN A2013 " " NAG F 1 " - " ASN A2122 " " NAG G 1 " - " ASN A2295 " " NAG H 1 " - " ASN A2582 " " NAG I 1 " - " ASN B 484 " " NAG J 1 " - " ASN B1716 " " NAG K 1 " - " ASN B2013 " " NAG L 1 " - " ASN B2122 " " NAG M 1 " - " ASN B2295 " " NAG N 1 " - " ASN B2582 " Time building additional restraints: 16.87 Conformation dependent library (CDL) restraints added in 6.1 seconds 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9196 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 58 sheets defined 28.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.945A pdb=" N ARG A 152 " --> pdb=" O TYR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 291 removed outlier: 3.735A pdb=" N ARG A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.617A pdb=" N THR A 349 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG A 350 " --> pdb=" O HIS A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'A' and resid 364 through 376 Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.869A pdb=" N MET A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 removed outlier: 3.528A pdb=" N PHE A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.506A pdb=" N ALA A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.751A pdb=" N ASN A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.741A pdb=" N GLU A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.651A pdb=" N LEU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 605 Processing helix chain 'A' and resid 606 through 608 No H-bonds generated for 'chain 'A' and resid 606 through 608' Processing helix chain 'A' and resid 660 through 674 Processing helix chain 'A' and resid 728 through 746 Processing helix chain 'A' and resid 778 through 792 removed outlier: 3.596A pdb=" N ASN A 792 " --> pdb=" O TRP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 923 through 949 removed outlier: 3.718A pdb=" N ALA A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 943 " --> pdb=" O THR A 939 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 949 " --> pdb=" O ALA A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 962 Processing helix chain 'A' and resid 967 through 971 Processing helix chain 'A' and resid 978 through 986 removed outlier: 3.809A pdb=" N PHE A 982 " --> pdb=" O PRO A 978 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1009 Processing helix chain 'A' and resid 1075 through 1087 removed outlier: 3.708A pdb=" N SER A1080 " --> pdb=" O THR A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1158 removed outlier: 3.521A pdb=" N VAL A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1314 through 1328 Processing helix chain 'A' and resid 1382 through 1392 Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 3.535A pdb=" N THR A1400 " --> pdb=" O LEU A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1457 removed outlier: 3.883A pdb=" N GLY A1456 " --> pdb=" O SER A1453 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A1457 " --> pdb=" O GLN A1454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1453 through 1457' Processing helix chain 'A' and resid 1506 through 1510 removed outlier: 3.535A pdb=" N CYS A1510 " --> pdb=" O GLN A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1517 removed outlier: 3.965A pdb=" N ASN A1517 " --> pdb=" O ASP A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1557 removed outlier: 4.405A pdb=" N THR A1556 " --> pdb=" O PRO A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1579 Processing helix chain 'A' and resid 1598 through 1607 Processing helix chain 'A' and resid 1718 through 1731 Processing helix chain 'A' and resid 1888 through 1900 Processing helix chain 'A' and resid 1988 through 2003 removed outlier: 4.180A pdb=" N PHE A1994 " --> pdb=" O SER A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2097 through 2099 No H-bonds generated for 'chain 'A' and resid 2097 through 2099' Processing helix chain 'A' and resid 2122 through 2137 removed outlier: 3.695A pdb=" N VAL A2126 " --> pdb=" O ASN A2122 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A2137 " --> pdb=" O GLU A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2319 through 2327 Processing helix chain 'A' and resid 2353 through 2369 Processing helix chain 'A' and resid 2370 through 2373 Processing helix chain 'A' and resid 2393 through 2398 Processing helix chain 'A' and resid 2425 through 2441 Processing helix chain 'A' and resid 2446 through 2455 Processing helix chain 'A' and resid 2458 through 2472 removed outlier: 4.171A pdb=" N VAL A2472 " --> pdb=" O LYS A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2473 through 2478 removed outlier: 6.394A pdb=" N PHE A2476 " --> pdb=" O SER A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2491 through 2496 Processing helix chain 'A' and resid 2497 