Starting phenix.real_space_refine on Sun Nov 19 08:34:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs1_7579/11_2023/6cs1_7579.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs1_7579/11_2023/6cs1_7579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs1_7579/11_2023/6cs1_7579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs1_7579/11_2023/6cs1_7579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs1_7579/11_2023/6cs1_7579.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cs1_7579/11_2023/6cs1_7579.pdb" } resolution = 4.6 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= 0.006 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 138 5.16 5 C 16537 2.51 5 N 4189 2.21 5 O 5131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 25995 Number of models: 1 Model: "" Number of chains: 27 Chain: "B" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8342 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "C" Number of atoms: 8339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8339 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "A" Number of atoms: 8327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8327 Classifications: {'peptide': 1066} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 13.26, per 1000 atoms: 0.51 Number of scatterers: 25995 At special positions: 0 Unit cell: (148.32, 148.32, 186.43, 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 138 16.00 O 5131 8.00 N 4189 7.00 C 16537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.02 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1307 " - " ASN A 589 " " NAG A1316 " - " ASN A1056 " " NAG A1317 " - " ASN A1116 " " NAG A1323 " - " ASN A 691 " " NAG B1301 " - " ASN B1056 " " NAG B1302 " - " ASN B 65 " " NAG B1322 " - " ASN B1116 " " NAG B1323 " - " ASN B 691 " " NAG C1308 " - " ASN C 589 " " NAG C1321 " - " ASN C1056 " " NAG C1327 " - " ASN C 691 " " NAG D 1 " - " ASN B 269 " " NAG E 1 " - " ASN B 318 " " NAG F 1 " - " ASN B 589 " " NAG G 1 " - " ASN B 699 " " NAG H 1 " - " ASN B 783 " " NAG I 1 " - " ASN B1080 " " NAG J 1 " - " ASN B 602 " " NAG K 1 " - " ASN C 65 " " NAG L 1 " - " ASN C 269 " " NAG M 1 " - " ASN C 318 " " NAG N 1 " - " ASN C 602 " " NAG O 1 " - " ASN C 699 " " NAG P 1 " - " ASN C 783 " " NAG Q 1 " - " ASN C1080 " " NAG R 1 " - " ASN C1116 " " NAG S 1 " - " ASN A 269 " " NAG T 1 " - " ASN A 602 " " NAG U 1 " - " ASN A 699 " " NAG V 1 " - " ASN A 783 " " NAG W 1 " - " ASN A1080 " " NAG X 1 " - " ASN A 318 " Time building additional restraints: 10.75 Conformation dependent library (CDL) restraints added in 4.5 seconds 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 52 sheets defined 22.3% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.155A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.932A pdb=" N ASP B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 377' Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 603 through 612 removed outlier: 3.650A pdb=" N SER B 607 " --> pdb=" O CYS B 603 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.735A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 734 " --> pdb=" O GLU B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 743 through 765 removed outlier: 4.045A pdb=" N ALA B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 removed outlier: 3.513A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 866 through 870 removed outlier: 4.196A pdb=" N THR B 869 " --> pdb=" O ALA B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.700A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 887 " --> pdb=" O GLN B 883 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.550A pdb=" N ALA B 906 " --> pdb=" O GLN B 902 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 946 removed outlier: 3.774A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 940 " --> pdb=" O GLN B 936 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 941 " --> pdb=" O ASN B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.650A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1016 removed outlier: 3.703A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 985 " --> pdb=" O GLY B 981 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYS B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.882A pdb=" N LEU C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 390 through 395 removed outlier: 4.267A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.710A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.554A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 removed outlier: 3.597A pdb=" N ILE C 724 " --> pdb=" O CYS C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 734 removed outlier: 4.095A pdb=" N LEU C 734 " --> pdb=" O GLU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.737A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 removed outlier: 3.732A pdb=" N LEU C 804 " --> pdb=" O ILE C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 removed outlier: 3.620A pdb=" N ALA C 853 " --> pdb=" O ASP C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.877A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 903 through 922 removed outlier: 3.733A pdb=" N GLN C 908 " --> pdb=" O GLN C 904 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 914 " --> pdb=" O ASN C 910 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 917 " --> pdb=" O ILE C 913 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.579A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.513A pdb=" N GLU C 972 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.505A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.775A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.804A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.831A pdb=" N TYR A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.814A pdb=" N THR A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.792A pdb=" N ILE A 724 " --> pdb=" O CYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 4.082A pdb=" N ALA A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 764 removed outlier: 3.546A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 removed outlier: 3.547A pdb=" N PHE A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.523A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 removed outlier: 4.343A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.741A pdb=" N GLN A 883 " --> pdb=" O PRO A 879 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 890 " --> pdb=" O TYR A 886 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.052A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.567A pdb=" N LYS A 911 " --> pdb=" O ASN A 907 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 4.256A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.657A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.555A pdb=" N GLU A 972 " --> pdb=" O PRO A 968 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 34 removed outlier: 9.288A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 92 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 87 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 34 