Starting phenix.real_space_refine on Tue Feb 20 05:52:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwy_30889/02_2024/7dwy_30889_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwy_30889/02_2024/7dwy_30889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwy_30889/02_2024/7dwy_30889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwy_30889/02_2024/7dwy_30889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwy_30889/02_2024/7dwy_30889_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dwy_30889/02_2024/7dwy_30889_neut_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 120 5.16 5 C 17151 2.51 5 N 4389 2.21 5 O 5319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26979 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 Chain: "B" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 Chain: "C" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 53, 'TRANS': 1045} Chain breaks: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "H" 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: "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: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" 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: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 286 Unusual residues: {'EIC': 1, 'NAG': 19} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Chain: "B" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 314 Unusual residues: {'EIC': 1, 'NAG': 21} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 21 Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 286 Unusual residues: {'EIC': 1, 'NAG': 19} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 13.27, per 1000 atoms: 0.49 Number of scatterers: 26979 At special positions: 0 Unit cell: (145.658, 146.745, 169.572, 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 120 16.00 O 5319 8.00 N 4389 7.00 C 17151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.78 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.48 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.49 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.78 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.48 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.49 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=1.78 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.48 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.49 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1401 " - " NAG A1402 " " NAG A1409 " - " NAG A1410 " " NAG A1412 " - " NAG A1413 " " NAG A1416 " - " NAG A1417 " " NAG A1418 " - " NAG A1419 " " NAG B1401 " - " NAG B1402 " " NAG B1409 " - " NAG B1410 " " NAG B1412 " - " NAG B1413 " " NAG B1416 " - " NAG B1417 " " NAG B1418 " - " NAG B1419 " " NAG B1420 " - " NAG B1421 " " NAG C1401 " - " NAG C1402 " " NAG C1410 " - " NAG C1411 " " NAG C1414 " - " NAG C1415 " " NAG C1416 " - " NAG C1417 " " NAG C1418 " - " NAG C1419 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1401 " - " ASN A 17 " " NAG A1403 " - " ASN A 61 " " NAG A1404 " - " ASN A 122 " " NAG A1405 " - " ASN A 149 " " NAG A1406 " - " ASN A 165 " " NAG A1407 " - " ASN A 234 " " NAG A1408 " - " ASN A 282 " " NAG A1409 " - " ASN A 343 " " NAG A1411 " - " ASN A 603 " " NAG A1412 " - " ASN A 616 " " NAG A1414 " - " ASN A 657 " " NAG A1415 " - " ASN A 709 " " NAG A1416 " - " ASN A 801 " " NAG A1418 " - " ASN A1134 " " NAG B1401 " - " ASN B 17 " " NAG B1403 " - " ASN B 61 " " NAG B1404 " - " ASN B 122 " " NAG B1405 " - " ASN B 149 " " NAG B1406 " - " ASN B 165 " " NAG B1407 " - " ASN B 234 " " NAG B1408 " - " ASN B 282 " " NAG B1409 " - " ASN B 343 " " NAG B1411 " - " ASN B 603 " " NAG B1412 " - " ASN B 616 " " NAG B1414 " - " ASN B 657 " " NAG B1415 " - " ASN B 709 " " NAG B1416 " - " ASN B 801 " " NAG B1418 " - " ASN B1074 " " NAG B1420 " - " ASN B1134 " " NAG C1401 " - " ASN C 17 " " NAG C1403 " - " ASN C 61 " " NAG C1404 " - " ASN C 122 " " NAG C1405 " - " ASN C 149 " " NAG C1406 " - " ASN C 165 " " NAG C1407 " - " ASN C 234 " " NAG C1408 " - " ASN C 282 " " NAG C1409 " - " ASN C 603 " " NAG C1410 " - " ASN C 616 " " NAG C1412 " - " ASN C 657 " " NAG C1413 " - " ASN C 709 " " NAG C1414 " - " ASN C 801 " " NAG C1416 " - " ASN C1074 " " NAG C1418 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN C 331 " " NAG L 1 " - " ASN C 343 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 4.9 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 39 sheets defined 20.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.43 Creating SS restraints... Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.781A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.511A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.099A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.477A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.781A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.784A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.511A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.099A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 981 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.477A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1145 Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.781A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 removed outlier: 3.786A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 837 through 840 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.512A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 4.099A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 981 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.477A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1145 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.208A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 242 through 247 removed outlier: 6.109A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.153A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.490A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.688A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.052A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.208A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 242 through 247 removed outlier: 6.109A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.656A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.153A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.491A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.688A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.051A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AA, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.207A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 242 through 247 removed outlier: 6.109A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.152A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AI, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.490A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.687A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.051A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 1088 through 1090 963 hydrogen bonds defined for protein. 2682 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: 10.84 Time building geometry restraints manager: 11.71 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: 8394 1.33 - 1.46: 6351 1.46 - 1.58: 12681 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 27576 Sorted by residual: bond pdb=" C1 NAG B1410 " pdb=" C2 NAG B1410 " ideal model delta sigma weight residual 1.532 1.418 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C1 NAG A1410 " pdb=" C2 NAG A1410 " ideal model delta sigma weight residual 1.532 1.418 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C1 NAG L 2 " pdb=" C2 NAG L 2 " ideal model delta sigma weight residual 1.532 1.418 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.302 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.303 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 27571 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.56: 728 106.56 - 113.44: 15458 113.44 - 120.31: 9836 120.31 - 127.19: 11238 127.19 - 134.07: 243 Bond angle restraints: 37503 Sorted by residual: angle pdb=" N ARG B 847 " pdb=" CA ARG B 847 " pdb=" C ARG B 847 " ideal model delta sigma weight residual 114.56 107.64 6.92 1.27e+00 6.20e-01 2.97e+01 angle pdb=" N ARG C 847 " pdb=" CA ARG C 847 " pdb=" C ARG C 847 " ideal model delta sigma weight residual 114.56 107.68 6.88 1.27e+00 6.20e-01 2.94e+01 angle pdb=" N ARG A 847 " pdb=" CA ARG A 847 " pdb=" C ARG A 847 " ideal model delta sigma weight residual 114.56 107.70 6.86 1.27e+00 6.20e-01 2.92e+01 angle pdb=" CA GLN C1142 " pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 120.79 116.42 4.37 9.70e-01 1.06e+00 2.03e+01 angle pdb=" CA GLN B1142 " pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 120.79 116.45 4.34 9.70e-01 1.06e+00 2.00e+01 ... (remaining 37498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 15163 17.54 - 35.09: 1478 35.09 - 52.63: 563 52.63 - 70.17: 231 70.17 - 87.72: 37 Dihedral angle restraints: 17472 sinusoidal: 7881 harmonic: 9591 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.58 80.58 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 17469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 4412 0.304 - 0.609: 16 0.609 - 0.913: 12 0.913 - 1.218: 12 1.218 - 1.522: 9 Chirality restraints: 4461 Sorted by residual: chirality pdb=" C1 NAG B1413 " pdb=" O4 NAG B1412 " pdb=" C2 NAG B1413 " pdb=" O5 NAG B1413 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.50e+03 chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.50e+03 chirality pdb=" C1 NAG A1413 " pdb=" O4 NAG A1412 " pdb=" C2 NAG A1413 " pdb=" O5 NAG A1413 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 ... (remaining 4458 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN B 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG B1414 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG A1414 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN C 657 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.577 2.00e-02 2.50e+03 pdb=" C1 NAG C1412 " -0.391 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 148 2.51 - 3.11: 18706 3.11 - 3.70: 37315 3.70 - 4.30: 58945 4.30 - 4.90: 99562 Nonbonded interactions: 214676 Sorted by model distance: nonbonded pdb=" O SER B 940 " pdb=" OG1 THR B 941 " model vdw 1.911 2.440 nonbonded pdb=" O SER A 940 " pdb=" OG1 THR A 941 " model vdw 1.911 2.440 nonbonded pdb=" O SER C 940 " pdb=" OG1 THR C 941 " model vdw 1.911 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.195 2.440 ... (remaining 214671 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' and (resid 14 through 1146 or resid 1401 through 1419)) selection = (chain 'B' and (resid 14 through 1146 or resid 1401 through 1419)) selection = (chain 'C' and (resid 14 through 1146 or resid 1401 through 1419)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' 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=1.00 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: 1.140 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: 6.490 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 70.980 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.280 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 27576 Z= 0.572 Angle : 0.860 8.344 37503 Z= 0.471 Chirality : 0.110 1.522 4461 Planarity : 0.011 0.279 4755 Dihedral : 17.257 87.718 11175 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.42 % Favored : 94.21 % Rotamer: Outliers : 12.02 % Allowed : 13.34 % Favored : 74.64 % 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: -2.54 (0.12), residues: 3267 helix: -0.88 (0.18), residues: 714 sheet: -0.12 (0.18), residues: 765 loop : -2.88 (0.11), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 PHE 0.016 0.002 PHE A 133 TYR 0.023 0.002 TYR B 756 ARG 0.003 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 352 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 66 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6449 (p-80) REVERT: A 208 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 471 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: B 185 ASN cc_start: 0.6177 (OUTLIER) cc_final: 0.5799 (t0) REVERT: B 212 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6478 (tp) REVERT: B 900 MET cc_start: 0.8728 (mtp) cc_final: 0.8483 (mtm) REVERT: C 66 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6668 (p-80) REVERT: C 212 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (tm) REVERT: C 258 TRP cc_start: 0.8542 (p-90) cc_final: 0.8253 (p-90) REVERT: C 259 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8196 (m) REVERT: C 462 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8304 (mmtt) REVERT: C 606 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7599 (p0) outliers start: 345 outliers final: 46 residues processed: 609 average time/residue: 1.0538 time to fit residues: 773.6832 Evaluate side-chains 248 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 192 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 207 HIS A 239 GLN A 314 GLN A 317 ASN A 448 ASN A 532 ASN A 544 ASN A 556 ASN A 564 GLN A 606 ASN A 613 GLN A 644 GLN A 751 ASN A 919 ASN A 925 ASN A1010 GLN A1023 ASN A1036 GLN A1054 GLN A1064 HIS A1125 ASN B 207 HIS B 239 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 370 ASN B 440 ASN B 448 ASN B 498 GLN B 544 ASN B 556 ASN B 564 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 644 GLN B 751 ASN B 804 GLN B 856 ASN B 919 ASN B 925 ASN B1023 ASN B1036 GLN B1054 GLN B1064 HIS C 121 ASN C 185 ASN C 207 HIS C 239 GLN C 314 GLN C 317 ASN C 440 ASN C 448 ASN C 450 ASN C 498 GLN C 544 ASN C 556 ASN C 564 GLN C 613 GLN C 644 GLN C 751 ASN C 919 ASN C 925 ASN C1023 ASN C1036 GLN C1054 GLN C1064 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27576 Z= 0.311 Angle : 0.711 11.716 37503 Z= 0.347 Chirality : 0.056 0.768 4461 Planarity : 0.004 0.052 4755 Dihedral : 9.476 80.572 5368 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.60 % Allowed : 17.24 % Favored : 78.16 % 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: -1.79 (0.13), residues: 3267 helix: 0.21 (0.20), residues: 705 sheet: 0.50 (0.19), residues: 681 loop : -2.56 (0.11), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 152 HIS 0.004 0.001 HIS A1048 PHE 0.018 0.002 PHE C 592 TYR 0.021 0.002 TYR C 837 ARG 0.007 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 218 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6613 (p-80) REVERT: A 197 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7339 (mp) REVERT: A 213 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8350 (t) REVERT: A 574 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7897 (p0) REVERT: A 900 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8709 (mtm) REVERT: A 916 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8417 (tp) REVERT: A 1005 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: B 66 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6159 (p-80) REVERT: B 185 ASN cc_start: 0.6325 (OUTLIER) cc_final: 0.6030 (t0) REVERT: B 197 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7663 (mp) REVERT: B 212 LEU cc_start: 0.6854 (tp) cc_final: 0.6519 (tp) REVERT: B 900 MET cc_start: 0.8690 (mtp) cc_final: 0.8449 (mtm) REVERT: C 216 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7382 (tp) REVERT: C 259 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8057 (m) REVERT: C 462 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8280 (mmtt) REVERT: C 606 ASN cc_start: 0.7789 (m-40) cc_final: 0.7380 (p0) REVERT: C 913 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: C 954 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7895 (mt0) outliers start: 132 outliers final: 53 residues processed: 324 average time/residue: 1.1775 time to fit residues: 455.1698 Evaluate side-chains 239 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 172 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 