through 2499 No H-bonds generated for 'chain 'A' and resid 2497 through 2499' Processing helix chain 'A' and resid 2517 through 2519 No H-bonds generated for 'chain 'A' and resid 2517 through 2519' Processing helix chain 'A' and resid 2520 through 2531 Processing helix chain 'A' and resid 2536 through 2548 removed outlier: 3.809A pdb=" N GLY A2548 " --> pdb=" O GLN A2544 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2564 removed outlier: 3.540A pdb=" N TYR A2564 " --> pdb=" O ALA A2560 " (cutoff:3.500A) Processing helix chain 'A' and resid 2572 through 2589 removed outlier: 4.088A pdb=" N PHE A2576 " --> pdb=" O ASP A2572 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2603 removed outlier: 4.144A pdb=" N ARG A2603 " --> pdb=" O ALA A2599 " (cutoff:3.500A) Processing helix chain 'A' and resid 2625 through 2632 Processing helix chain 'A' and resid 2633 through 2637 removed outlier: 3.585A pdb=" N PHE A2636 " --> pdb=" O GLY A2633 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2665 Processing helix chain 'A' and resid 2711 through 2720 Processing helix chain 'A' and resid 2720 through 2727 removed outlier: 3.637A pdb=" N SER A2724 " --> pdb=" O LYS A2720 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 44 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.954A pdb=" N ARG B 152 " --> pdb=" O TYR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.733A pdb=" N ARG B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.620A pdb=" N THR B 349 " --> pdb=" O MET B 346 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG B 350 " --> pdb=" O HIS B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 350' Processing helix chain 'B' and resid 364 through 376 Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.868A pdb=" N MET B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 removed outlier: 3.524A pdb=" N PHE B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 removed outlier: 3.506A pdb=" N ALA B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 Processing helix chain 'B' and resid 475 through 482 removed outlier: 3.755A pdb=" N ASN B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 573 removed outlier: 3.742A pdb=" N GLU B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 586 removed outlier: 3.651A pdb=" N LEU B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 605 Processing helix chain 'B' and resid 606 through 608 No H-bonds generated for 'chain 'B' and resid 606 through 608' Processing helix chain 'B' and resid 660 through 674 Processing helix chain 'B' and resid 728 through 746 Processing helix chain 'B' and resid 778 through 792 removed outlier: 3.590A pdb=" N ASN B 792 " --> pdb=" O TRP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 923 through 949 removed outlier: 3.717A pdb=" N ALA B 928 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 948 " --> pdb=" O SER B 944 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 949 " --> pdb=" O ALA B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 962 Processing helix chain 'B' and resid 967 through 971 Processing helix chain 'B' and resid 978 through 986 removed outlier: 3.809A pdb=" N PHE B 982 " --> pdb=" O PRO B 978 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 986 " --> pdb=" O PHE B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1009 Processing helix chain 'B' and resid 1075 through 1088 removed outlier: 3.711A pdb=" N SER B1080 " --> pdb=" O THR B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1158 removed outlier: 3.521A pdb=" N VAL B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 1300 through 1304 Processing helix chain 'B' and resid 1314 through 1328 Processing helix chain 'B' and resid 1382 through 1392 Processing helix chain 'B' and resid 1395 through 1405 removed outlier: 3.537A pdb=" N THR B1400 " --> pdb=" O LEU B1396 " (cutoff:3.500A) Processing helix chain 'B' and resid 1453 through 1457 removed outlier: 3.885A pdb=" N GLY B1456 " --> pdb=" O SER B1453 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B1457 " --> pdb=" O GLN B1454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1453 through 1457' Processing helix chain 'B' and resid 1506 through 1510 removed outlier: 3.553A pdb=" N CYS B1510 " --> pdb=" O GLN B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1512 through 1517 removed outlier: 3.965A pdb=" N ASN B1517 " --> pdb=" O ASP B1513 " (cutoff:3.500A) Processing helix chain 'B' and resid 1552 through 1557 removed outlier: 4.392A pdb=" N THR B1556 " --> pdb=" O PRO B1552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1575 through 1579 Processing helix chain 'B' and resid 1598 through 1607 Processing helix chain 'B' and resid 1718 through 1731 Processing helix chain 'B' and resid 1888 through 1900 Processing helix chain 