removed outlier: 9.288A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 92 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 87 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.262A pdb=" N PHE B 47 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 56 removed outlier: 3.812A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 266 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.008A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 98 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 82 removed outlier: 15.087A pdb=" N PHE B 231 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 12.850A pdb=" N ASP B 134 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ALA B 233 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU B 235 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 615 through 616 removed outlier: 5.827A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 581 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 579 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.323A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 344 through 345 removed outlier: 3.867A pdb=" N ILE B 345 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.018A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 365 through 366 removed outlier: 3.525A pdb=" N VAL B 497 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 387 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 498 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 385 " --> pdb=" O VAL B 498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AB4, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.315A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 677 " --> pdb=" O CYS B 657 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS B 657 " --> pdb=" O TYR B 677 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 684 through 685 Processing sheet with id=AB6, first strand: chain 'B' and resid 693 through 709 removed outlier: 6.801A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 693 through 709 removed outlier: 6.801A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AB9, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AC1, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AC2, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 3.708A pdb=" N SER B1105 " --> pdb=" O ALA B1069 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.746A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 67 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 93 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS C 180 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 52 through 59 removed outlier: 7.697A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.588A pdb=" N VAL C 140 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS C 149 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N SER C 141 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN C 147 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.700A pdb=" N ARG C 232 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 98 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.888A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 582 " --> pdb=" O LEU C 597 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 312 through 314 removed outlier: 6.559A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 574 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 344 through 345 removed outlier: 3.563A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 365 through 366 removed outlier: 3.698A pdb=" N TRP C 423 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C 495 " --> pdb=" O TRP C 423 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR C 494 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 387 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AD3, first strand: chain 'C' and resid 640 through 646 removed outlier: 4.525A pdb=" N THR C 678 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C 644 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 683 through 685 Processing sheet with id=AD5, first strand: chain 'C' and resid 693 through 709 removed outlier: 6.946A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 703 " --> pdb=" O THR C1048 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1030 through 1033 removed outlier: 7.114A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C1076 " --> pdb=" O THR C1087 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C1087 " --> pdb=" O VAL C1076 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AD8, first strand: chain 'C' and resid 821 through 823 Processing sheet with id=AD9, first strand: chain 'C' and resid 1063 through 1065 Processing sheet with id=AE1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.814A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 253 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 52 through 59 removed outlier: 7.781A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.252A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 12.446A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AE5, first strand: chain 'A' and resid 300 through 301 removed outlier: 3.587A pdb=" N TYR A 300 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 583 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AE7, first strand: chain 'A' and resid 312 through 314 removed outlier: 6.366A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 539 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.509A pdb=" N SER A 386 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 343 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 497 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 499 " --> pdb=" O CYS A 419 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 365 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.800A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AF2, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.217A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 677 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.465A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 703 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 1029 through 1033 removed outlier: 7.090A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AF6, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AF7, first strand: chain 'A' and resid 1103 through 1104 removed outlier: 6.720A pdb=" N ALA A1062 " --> pdb=" O ILE A1115 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2466 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: 11.93 Time building geometry restraints manager: 11.