321 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 238 optimal weight: 0.0570 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 540 ASN A 606 ASN A 804 GLN A1002 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1083 HIS B1125 ASN C 188 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27576 Z= 0.269 Angle : 0.644 16.580 37503 Z= 0.318 Chirality : 0.050 0.566 4461 Planarity : 0.004 0.040 4755 Dihedral : 8.468 81.745 5320 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.18 % Allowed : 17.31 % Favored : 78.51 % 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: -1.43 (0.13), residues: 3267 helix: 0.60 (0.20), residues: 711 sheet: 0.68 (0.20), residues: 657 loop : -2.31 (0.11), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 152 HIS 0.003 0.001 HIS C 146 PHE 0.017 0.002 PHE A 157 TYR 0.015 0.001 TYR C1067 ARG 0.005 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 193 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8628 (mtm) REVERT: A 916 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 1005 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: B 66 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6150 (p-80) REVERT: B 606 ASN cc_start: 0.7943 (m110) cc_final: 0.7700 (m110) REVERT: B 900 MET cc_start: 0.8709 (mtp) cc_final: 0.8458 (mtm) REVERT: C 259 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8109 (m) REVERT: C 462 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8277 (mmtt) REVERT: C 606 ASN cc_start: 0.7731 (m-40) cc_final: 0.7248 (p0) REVERT: C 646 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7824 (mtp85) REVERT: C 913 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8415 (pt0) REVERT: C 954 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7900 (mt0) outliers start: 120 outliers final: 58 residues processed: 289 average time/residue: 1.1103 time to fit residues: 385.4062 Evaluate side-chains 242 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 177 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 282 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 360 ASN A 606 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27576 Z= 0.291 Angle : 0.633 12.272 37503 Z= 0.314 Chirality : 0.049 0.476 4461 Planarity : 0.004 0.039 4755 Dihedral : 7.787 87.172 5307 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.25 % Allowed : 17.73 % Favored : 78.02 % 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: -1.25 (0.14), residues: 3267 helix: 0.76 (0.20), residues: 711 sheet: 0.73 (0.20), residues: 657 loop : -2.18 (0.12), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 152 HIS 0.004 0.001 HIS C 146 PHE 0.018 0.002 PHE B 759 TYR 0.016 0.002 TYR C1067 ARG 0.005 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 186 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8623 (mtm) REVERT: A 1005 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: B 66 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6245 (p-80) REVERT: B 96 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7561 (mt-10) REVERT: B 281 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: B 900 MET cc_start: 0.8730 (mtp) cc_final: 0.8490 (mtm) REVERT: C 259 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7972 (m) REVERT: C 462 LYS cc_start: 0.8590 (mmtp) cc_final: 0.8384 (mmtt) REVERT: C 606 ASN cc_start: 0.7600 (m-40) cc_final: 0.7081 (p0) REVERT: C 646 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7852 (mtp85) REVERT: C 828 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8396 (mp) REVERT: C 913 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8435 (pt0) outliers start: 122 outliers final: 63 residues processed: 284 average time/residue: 1.1195 time to fit residues: 383.5466 Evaluate side-chains 243 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 173 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 269 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 87 ASN B 218 GLN B 314 GLN B 644 GLN B 955 ASN B1005 GLN C 613 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 27576 Z= 0.501 Angle : 0.745 18.571 37503 Z= 0.373 Chirality : 0.054 0.526 4461 Planarity : 0.005 0.046 4755 Dihedral : 7.930 90.968 5302 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.53 % Allowed : 17.66 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.43 (0.13), residues: 3267 helix: 0.44 (0.20), residues: 711 sheet: 0.70 (0.19), residues: 681 loop : -2.29 (0.12), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.005 0.001 HIS B 655 PHE 0.019 0.002 PHE A 59 TYR 0.023 0.002 TYR A 756 ARG 0.008 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 179 time to evaluate : 2.894 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.6624 (p90) REVERT: A 900 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8647 (mtm) REVERT: A 1005 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: B 66 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6287 (p-80) REVERT: B 281 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7607 (pp20) REVERT: B 554 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: B 646 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7769 (ttm110) REVERT: B 900 MET cc_start: 0.8720 (mtp) cc_final: 0.8469 (mtm) REVERT: C 606 ASN cc_start: 0.7625 (m-40) cc_final: 0.7032 (p0) REVERT: C 646 