'B' and resid 1988 through 2003 removed outlier: 4.195A pdb=" N PHE B1994 " --> pdb=" O SER B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2097 through 2099 No H-bonds generated for 'chain 'B' and resid 2097 through 2099' Processing helix chain 'B' and resid 2122 through 2137 removed outlier: 3.622A pdb=" N VAL B2126 " --> pdb=" O ASN B2122 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B2137 " --> pdb=" O GLU B2133 " (cutoff:3.500A) Processing helix chain 'B' and resid 2319 through 2327 Processing helix chain 'B' and resid 2353 through 2369 Processing helix chain 'B' and resid 2370 through 2373 Processing helix chain 'B' and resid 2393 through 2398 Processing helix chain 'B' and resid 2425 through 2441 Processing helix chain 'B' and resid 2446 through 2455 Processing helix chain 'B' and resid 2458 through 2472 removed outlier: 4.172A pdb=" N VAL B2472 " --> pdb=" O LYS B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2473 through 2478 removed outlier: 6.388A pdb=" N PHE B2476 " --> pdb=" O SER B2473 " (cutoff:3.500A) Processing helix chain 'B' and resid 2491 through 2496 Processing helix chain 'B' and resid 2497 through 2499 No H-bonds generated for 'chain 'B' and resid 2497 through 2499' Processing helix chain 'B' and resid 2517 through 2519 No H-bonds generated for 'chain 'B' and resid 2517 through 2519' Processing helix chain 'B' and resid 2520 through 2531 Processing helix chain 'B' and resid 2536 through 2548 removed outlier: 3.815A pdb=" N GLY B2548 " --> pdb=" O GLN B2544 " (cutoff:3.500A) Processing helix chain 'B' and resid 2553 through 2564 removed outlier: 3.546A pdb=" N TYR B2564 " --> pdb=" O ALA B2560 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2589 removed outlier: 4.097A pdb=" N PHE B2576 " --> pdb=" O ASP B2572 " (cutoff:3.500A) Processing helix chain 'B' and resid 2589 through 2603 removed outlier: 4.145A pdb=" N ARG B2603 " --> pdb=" O ALA B2599 " (cutoff:3.500A) Processing helix chain 'B' and resid 2625 through 2632 Processing helix chain 'B' and resid 2633 through 2637 removed outlier: 3.569A pdb=" N PHE B2636 " --> pdb=" O GLY B2633 " (cutoff:3.500A) Processing helix chain 'B' and resid 2645 through 2665 Processing helix chain 'B' and resid 2711 through 2720 Processing helix chain 'B' and resid 2720 through 2727 removed outlier: 3.640A pdb=" N SER B2724 " --> pdb=" O LYS B2720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.560A pdb=" N SER A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 removed outlier: 3.519A pdb=" N TRP A 337 " --> pdb=" O GLN A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 629 through 632 Processing sheet with id=AA7, first strand: chain 'A' and resid 697 through 698 removed outlier: 3.574A pdb=" N TYR A 704 " --> pdb=" O GLN A 697 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 772 through 773 Processing sheet with id=AA9, first strand: chain 'A' and resid 1040 through 1042 Processing sheet with id=AB1, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AB2, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB3, first strand: chain 'A' and resid 1227 through 1230 Processing sheet with id=AB4, first strand: chain 'A' and resid 1254 through 1255 removed outlier: 3.600A pdb=" N GLN A1282 " --> pdb=" O TRP A1254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1285 Processing sheet with id=AB6, first strand: chain 'A' and resid 1365 through 1371 Processing sheet with id=AB7, first strand: chain 'A' and resid 1332 through 1337 Processing sheet with id=AB8, first strand: chain 'A' and resid 1466 through 1468 Processing sheet with id=AB9, first strand: chain 'A' and resid 1480 through 1481 Processing sheet with id=AC1, first strand: chain 'A' and resid 1532 through 1534 Processing sheet with id=AC2, first strand: chain 'A' and resid 1685 through 1686 removed outlier: 3.652A pdb=" N GLY A1736 " --> pdb=" O LEU A1752 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A1747 " --> pdb=" O PHE A1710 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1697 through 1700 removed outlier: 7.743A pdb=" N CYS A1760 " --> pdb=" O GLN A1698 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET A1700 " --> pdb=" O LEU A1758 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU A1758 " --> pdb=" O MET A1700 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS A1760 " --> pdb=" O HIS A1877 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS A1877 " --> pdb=" O CYS A1760 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1865 through 1866 removed outlier: 6.172A pdb=" N ILE A1865 " --> pdb=" O LEU A1943 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1966 through 1967 removed outlier: 7.018A pdb=" N SER A1977 " --> pdb=" O ASN A2028 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1966 through 