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8128 1.34 - 1.47: 6944 1.47 - 1.59: 11334 1.59 - 1.72: 0 1.72 - 1.84: 186 Bond restraints: 26592 Sorted by residual: bond pdb=" C1 MAN P 4 " pdb=" O5 MAN P 4 " ideal model delta sigma weight residual 1.399 1.482 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1 MAN P 4 " pdb=" C2 MAN P 4 " ideal model delta sigma weight residual 1.526 1.585 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sigma weight residual 1.417 1.466 -0.049 2.00e-02 2.50e+03 5.99e+00 ... (remaining 26587 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.11: 531 105.11 - 112.35: 13576 112.35 - 119.59: 8482 119.59 - 126.84: 13332 126.84 - 134.08: 260 Bond angle restraints: 36181 Sorted by residual: angle pdb=" C PHE B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C GLY A 625 " pdb=" N ASN A 626 " pdb=" CA ASN A 626 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C THR B 106 " pdb=" N MET B 107 " pdb=" CA MET B 107 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 112.08 107.65 4.43 1.01e+00 9.80e-01 1.92e+01 angle pdb=" C ARG B 207 " pdb=" N ASP B 208 " pdb=" CA ASP B 208 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 ... (remaining 36176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 14675 16.96 - 33.92: 434 33.92 - 50.88: 104 50.88 - 67.84: 11 67.84 - 84.81: 10 Dihedral angle restraints: 15234 sinusoidal: 5906 harmonic: 9328 Sorted by residual: dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual 93.00 177.81 -84.81 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 348 " pdb=" CB CYS C 348 " ideal model delta sinusoidal sigma weight residual -86.00 -169.89 83.89 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -169.71 83.71 1 1.00e+01 1.00e-02 8.55e+01 ... (remaining 15231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3910 0.095 - 0.190: 362 0.190 - 0.285: 24 0.285 - 0.380: 5 0.380 - 0.475: 4 Chirality restraints: 4305 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 699 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1116 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CB ILE C 72 " pdb=" CA ILE C 72 " pdb=" CG1 ILE C 72 " pdb=" CG2 ILE C 72 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 4302 not shown) Planarity restraints: 4600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 968 " -0.058 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO B 969 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 969 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 969 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 968 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO A 969 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 969 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 969 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C PHE A 83 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 84 " 0.015 2.00e-02 2.50e+03 ... (remaining 4597 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4173 2.76 - 3.30: 23536 3.30 - 3.83: 43820 3.83 - 4.37: 50526 4.37 - 4.90: 83547 Nonbonded interactions: 205602 Sorted by model distance: nonbonded pdb=" OG SER A 690 " pdb=" OD1 ASN A 692 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP C 557 " pdb=" OG SER A 949 " model vdw 2.252 2.440 nonbonded pdb=" OE1 GLN A 769 " pdb=" OH TYR A 771 " model vdw 2.275 2.440 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.281 2.440 nonbonded pdb=" O GLU C 647 " pdb=" OH TYR C 677 " model vdw 2.289 2.440 ... (remaining 205597 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 18 through 1120 or resid 1301 through 1316)) selection = (chain 'B' and (resid 18 through 662 or resid 672 through 823 or resid 832 throu \ gh 1120 or resid 1301 through 1322)) selection = (chain 'C' and (resid 18 through 823 or resid 832 through 1120 or resid 1308 thr \ ough 1327)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'R' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.510 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 70.010 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26592 Z= 0.368 Angle : 0.917 9.786 36181 Z= 0.484 Chirality : 0.058 0.475 4305 Planarity : 0.006 0.086 4567 Dihedral : 8.767 75.000 9099 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.20 (0.12), residues: 3160 helix: -3.54 (0.13), residues: 578 sheet: -1.99 (0.18), residues: 616 loop : -2.96 (0.11), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.4143 time to fit residues: 292.8020 Evaluate side-chains 224 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 249 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 chunk 151 optimal weight: 30.0000 chunk 185 optimal weight: 0.0670 chunk 288 optimal weight: 0.7980 overall best weight: 1.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN B 746 ASN B 766 GLN B 806 ASN B 987 GLN B1036 GLN B1088 GLN C 29 ASN C 201 GLN C 280 GLN C 357 ASN C 375 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 GLN C 947 GLN C 984 GLN C1101 ASN A 96 ASN A 122 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 733 ASN A 737 GLN A 744 GLN A 759 ASN A 806 ASN A 910 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN A 993 GLN A1030 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3458 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26592 Z= 0.203 Angle : 0.667 8.936 36181 Z= 0.351 Chirality : 0.046 0.342 4305 Planarity : 0.005 0.065 4567 Dihedral : 5.980 36.437 3436 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.18 % Allowed : 1.91 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -3.09 (0.13), residues: 3160 helix: -1.50 (0.18), residues: 602 sheet: -1.50 (0.18), residues: 661 loop : -2.55 (0.12), residues: 1897 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 287 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 290 average time/residue: 0.4191 time to fit residues: 191.2522 Evaluate side-chains 181 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 2.739 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2976 time to fit residues: 4.3470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.0770 chunk 89 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 30.0000 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN B 759 ASN B 766 GLN B 935 ASN B 936 GLN ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 158 ASN C 181 HIS C 201 GLN ** C 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 733 ASN C 786 GLN C 877 GLN C 896 ASN C 907 ASN C 917 GLN C 947 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C 993 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 744 GLN A 759 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4169 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 26592 Z= 0.308 Angle : 0.803 11.228 36181 Z= 0.416 Chirality : 0.051 0.420 4305 Planarity : 0.006 0.108 4567 Dihedral : 5.861 30.255 3436 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.25 % Allowed : 3.53 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.79 (0.13), residues: 3160 helix: -1.08 (0.19), residues: 632 sheet: -1.51 (0.19), residues: 637 loop : -2.33 (0.13), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 272 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 277 average time/residue: 0.3780 time to fit residues: 166.7846 Evaluate side-chains 198 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 2.940 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2382 time to fit residues: 5.0384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.4980 chunk 217 optimal weight: 20.0000 chunk 150 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 290 optimal weight: 20.0000 