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7886 (mtp180) REVERT: C 762 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7849 (mt0) outliers start: 130 outliers final: 76 residues processed: 290 average time/residue: 1.0936 time to fit residues: 380.7583 Evaluate side-chains 253 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 169 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 0.6980 chunk 284 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 316 optimal weight: 0.9990 chunk 262 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 613 GLN C 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27576 Z= 0.179 Angle : 0.596 20.121 37503 Z= 0.296 Chirality : 0.047 0.358 4461 Planarity : 0.004 0.043 4755 Dihedral : 7.434 101.228 5301 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.24 % Allowed : 19.12 % Favored : 77.64 % 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: -1.06 (0.14), residues: 3267 helix: 1.01 (0.20), residues: 693 sheet: 0.75 (0.20), residues: 648 loop : -2.01 (0.12), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.000 HIS B 146 PHE 0.012 0.001 PHE A1121 TYR 0.016 0.001 TYR C 837 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 176 time to evaluate : 3.159 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7136 (ttm-80) REVERT: A 569 ILE cc_start: 0.8428 (tp) cc_final: 0.8113 (tp) REVERT: A 790 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7968 (pttt) REVERT: A 900 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8602 (mtm) REVERT: B 66 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.6428 (p-80) REVERT: B 88 ASP cc_start: 0.8119 (m-30) cc_final: 0.7917 (m-30) REVERT: B 281 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7566 (pp20) REVERT: B 554 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: B 571 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7930 (t0) REVERT: B 646 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7676 (ttm110) REVERT: B 900 MET cc_start: 0.8679 (mtp) cc_final: 0.8452 (mtm) REVERT: C 606 ASN cc_start: 0.7595 (m-40) cc_final: 0.6976 (p0) REVERT: C 646 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7857 (mtp180) outliers start: 93 outliers final: 52 residues processed: 254 average time/residue: 1.2336 time to fit residues: 372.3156 Evaluate side-chains 227 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 168 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 231 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 266 optimal weight: 0.0970 chunk 176 optimal weight: 0.3980 chunk 315 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 540 ASN B 613 GLN B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27576 Z= 0.144 Angle : 0.556 17.662 37503 Z= 0.275 Chirality : 0.046 0.484 4461 Planarity : 0.003 0.037 4755 Dihedral : 7.042 107.446 5300 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.61 % Allowed : 20.20 % Favored : 77.19 % 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: -0.84 (0.14), residues: 3267 helix: 1.25 (0.20), residues: 711 sheet: 0.78 (0.20), residues: 654 loop : -1.89 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.000 HIS C 146 PHE 0.011 0.001 PHE B 32 TYR 0.015 0.001 TYR C1067 ARG 0.008 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 191 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.7133 (ttm-80) REVERT: A 567 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7661 (mtp85) REVERT: A 900 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: A 916 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8335 (tp) REVERT: B 66 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.6480 (p-80) REVERT: B 197 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7316 (tp) REVERT: B 281 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7573 (pp20) REVERT: B 554 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: B 571 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7923 (t0) REVERT: B 646 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7591 (ttm110) REVERT: B 900 MET cc_start: 0.8683 (mtp) cc_final: 0.8396 (mtm) REVERT: C 393 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8154 (m) REVERT: C 606 ASN cc_start: 0.7566 (m-40) cc_final: 0.6975 (p0) REVERT: C 646 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7874 (mtp85) outliers start: 75 outliers final: 39 residues processed: 251 average time/residue: 1.2283 time to fit residues: 368.3985 Evaluate side-chains 225 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27576 Z= 0.260 Angle : 0.604 16.493 37503 Z= 0.300 Chirality : 0.048 0.335 4461 Planarity : 0.004 0.038 4755 Dihedral : 7.128 106.185 5294 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.86 % Allowed : 20.24 % Favored : 76.91 % 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: -0.91 (0.14), residues: 3267 helix: 1.14 (0.20), residues: 711 sheet: 0.78 (0.20), residues: 654 loop : -1.92 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.014 0.001 PHE C 592 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 178 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6559 (mmt180) REVERT: A 346 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.7106 (ttm-80) REVERT: A 569 ILE cc_start: 0.8395 (tp) cc_final: 0.8129 (tp) REVERT: A 916 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8463 (tp) REVERT: B 66 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.6581 (p-80) REVERT: B 88 ASP cc_start: 0.8133 (m-30) cc_final: 0.7932 (m-30) REVERT: B 281 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: B 554 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: B 646 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7692 (ttm110) REVERT: B 900 MET cc_start: 0.8719 (mtp) cc_final: 0.8485 (mtm) REVERT: C 606 ASN cc_start: 0.7610 (m-40) cc_final: 0.7004 (p0) outliers start: 82 outliers final: 61 residues processed: 248 average time/residue: 1.2758 time to fit residues: 382.7402 Evaluate side-chains 237 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 170 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 230 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 292 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 519 HIS B1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27576 Z= 0.206 Angle : 0.604 15.456 37503 Z= 0.300 Chirality : 0.048 0.495 4461 Planarity : 0.004 0.037 4755 Dihedral : 7.124 105.767 5294 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 20.31 % Favored : 76.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.86 (0.14), residues: 3267 helix: 1.20 (0.20), residues: 711 sheet: 0.77 (0.20), residues: 654 loop : -1.89 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS C 146 PHE 0.012 0.001 PHE C 592 TYR 0.015 0.001 TYR C1067 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 172 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.7099 (ttm-80) REVERT: A 569 ILE cc_start: 0.8440 (tp) cc_final: 0.8191 (tp) REVERT: A 916 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 66 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6551 (p-80) REVERT: B 197 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7311 (tp) REVERT: B 281 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: B 554 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: B 646 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7656 (ttm110) REVERT: B 900 MET cc_start: 0.8694 (mtp) cc_final: 0.8386 (mtm) REVERT: C 393 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8202 (m) REVERT: C 606 ASN cc_start: 0.7547 (m-40) cc_final: 0.7070 (p0) outliers start: 78 outliers final: 56 residues processed: 239 average time/residue: 1.2335 time to fit residues: 351.4447 Evaluate side-chains 234 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 171 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 325 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 259 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN B 519 HIS B1005 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27576 Z= 0.242 Angle : 0.608 14.678 37503 Z= 0.301 Chirality : 0.047 0.334 4461 Planarity : 0.004 0.040 4755 Dihedral : 7.341 105.777 5294 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.68 % Allowed : 20.34 % Favored : 76.98 % 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: -0.89 (0.14), residues: 3267 helix: 1.16 (0.20), residues: 711 sheet: 0.77 (0.20), residues: 654 loop : -1.90 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C 146 PHE 0.013 0.001 PHE C 592 TYR 0.017 0.001 TYR A 145 ARG 0.007 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 176 time to evaluate : 2.777 Fit side-chains revert: symmetry clash REVERT: A 346 ARG cc_start: 0.7363 (ttm-80) cc_final: 0.7110 (ttm-80) REVERT: A 569 ILE cc_start: 0.8410 (tp) cc_final: 0.8105 (tp) REVERT: A 916 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 66 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.6690 (p-80) REVERT: B 96 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 281 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7598 (pp20) REVERT: B 554 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: B 646 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7643 (ttm110) REVERT: B 900 MET cc_start: 0.8699 (mtp) cc_final: 0.8389 (mtm) REVERT: C 606 ASN cc_start: 0.7509 (m-40) cc_final: 0.7098 (p0) outliers start: 77 outliers final: 61 residues processed: 242 average time/residue: 1.2430 time to fit residues: 362.2509 Evaluate side-chains 238 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 172 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 239 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 266 optimal weight: 0.0030 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 0.0980 chunk 228 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 519 HIS B1005 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097748 restraints weight = 37327.322| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.39 r_work: 0.3098 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27576 Z= 0.153 Angle : 0.554 12.297 37503 Z= 0.274 Chirality : 0.045 0.294 4461 Planarity : 0.003 0.038 4755 Dihedral : 6.991 105.944 5294 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.09 % Allowed : 20.97 % Favored : 76.94 % 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: -0.71 (0.14), residues: 3267 helix: 1.47 (0.20), residues: 705 sheet: 0.81 (0.20), residues: 654 loop : -1.82 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS C 146 PHE 0.012 0.001 PHE B 32 TYR 0.020 0.001 TYR A 248 ARG 0.008 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7847.80 seconds wall clock time: 141 minutes 36.96 seconds (8496.96 seconds total)