1967 Processing sheet with id=AC7, first strand: chain 'A' and resid 1972 through 1973 removed outlier: 4.679A pdb=" N ILE A2183 " --> pdb=" O LEU A2096 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2101 through 2103 Processing sheet with id=AC9, first strand: chain 'A' and resid 2193 through 2195 removed outlier: 3.590A pdb=" N GLU A2195 " --> pdb=" O VAL A2198 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2212 through 2218 removed outlier: 10.268A pdb=" N ALA A2296 " --> pdb=" O PRO A2377 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG A2379 " --> pdb=" O ALA A2296 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A2298 " --> pdb=" O ARG A2379 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A2385 " --> pdb=" O PHE A2302 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A2409 " --> pdb=" O ARG A2378 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A2380 " --> pdb=" O ARG A2409 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL A2411 " --> pdb=" O VAL A2380 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A2382 " --> pdb=" O VAL A2411 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET A2413 " --> pdb=" O LEU A2382 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A2384 " --> pdb=" O MET A2413 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA A2410 " --> pdb=" O LEU A2507 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY A2509 " --> pdb=" O ALA A2410 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A2412 " --> pdb=" O GLY A2509 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N LYS A2698 " --> pdb=" O VAL A2608 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET A2610 " --> pdb=" O LYS A2698 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 2231 through 2232 Processing sheet with id=AD3, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.603A pdb=" N SER B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AD5, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AD7, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.519A pdb=" N TRP B 337 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 629 through 632 Processing sheet with id=AD9, first strand: chain 'B' and resid 697 through 698 removed outlier: 3.573A pdb=" N TYR B 704 " --> pdb=" O GLN B 697 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 772 through 773 Processing sheet with id=AE2, first strand: chain 'B' and resid 1040 through 1042 Processing sheet with id=AE3, first strand: chain 'B' and resid 1091 through 1092 Processing sheet with id=AE4, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AE5, first strand: chain 'B' and resid 1227 through 1230 Processing sheet with id=AE6, first strand: chain 'B' and resid 1254 through 1255 removed outlier: 3.602A pdb=" N GLN B1282 " --> pdb=" O TRP B1254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1284 through 1285 Processing sheet with id=AE8, first strand: chain 'B' and resid 1365 through 1371 Processing sheet with id=AE9, first strand: chain 'B' and resid 1332 through 1337 Processing sheet with id=AF1, first strand: chain 'B' and resid 1466 through 1468 Processing sheet with id=AF2, first strand: chain 'B' and resid 1480 through 1481 Processing sheet with id=AF3, first strand: chain 'B' and resid 1532 through 1534 Processing sheet with id=AF4, first strand: chain 'B' and resid 1685 through 1686 removed outlier: 3.647A pdb=" N GLY B1736 " --> pdb=" O LEU B1752 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B1747 " --> pdb=" O PHE B1710 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1697 through 1700 removed outlier: 7.758A pdb=" N CYS B1760 " --> pdb=" O GLN B1698 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET B1700 " --> pdb=" O LEU B1758 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B1758 " --> pdb=" O MET B1700 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS B1760 " --> pdb=" O HIS B1877 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N HIS B1877 " --> pdb=" O CYS B1760 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1865 through 1866 removed outlier: 6.188A pdb=" N ILE B1865 " --> pdb=" O LEU B1943 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 1966 through 1967 removed outlier: 7.018A pdb=" N SER B1977 " --> pdb=" O ASN B2028 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1966 through 1967 Processing sheet with id=AF9, first strand: chain 'B' and resid 1972 through 1973 removed outlier: 4.675A pdb=" N ILE B2183 " --> pdb=" O LEU B2096 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 2101 through 2103 Processing sheet with id=AG2, first strand: chain 'B' and resid 2193 through 2195 removed outlier: 3.592A pdb=" N GLU B2195 " --> pdb=" O VAL B2198 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 2212 through 2218 removed