chunk 307 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 275 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN C 896 ASN C 947 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 304 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4073 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 26592 Z= 0.163 Angle : 0.597 7.850 36181 Z= 0.309 Chirality : 0.045 0.347 4305 Planarity : 0.004 0.099 4567 Dihedral : 5.263 36.809 3436 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.31 (0.14), residues: 3160 helix: -0.29 (0.20), residues: 634 sheet: -1.19 (0.19), residues: 650 loop : -2.19 (0.13), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3844 time to fit residues: 160.4302 Evaluate side-chains 190 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.710 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 424 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 330 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 896 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 HIS A1088 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 26592 Z= 0.375 Angle : 0.939 16.536 36181 Z= 0.482 Chirality : 0.056 0.562 4305 Planarity : 0.007 0.097 4567 Dihedral : 6.304 30.568 3436 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 30.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.05 % Favored : 90.92 % Rotamer: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.98 (0.13), residues: 3160 helix: -1.44 (0.18), residues: 630 sheet: -1.57 (0.20), residues: 626 loop : -2.41 (0.13), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 255 average time/residue: 0.3712 time to fit residues: 154.9803 Evaluate side-chains 191 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5839 time to fit residues: 4.5154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 307 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 896 ASN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN A1088 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4643 moved from start: 0.7699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26592 Z= 0.191 Angle : 0.641 9.882 36181 Z= 0.330 Chirality : 0.046 0.380 4305 Planarity : 0.004 0.068 4567 Dihedral : 5.532 27.621 3436 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.44 (0.14), residues: 3160 helix: -0.39 (0.20), residues: 627 sheet: -1.38 (0.20), residues: 613 loop : -2.23 (0.13), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3803 time to fit residues: 150.4902 Evaluate side-chains 180 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 259 optimal weight: 40.0000 chunk 171 optimal weight: 0.5980 chunk 306 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS B 947 GLN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 HIS ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 158 ASN C 330 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 632 GLN A 910 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 0.8905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 26592 Z= 0.288 Angle : 0.785 19.762 36181 Z= 0.400 Chirality : 0.051 0.468 4305 Planarity : 0.006 0.086 4567 Dihedral : 5.853 34.884 3436 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.63 (0.14), residues: 3160 helix: -0.69 (0.20), residues: 620 sheet: -1.73 (0.20), residues: 608 loop : -2.20 (0.13), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3608 time to fit residues: 138.4114 Evaluate side-chains 173 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 877 GLN C 904 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 910 ASN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4857 moved from start: 0.9022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26592 Z= 0.182 Angle : 0.635 9.440 36181 Z= 0.326 Chirality : 0.046 0.264 4305 Planarity : 0.004 0.065 4567 Dihedral : 5.441 27.970 3436 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.32 (0.14), residues: 3160 helix: -0.21 (0.21), residues: 629 sheet: -1.49 (0.20), residues: 619 loop : -2.10 (0.13), residues: 1912 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3632 time to fit residues: 138.4207 Evaluate side-chains 168 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 0.0470 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 284 optimal weight: 0.4980 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 546 GLN ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4893 moved from start: 0.9285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26592 Z= 0.181 Angle : 0.630 9.386 36181 Z= 0.323 Chirality : 0.046 0.279 4305 Planarity : 0.005 0.072 4567 Dihedral : 5.309 28.593 3436 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.31 (0.14), residues: 3160 helix: -0.19 (0.20), residues: 627 sheet: -1.53 (0.20), residues: 617 loop : -2.08 (0.13), residues: 1916 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.3947 time to fit residues: 149.4743 Evaluate side-chains 163 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 20.0000 chunk 302 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 chunk 209 optimal weight: 8.9990 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 0.4980 chunk 252 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 ASN ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 877 GLN ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5037 moved from start: 0.9989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 26592 Z= 0.212 Angle : 0.674 10.846 36181 Z= 0.347 Chirality : 0.047 0.261 4305 Planarity : 0.005 0.062 4567 Dihedral : 5.443 28.401 3436 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.32 (0.14), residues: 3160 helix: -0.25 (0.20), residues: 623 sheet: -1.53 (0.20), residues: 606 loop : -2.07 (0.13), residues: 1931 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3662 time to fit residues: 140.6147 Evaluate side-chains 167 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 259 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 330 ASN C 357 ASN ** C 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1101 ASN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 917 GLN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.139098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.121759 restraints weight = 195574.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.120939 restraints weight = 191008.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.121256 restraints weight = 171829.488| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 1.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 26592 Z= 0.448 Angle : 1.023 14.025 36181 Z= 0.533 Chirality : 0.059 0.412 4305 Planarity : 0.007 0.074 4567 Dihedral : 6.927 33.479 3436 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 35.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.68 % Favored : 88.29 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.21 (0.13), residues: 3160 helix: -1.51 (0.18), residues: 599 sheet: -2.07 (0.19), residues: 641 loop : -2.45 (0.13), residues: 1920 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4705.44 seconds wall clock time: 87 minutes 59.01 seconds (5279.01 seconds total)