outlier: 10.265A pdb=" N ALA B2296 " --> pdb=" O PRO B2377 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG B2379 " --> pdb=" O ALA B2296 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B2298 " --> pdb=" O ARG B2379 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP B2385 " --> pdb=" O PHE B2302 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG B2409 " --> pdb=" O ARG B2378 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B2380 " --> pdb=" O ARG B2409 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B2411 " --> pdb=" O VAL B2380 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B2382 " --> pdb=" O VAL B2411 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET B2413 " --> pdb=" O LEU B2382 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B2384 " --> pdb=" O MET B2413 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B2410 " --> pdb=" O LEU B2507 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY B2509 " --> pdb=" O ALA B2410 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B2412 " --> pdb=" O GLY B2509 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N LYS B2698 " --> pdb=" O VAL B2608 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET B2610 " --> pdb=" O LYS B2698 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 2231 through 2232 1236 hydrogen bonds defined for protein. 3360 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: 25.42 Time building geometry restraints manager: 18.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10730 1.33 - 1.46: 10775 1.46 - 1.59: 18153 1.59 - 1.72: 0 1.72 - 1.85: 374 Bond restraints: 40032 Sorted by residual: bond pdb=" C1 MAN H 6 " pdb=" O5 MAN H 6 " ideal model delta sigma weight residual 1.399 1.495 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C5 MAN N 6 " pdb=" O5 MAN N 6 " ideal model delta sigma weight residual 1.418 1.504 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 MAN N 6 " pdb=" O5 MAN N 6 " ideal model delta sigma weight residual 1.399 1.483 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C5 MAN H 6 " pdb=" O5 MAN H 6 " ideal model delta sigma weight residual 1.418 1.491 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.86e+00 ... (remaining 40027 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.59: 1554 106.59 - 113.83: 21221 113.83 - 121.08: 18860 121.08 - 128.32: 12318 128.32 - 135.57: 383 Bond angle restraints: 54336 Sorted by residual: angle pdb=" N VAL A1840 " pdb=" CA VAL A1840 " pdb=" C VAL A1840 " ideal model delta sigma weight residual 109.02 103.76 5.26 9.30e-01 1.16e+00 3.20e+01 angle pdb=" C VAL A1840 " pdb=" CA VAL A1840 " pdb=" CB VAL A1840 " ideal model delta sigma weight residual 111.00 116.26 -5.26 9.80e-01 1.04e+00 2.89e+01 angle pdb=" C VAL B1840 " pdb=" CA VAL B1840 " pdb=" CB VAL B1840 " ideal model delta sigma weight residual 111.00 116.17 -5.17 9.80e-01 1.04e+00 2.78e+01 angle pdb=" C GLY A2348 " pdb=" N GLU A2349 " pdb=" CA GLU A2349 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C GLY B2348 " pdb=" N GLU B2349 " pdb=" CA GLU B2349 " ideal model delta sigma weight residual 121.54 131.54 -10.00 1.91e+00 2.74e-01 2.74e+01 ... (remaining 54331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21424 17.90 - 35.79: 2078 35.79 - 53.69: 367 53.69 - 71.58: 91 71.58 - 89.48: 52 Dihedral angle restraints: 24012 sinusoidal: 9754 harmonic: 14258 Sorted by residual: dihedral pdb=" CB CYS B 140 " pdb=" SG CYS B 140 " pdb=" SG CYS B 160 " pdb=" CB CYS B 160 " ideal model delta sinusoidal sigma weight residual -86.00 -172.33 86.33 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual -86.00 -172.32 86.32 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS B1462 " pdb=" SG CYS B1462 " pdb=" SG CYS B1473 " pdb=" CB CYS B1473 " ideal model delta sinusoidal sigma weight residual -86.00 -168.69 82.69 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 24009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 5492 0.105 - 0.210: 497 0.210 - 0.316: 37 0.316 - 0.421: 12 0.421 - 0.526: 2 Chirality restraints: 6040 Sorted by residual: chirality pdb=" CB VAL A2055 " pdb=" CA VAL A2055 " pdb=" CG1 VAL A2055 " pdb=" CG2 VAL A2055 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB VAL B2055 " pdb=" CA VAL B2055 " pdb=" CG1 VAL B2055 " pdb=" CG2 VAL B2055 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 6037 not shown) Planarity restraints: 7150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B2122 " -0.011 2.00e-02 2.50e+03 6.90e-02 5.94e+01 pdb=" CG ASN B2122 " 0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN B2122 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN B2122 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 484 " 0.059 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN B 484 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN B 484 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 484 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B2122 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.46e+01 pdb=" CG ASN B2122 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B2122 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN B2122 " -0.022 2.00e-02 2.50e+03 ... (remaining 7147 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 9662 2.80 - 3.32: 36101 3.32 - 3.85: 63219 3.85 - 4.37: 70018 4.37 - 4.90: 120772 Nonbonded interactions: 299772 Sorted by model distance: nonbonded pdb=" OH TYR A2058 " pdb=" OD1 ASN B 168 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASN A 168 " pdb=" OH TYR B2058 " model vdw 2.279 2.440 nonbonded pdb=" O PRO A2267 " pdb=" OG1 THR A2467 " model vdw 2.284 2.440 nonbonded pdb=" O PRO B2267 " pdb=" OG1 THR B2467 " model vdw 2.284 2.440 nonbonded pdb=" OH TYR A2658 " pdb=" O THR A2683 " model vdw 2.291 2.440 ... (remaining 299767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.74 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.030 Extract box with map and model: 10.760 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 109.490 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.006 0.096 40032 Z= 0.363 Angle : 1.114 15.025 54336 Z= 0.576 Chirality : 0.063 0.526 6040 Planarity : 0.007 0.073 7122 Dihedral : 14.586 89.475 14474 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.63 % Favored : 91.34 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 4922 helix: -0.65 (0.12), residues: 1236 sheet: -1.18 (0.22), residues: 578 loop : -2.06 (0.11), residues: 3108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 308 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 310 average time/residue: 0.5115 time to fit residues: 263.3743 Evaluate side-chains 205 residues out of total 4244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.714 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 418 optimal weight: 7.9990 chunk 375 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 253 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 450 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 362 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 GLN ** A1877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2568 HIS B 212 ASN B 362 GLN B1043 HIS ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 40032 Z= 0.450 Angle : 0.756 11.605 54336 Z= 0.376 Chirality : 0.047 0.358 6040 Planarity : 0.005 0.058 7122 Dihedral : 5.696 25.155 5340 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4922 helix: 0.64 (0.14), residues: 1242 sheet: -1.19 (0.21), residues: 616 loop : -2.07 (0.11), residues: 3064 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 231 time to evaluate : 5.226 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 27 residues processed: 251 average time/residue: 0.5348 time to fit residues: 225.4357 Evaluate side-chains 228 residues out of total 4244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 4.409 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3782 time to fit residues: 25.9398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 250 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 374 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 451 optimal weight: 2.9990 chunk 487 optimal weight: 0.6980 chunk 401 optimal weight: 0.6980 chunk 447 optimal weight: 0.0170 chunk 153 optimal weight: 0.9990 chunk 361 optimal weight: 9.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN ** A1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 40032 Z= 0.211 Angle : 0.656 10.561 54336 Z= 0.320 Chirality : 0.043 0.298 6040 Planarity : 0.004 0.053 7122 Dihedral : 5.358 24.274 5340 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4922 helix: 1.03 (0.14), residues: 1250 sheet: -1.07 (0.21), residues: 638 loop : -1.99 (0.11), residues: 3034 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9844 Ramachandran restraints generated. 4922 Oldfield, 0 Emsley, 4922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 5.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 237 average time/residue: 0.5442 time to fit residues: 215.3267 Evaluate side-chains 216 residues out of total 4244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 4.126 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3609 time to fit residues: 13.6323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 445 optimal weight: 0.7980 chunk 339 optimal weight: 0.0570 chunk 234 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 302 optimal weight: 6.9990 chunk 452 optimal weight: 1.9990 chunk 479 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 429 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: