Starting phenix.real_space_refine on Fri Mar 22 18:03:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/03_2024/7whd_32499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/03_2024/7whd_32499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/03_2024/7whd_32499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/03_2024/7whd_32499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/03_2024/7whd_32499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/03_2024/7whd_32499.pdb" } resolution = 2.65 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 ------------------------------------------------------------------------------- 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= 0.002 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 147 5.16 5 C 21677 2.51 5 N 5644 2.21 5 O 6741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34209 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "K" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 18.30, per 1000 atoms: 0.53 Number of scatterers: 34209 At special positions: 0 Unit cell: (175.664, 164.685, 252.517, 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 147 16.00 O 6741 8.00 N 5644 7.00 C 21677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.49 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.08 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 282 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 616 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A 165 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 282 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 616 " " NAG B1405 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 282 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 13.98 Conformation dependent library (CDL) restraints added in 6.1 seconds 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8054 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 80 sheets defined 18.5% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.969A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.349A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.492A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.178A pdb=" N THR A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.528A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.552A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.005A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.999A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.667A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.522A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.469A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.456A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.692A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.531A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.545A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.577A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.115A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.786A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.714A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.547A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1145' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.229A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.859A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.520A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.786A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.117A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.613A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.028A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.622A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.439A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.936A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.055A pdb=" N SER E 127 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.577A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.850A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'H' and resid 150 through 153 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.800A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 Processing helix chain 'K' and resid 182 through 188 removed outlier: 3.525A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.153A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.708A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.555A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.859A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.936A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.694A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.587A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.181A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.661A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.126A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.602A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.102A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 225 through 229 removed outlier: 6.757A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 114 through 116 removed outlier: 4.248A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.409A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 323 through 326 removed outlier: 5.703A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 395 through 402 Processing sheet with id=AD1, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.565A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.837A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.810A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.810A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.436A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.238A pdb=" N GLY C 89 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.474A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.651A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 removed outlier: 6.633A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.453A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.714A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.163A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.176A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.828A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.828A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.978A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 57 through 60 removed outlier: 5.071A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 57 through 60 removed outlier: 5.071A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 92 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 68 through 73 Processing sheet with id=AF8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.594A pdb=" N GLY D 147 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.594A pdb=" N GLY D 147 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 158 through 162 removed outlier: 3.861A pdb=" N THR D 159 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 215 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.608A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.099A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 144 through 148 Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.862A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA G 92 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR G 94 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 68 through 73 Processing sheet with id=AH1, first strand: chain 'G' and resid 128 through 130 removed outlier: 3.533A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU G 149 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER G 188 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS G 151 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU G 186 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 144 through 146 removed outlier: 3.651A pdb=" N VAL G 177 " --> pdb=" O SER G 185 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.662A pdb=" N THR G 159 " --> pdb=" O ASN G 207 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.505A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.683A pdb=" N ARG H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.875A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 145 through 148 removed outlier: 3.530A pdb=" N LYS H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.804A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL J 20 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.640A pdb=" N GLU J 10 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR J 118 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS J 12 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 92 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.640A pdb=" N GLU J 10 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR J 118 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS J 12 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 92 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL J 110 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 128 through 130 removed outlier: 6.240A pdb=" N TYR J 184 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AI4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AI5, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.551A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.521A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.509A pdb=" N SER K 114 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER K 177 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 153 through 155 removed outlier: 3.813A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS K 145 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3228 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: 15.62 Time building geometry restraints manager: 15.19 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: 10926 1.34 - 1.47: 8730 1.47 - 1.59: 15112 1.59 - 1.71: 0 1.71 - 1.83: 183 Bond restraints: 34951 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C ALA G 102 " pdb=" N PHE G 103 " ideal model delta sigma weight residual 1.332 1.293 0.039 1.40e-02 5.10e+03 7.79e+00 bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 ... (remaining 34946 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.13: 650 105.13 - 112.35: 18145 112.35 - 119.57: 10797 119.57 - 126.79: 17571 126.79 - 134.01: 367 Bond angle restraints: 47530 Sorted by residual: angle pdb=" C ASN A 125 " pdb=" CA ASN A 125 " pdb=" CB ASN A 125 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" CA PHE J 130 " pdb=" C PHE J 130 " pdb=" N PRO J 131 " ideal model delta sigma weight residual 119.06 114.33 4.73 1.05e+00 9.07e-01 2.03e+01 angle pdb=" CA ASN A 125 " pdb=" C ASN A 125 " pdb=" N VAL A 126 " ideal model delta sigma weight residual 119.52 116.30 3.22 7.90e-01 1.60e+00 1.66e+01 angle pdb=" N ASP C 389 " pdb=" CA ASP C 389 " pdb=" C ASP C 389 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 angle pdb=" N TYR A 380 " pdb=" CA TYR A 380 " pdb=" C TYR A 380 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 ... (remaining 47525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19490 17.97 - 35.93: 1645 35.93 - 53.90: 309 53.90 - 71.87: 99 71.87 - 89.83: 40 Dihedral angle restraints: 21583 sinusoidal: 9051 harmonic: 12532 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -175.21 89.21 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 4.38 88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -5.11 -80.89 1 1.00e+01 1.00e-02 8.08e+01 ... (remaining 21580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 5399 0.112 - 0.223: 153 0.223 - 0.334: 6 0.334 - 0.446: 2 0.446 - 0.557: 1 Chirality restraints: 5561 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 5558 not shown) Planarity restraints: 6109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " 0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO B 139 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.004 2.00e-02 2.50e+03 3.01e-02 1.13e+01 pdb=" CG ASN A 616 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.022 2.00e-02 2.50e+03 1.85e-02 8.54e+00 pdb=" CG TRP B 64 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.000 2.00e-02 2.50e+03 ... (remaining 6106 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 13 2.22 - 2.89: 14198 2.89 - 3.56: 46062 3.56 - 4.23: 76011 4.23 - 4.90: 130954 Nonbonded interactions: 267238 Sorted by model distance: nonbonded pdb=" CE LYS A 129 " pdb=" CB CYS A 131 " model vdw 1.554 3.840 nonbonded pdb=" CE2 TYR A 660 " pdb=" OE1 GLN A 675 " model vdw 1.889 3.340 nonbonded pdb=" OH TYR B 38 " pdb=" OG1 THR B 284 " model vdw 2.046 2.440 nonbonded pdb=" OD1 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 2.103 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.124 2.440 ... (remaining 267233 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 27 through 620 or resid 641 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1405)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1405)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1405)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.670 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 93.220 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.510 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3516 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 0.057 34951 Z= 0.370 Angle : 0.713 10.150 47530 Z= 0.376 Chirality : 0.049 0.557 5561 Planarity : 0.005 0.100 6072 Dihedral : 14.145 89.832 13376 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.83 % Rotamer: Outliers : 0.93 % Allowed : 0.93 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 4265 helix: 1.23 (0.21), residues: 662 sheet: -1.16 (0.15), residues: 1268 loop : -2.10 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 64 HIS 0.007 0.001 HIS C1048 PHE 0.037 0.002 PHE C 906 TYR 0.034 0.002 TYR A 508 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 910 time to evaluate : 3.674 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: A 139 PRO cc_start: 0.6416 (Cg_endo) cc_final: 0.5394 (Cg_exo) REVERT: A 153 MET cc_start: 0.1620 (mmp) cc_final: 0.0727 (ptp) REVERT: A 197 ILE cc_start: 0.5849 (mp) cc_final: 0.5566 (mp) REVERT: A 726 ILE cc_start: 0.5887 (mp) cc_final: 0.5358 (pt) REVERT: A 781 VAL cc_start: 0.2720 (t) cc_final: 0.2509 (t) REVERT: B 245 HIS cc_start: 0.2519 (m-70) cc_final: 0.0771 (p90) REVERT: B 406 GLU cc_start: 0.4980 (pm20) cc_final: 0.3718 (pp20) REVERT: C 329 PHE cc_start: 0.5358 (m-80) cc_final: 0.4960 (p90) REVERT: C 1027 THR cc_start: 0.0805 (m) cc_final: -0.0267 (p) REVERT: C 1095 PHE cc_start: 0.1286 (m-80) cc_final: 0.0929 (m-80) REVERT: K 210 ASN cc_start: 0.6953 (t0) cc_final: 0.6633 (t0) outliers start: 35 outliers final: 7 residues processed: 935 average time/residue: 1.0767 time to fit residues: 1260.8184 Evaluate side-chains 550 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 543 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 160 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 336 optimal weight: 0.7980 chunk 130 optimal weight: 0.0040 chunk 204 optimal weight: 6.9990 chunk 250 optimal weight: 0.1980 chunk 389 optimal weight: 4.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 542 ASN A 690 GLN A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1125 ASN C 66 HIS C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN C 955 ASN D 39 GLN E 158 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 166 GLN J 163 ASN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4213 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 34951 Z= 0.240 Angle : 0.768 15.388 47530 Z= 0.382 Chirality : 0.049 0.574 5561 Planarity : 0.005 0.073 6072 Dihedral : 7.506 59.781 5772 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 3.84 % Allowed : 14.86 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 4265 helix: 1.25 (0.21), residues: 676 sheet: -0.98 (0.15), residues: 1261 loop : -2.04 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 148 HIS 0.010 0.001 HIS C1058 PHE 0.026 0.002 PHE K 209 TYR 0.021 0.002 TYR B1067 ARG 0.023 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 657 time to evaluate : 3.587 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: A 153 MET cc_start: 0.1523 (mmp) cc_final: 0.0499 (ptp) REVERT: A 220 PHE cc_start: 0.4515 (OUTLIER) cc_final: 0.3866 (m-80) REVERT: A 720 ILE cc_start: 0.0972 (OUTLIER) cc_final: 0.0504 (tp) REVERT: A 726 ILE cc_start: 0.6496 (mp) cc_final: 0.5807 (pp) REVERT: B 245 HIS cc_start: 0.2669 (m-70) cc_final: 0.0952 (p90) REVERT: B 394 ASN cc_start: 0.3556 (t0) cc_final: 0.3334 (t0) REVERT: B 770 ILE cc_start: 0.4737 (OUTLIER) cc_final: 0.4396 (mm) REVERT: C 153 MET cc_start: 0.3241 (ptm) cc_final: 0.2053 (pp-130) REVERT: C 1009 THR cc_start: 0.2427 (t) cc_final: 0.2082 (m) REVERT: C 1027 THR cc_start: 0.1613 (m) cc_final: 0.0362 (p) REVERT: G 34 ILE cc_start: 0.1615 (OUTLIER) cc_final: 0.0768 (mm) REVERT: H 148 TRP cc_start: 0.1641 (m100) cc_final: 0.1134 (m100) REVERT: K 4 LEU cc_start: 0.3509 (mp) cc_final: 0.3033 (mt) REVERT: K 210 ASN cc_start: 0.7109 (t0) cc_final: 0.6842 (p0) REVERT: K 211 ARG cc_start: 0.7795 (ptm160) cc_final: 0.7558 (ppp80) outliers start: 144 outliers final: 52 residues processed: 731 average time/residue: 1.0126 time to fit residues: 944.3444 Evaluate side-chains 573 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 517 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 782 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 324 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 390 optimal weight: 0.0060 chunk 421 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 387 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 313 optimal weight: 0.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 321 GLN A 474 GLN A 536 ASN A 542 ASN A 751 ASN A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 926 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1108 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 321 GLN B 414 GLN B 450 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 784 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 87 ASN C 422 ASN C 540 ASN C 544 ASN C 607 GLN C 613 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 38 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN J 172 HIS ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.227 34951 Z= 0.496 Angle : 1.175 33.522 47530 Z= 0.584 Chirality : 0.063 0.834 5561 Planarity : 0.008 0.119 6072 Dihedral : 7.866 59.923 5759 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.03 % Favored : 90.83 % Rotamer: Outliers : 8.06 % Allowed : 18.20 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.46 (0.12), residues: 4265 helix: -0.49 (0.18), residues: 664 sheet: -1.02 (0.15), residues: 1175 loop : -2.37 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP C1102 HIS 0.018 0.003 HIS A1048 PHE 0.050 0.004 PHE B 377 TYR 0.054 0.004 TYR A1047 ARG 0.019 0.002 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 865 time to evaluate : 3.743 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 revert: symmetry clash REVERT: A 153 MET cc_start: 0.1526 (mmp) cc_final: 0.0170 (ptp) REVERT: A 198 ASP cc_start: 0.6822 (p0) cc_final: 0.6621 (p0) REVERT: A 294 ASP cc_start: 0.3758 (OUTLIER) cc_final: 0.3472 (p0) REVERT: A 332 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6244 (mp) REVERT: A 1006 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7395 (t) REVERT: B 394 ASN cc_start: 0.4704 (t0) cc_final: 0.4376 (t0) REVERT: C 153 MET cc_start: 0.2976 (ptm) cc_final: 0.2250 (ptt) REVERT: C 398 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.6105 (m-30) REVERT: C 674 TYR cc_start: 0.7181 (t80) cc_final: 0.6953 (t80) REVERT: D 81 MET cc_start: 0.5385 (tmm) cc_final: 0.5149 (tmm) REVERT: E 104 VAL cc_start: 0.4927 (OUTLIER) cc_final: 0.4563 (m) REVERT: E 125 LEU cc_start: 0.8101 (pp) cc_final: 0.7896 (tm) REVERT: G 59 ASN cc_start: 0.6093 (OUTLIER) cc_final: 0.5851 (p0) REVERT: G 99 GLU cc_start: 0.6923 (pt0) cc_final: 0.6723 (pt0) REVERT: H 46 LEU cc_start: 0.5854 (tt) cc_final: 0.5466 (tp) REVERT: H 185 ASP cc_start: 0.6720 (t70) cc_final: 0.6403 (t70) REVERT: H 210 ASN cc_start: 0.6407 (OUTLIER) cc_final: 0.6008 (p0) REVERT: K 4 LEU cc_start: 0.5233 (mp) cc_final: 0.4922 (mt) REVERT: K 170 ASP cc_start: 0.8192 (t0) cc_final: 0.7688 (t0) REVERT: K 195 GLU cc_start: 0.5886 (tp30) cc_final: 0.5502 (tm-30) REVERT: K 211 ARG cc_start: 0.8124 (ptm160) cc_final: 0.7535 (ppp80) outliers start: 302 outliers final: 75 residues processed: 1069 average time/residue: 1.0444 time to fit residues: 1417.9772 Evaluate side-chains 677 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 595 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 391 optimal weight: 0.6980 chunk 414 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 644 GLN A 784 GLN A 804 GLN A 954 GLN A 992 GLN A1083 HIS B 207 HIS B 414 GLN B 422 ASN B 450 ASN B 540 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 907 ASN B 935 GLN B1010 GLN B1119 ASN B1142 GLN C 81 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 59 ASN E 160 GLN E 166 GLN G 31 ASN G 39 GLN H 38 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 1.0478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 34951 Z= 0.315 Angle : 0.858 15.638 47530 Z= 0.422 Chirality : 0.052 0.453 5561 Planarity : 0.006 0.088 6072 Dihedral : 6.956 57.169 5759 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 6.56 % Allowed : 24.17 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 4265 helix: 0.51 (0.20), residues: 660 sheet: -0.89 (0.14), residues: 1242 loop : -2.11 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 94 HIS 0.014 0.002 HIS D 208 PHE 0.029 0.002 PHE D 130 TYR 0.030 0.002 TYR A 380 ARG 0.019 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 682 time to evaluate : 3.323 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: A 134 GLN cc_start: 0.5838 (mm-40) cc_final: 0.5471 (tp40) REVERT: A 153 MET cc_start: 0.1757 (mmp) cc_final: 0.0611 (ptp) REVERT: A 332 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6133 (mp) REVERT: A 642 VAL cc_start: 0.8039 (m) cc_final: 0.7815 (t) REVERT: A 1001 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8411 (tp) REVERT: B 128 ILE cc_start: 0.5962 (mp) cc_final: 0.5674 (mt) REVERT: B 697 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7189 (ptm) REVERT: B 1031 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: C 153 MET cc_start: 0.3246 (ptm) cc_final: 0.2559 (ptt) REVERT: C 303 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6256 (mt) REVERT: C 464 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6905 (t80) REVERT: C 756 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7116 (t80) REVERT: C 1050 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7936 (ptp) REVERT: C 1058 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7188 (t-90) REVERT: G 130 PHE cc_start: 0.6761 (m-80) cc_final: 0.6538 (m-10) REVERT: G 222 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5567 (mptt) REVERT: H 188 LYS cc_start: 0.8428 (pptt) cc_final: 0.8192 (pptt) REVERT: J 67 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7218 (mtm180) REVERT: J 69 THR cc_start: 0.7693 (t) cc_final: 0.6899 (p) REVERT: K 170 ASP cc_start: 0.8049 (t0) cc_final: 0.7665 (t0) REVERT: K 186 TYR cc_start: 0.7807 (t80) cc_final: 0.7320 (t80) REVERT: K 211 ARG cc_start: 0.7759 (ptm160) cc_final: 0.7371 (ppp80) outliers start: 246 outliers final: 84 residues processed: 855 average time/residue: 1.0360 time to fit residues: 1126.0006 Evaluate side-chains 645 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 550 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 163 ASN Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 171 optimal weight: 0.0870 chunk 353 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 372 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 895 GLN A 992 GLN B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 450 ASN B 540 ASN B 710 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 271 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1010 GLN C1036 GLN D 59 ASN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 39 GLN H 38 GLN ** H 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN J 163 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 1.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 34951 Z= 0.385 Angle : 0.888 16.195 47530 Z= 0.445 Chirality : 0.056 1.258 5561 Planarity : 0.006 0.080 6072 Dihedral : 6.793 58.915 5759 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.44 % Favored : 91.47 % Rotamer: Outliers : 7.39 % Allowed : 25.75 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4265 helix: 0.23 (0.20), residues: 690 sheet: -0.99 (0.14), residues: 1226 loop : -2.22 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 162 HIS 0.012 0.002 HIS B 207 PHE 0.040 0.002 PHE A 562 TYR 0.030 0.002 TYR C 265 ARG 0.020 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 612 time to evaluate : 3.993 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: A 153 MET cc_start: 0.1105 (mmp) cc_final: 0.0495 (pmt) REVERT: A 332 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6572 (mp) REVERT: A 417 LYS cc_start: 0.7459 (tppt) cc_final: 0.7117 (tptt) REVERT: A 421 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6146 (p90) REVERT: A 483 VAL cc_start: 0.6348 (p) cc_final: 0.6071 (p) REVERT: A 642 VAL cc_start: 0.8625 (m) cc_final: 0.8376 (t) REVERT: A 1050 MET cc_start: 0.8444 (pmm) cc_final: 0.8147 (pmm) REVERT: B 108 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.5596 (t) REVERT: B 697 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7749 (ptm) REVERT: B 869 MET cc_start: 0.8138 (mtm) cc_final: 0.7860 (ttm) REVERT: B 882 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8549 (mt) REVERT: B 1031 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: C 153 MET cc_start: 0.3435 (ptm) cc_final: 0.2728 (ptt) REVERT: C 223 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6944 (pp) REVERT: C 267 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7258 (t) REVERT: C 303 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7468 (mt) REVERT: C 314 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: C 464 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7191 (t80) REVERT: C 466 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.5267 (ttp-170) REVERT: D 113 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7241 (pt0) REVERT: E 82 ASP cc_start: 0.7398 (m-30) cc_final: 0.7084 (m-30) REVERT: E 183 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8529 (ptmt) REVERT: G 106 TYR cc_start: 0.8177 (t80) cc_final: 0.7871 (t80) REVERT: G 205 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6756 (p0) REVERT: G 222 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5879 (mptt) REVERT: K 170 ASP cc_start: 0.8307 (t0) cc_final: 0.7831 (t0) REVERT: K 195 GLU cc_start: 0.6236 (tp30) cc_final: 0.5863 (tm-30) outliers start: 277 outliers final: 115 residues processed: 818 average time/residue: 1.0908 time to fit residues: 1124.2442 Evaluate side-chains 591 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 461 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 0.0980 chunk 373 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 415 optimal weight: 4.9990 chunk 344 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 207 HIS B 394 ASN B 422 ASN B 925 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN D 59 ASN D 163 ASN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 199 GLN G 31 ASN G 39 GLN G 43 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 1.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 34951 Z= 0.438 Angle : 0.911 17.683 47530 Z= 0.450 Chirality : 0.056 0.650 5561 Planarity : 0.006 0.100 6072 Dihedral : 7.444 59.926 5759 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.74 % Favored : 92.22 % Rotamer: Outliers : 6.80 % Allowed : 28.20 % Favored : 64.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4265 helix: 0.34 (0.20), residues: 688 sheet: -1.08 (0.14), residues: 1241 loop : -2.19 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 162 HIS 0.011 0.002 HIS B 207 PHE 0.039 0.003 PHE C 377 TYR 0.037 0.003 TYR H 140 ARG 0.013 0.001 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 529 time to evaluate : 4.060 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: A 153 MET cc_start: 0.1543 (mmp) cc_final: 0.0791 (ptp) REVERT: A 421 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6108 (p90) REVERT: A 994 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7210 (t0) REVERT: B 84 LEU cc_start: 0.7415 (tp) cc_final: 0.6986 (mt) REVERT: B 135 PHE cc_start: 0.4434 (OUTLIER) cc_final: 0.3798 (p90) REVERT: B 869 MET cc_start: 0.8342 (mtm) cc_final: 0.8125 (mtm) REVERT: B 1031 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: C 91 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6518 (t80) REVERT: C 153 MET cc_start: 0.3304 (ptm) cc_final: 0.2855 (ptt) REVERT: C 267 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.7452 (t) REVERT: C 466 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6051 (ttp-170) REVERT: D 204 CYS cc_start: 0.4636 (t) cc_final: 0.4406 (t) REVERT: E 75 ILE cc_start: 0.7392 (mm) cc_final: 0.6859 (mt) REVERT: G 48 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7565 (mtp) REVERT: G 205 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7002 (p0) REVERT: G 222 LYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5895 (mptt) REVERT: H 188 LYS cc_start: 0.8492 (pptt) cc_final: 0.8290 (pptt) REVERT: H 189 HIS cc_start: 0.7247 (m170) cc_final: 0.6555 (m90) REVERT: J 69 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7847 (p) REVERT: K 82 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6248 (t0) REVERT: K 170 ASP cc_start: 0.8431 (t0) cc_final: 0.7960 (t0) outliers start: 255 outliers final: 129 residues processed: 722 average time/residue: 1.1414 time to fit residues: 1026.3688 Evaluate side-chains 571 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 430 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 194 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 205 ASN Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 163 ASN Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 349 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 413 optimal weight: 0.9980 chunk 258 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 190 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B1005 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 1.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34951 Z= 0.246 Angle : 0.803 12.596 47530 Z= 0.389 Chirality : 0.050 0.612 5561 Planarity : 0.005 0.077 6072 Dihedral : 6.922 58.102 5759 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.17 % Favored : 92.80 % Rotamer: Outliers : 4.86 % Allowed : 31.14 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.12), residues: 4265 helix: 0.61 (0.20), residues: 689 sheet: -0.82 (0.15), residues: 1219 loop : -2.12 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 162 HIS 0.010 0.001 HIS B 207 PHE 0.032 0.002 PHE A 562 TYR 0.031 0.002 TYR H 140 ARG 0.012 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 473 time to evaluate : 3.924 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: A 153 MET cc_start: 0.1447 (mmp) cc_final: 0.0851 (ptp) REVERT: A 421 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6234 (p90) REVERT: A 697 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7333 (mtp) REVERT: A 994 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7100 (t0) REVERT: B 135 PHE cc_start: 0.4322 (OUTLIER) cc_final: 0.3848 (p90) REVERT: B 138 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6839 (p0) REVERT: B 394 ASN cc_start: 0.5178 (t0) cc_final: 0.4867 (m-40) REVERT: B 508 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: B 1031 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: C 153 MET cc_start: 0.3360 (ptm) cc_final: 0.2859 (ptt) REVERT: E 75 ILE cc_start: 0.7560 (mm) cc_final: 0.7244 (mt) REVERT: E 147 GLN cc_start: 0.7192 (tp40) cc_final: 0.6967 (tt0) REVERT: H 189 HIS cc_start: 0.7184 (m170) cc_final: 0.6223 (m90) REVERT: J 67 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7182 (mtm180) REVERT: K 123 GLU cc_start: 0.8338 (tp30) cc_final: 0.7526 (pp20) outliers start: 182 outliers final: 92 residues processed: 610 average time/residue: 1.1061 time to fit residues: 849.7204 Evaluate side-chains 523 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 423 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 246 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 262 optimal weight: 0.9990 chunk 281 optimal weight: 0.8980 chunk 204 optimal weight: 0.0870 chunk 38 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1106 GLN B 207 HIS B 394 ASN B 540 ASN B 613 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 764 ASN C 935 GLN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN G 39 GLN H 38 GLN H 53 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 1.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34951 Z= 0.231 Angle : 0.791 12.311 47530 Z= 0.383 Chirality : 0.049 0.593 5561 Planarity : 0.005 0.077 6072 Dihedral : 6.563 56.977 5759 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.41 % Favored : 92.57 % Rotamer: Outliers : 4.27 % Allowed : 31.70 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4265 helix: 0.83 (0.20), residues: 685 sheet: -0.72 (0.15), residues: 1216 loop : -2.04 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 162 HIS 0.011 0.001 HIS B 207 PHE 0.026 0.002 PHE C 486 TYR 0.046 0.002 TYR A 380 ARG 0.012 0.001 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 450 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2136 (mmp) cc_final: 0.1464 (pmt) REVERT: A 421 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6145 (p90) REVERT: B 84 LEU cc_start: 0.7416 (mt) cc_final: 0.7055 (mt) REVERT: B 135 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.4468 (p90) REVERT: B 138 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7001 (p0) REVERT: B 421 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.6722 (p90) REVERT: C 92 PHE cc_start: 0.7826 (t80) cc_final: 0.7408 (m-80) REVERT: C 95 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7340 (t) REVERT: C 153 MET cc_start: 0.3378 (ptm) cc_final: 0.2888 (ptt) REVERT: C 329 PHE cc_start: 0.7120 (m-80) cc_final: 0.5921 (p90) REVERT: C 410 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8428 (tp) REVERT: D 3 GLN cc_start: 0.7402 (pm20) cc_final: 0.7120 (pm20) REVERT: E 75 ILE cc_start: 0.7668 (mm) cc_final: 0.7361 (mt) REVERT: G 203 ILE cc_start: 0.8491 (pp) cc_final: 0.8267 (mm) REVERT: G 222 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5913 (mptt) REVERT: J 67 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7123 (mtp180) REVERT: K 123 GLU cc_start: 0.8331 (tp30) cc_final: 0.7513 (pp20) outliers start: 160 outliers final: 93 residues processed: 567 average time/residue: 1.0625 time to fit residues: 762.3163 Evaluate side-chains 505 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 404 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 0.5980 chunk 396 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 385 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 348 optimal weight: 0.8980 chunk 364 optimal weight: 3.9990 chunk 383 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1005 GLN B 207 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN D 208 HIS G 39 GLN H 53 ASN ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 1.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34951 Z= 0.292 Angle : 0.808 16.174 47530 Z= 0.394 Chirality : 0.050 0.643 5561 Planarity : 0.005 0.077 6072 Dihedral : 6.519 58.388 5759 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.67 % Favored : 92.31 % Rotamer: Outliers : 3.68 % Allowed : 32.34 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 4265 helix: 0.88 (0.20), residues: 676 sheet: -0.75 (0.15), residues: 1218 loop : -2.01 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 162 HIS 0.036 0.002 HIS B 207 PHE 0.044 0.002 PHE H 139 TYR 0.040 0.002 TYR H 140 ARG 0.014 0.001 ARG J 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 438 time to evaluate : 4.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1589 (mmp) cc_final: 0.1063 (ptp) REVERT: A 421 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6277 (p90) REVERT: A 1050 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7505 (pmm) REVERT: B 84 LEU cc_start: 0.7604 (mt) cc_final: 0.7288 (mt) REVERT: B 138 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6966 (p0) REVERT: B 421 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.6550 (p90) REVERT: C 153 MET cc_start: 0.2939 (ptm) cc_final: 0.2516 (ptt) REVERT: D 3 GLN cc_start: 0.7481 (pm20) cc_final: 0.7216 (pm20) REVERT: E 10 THR cc_start: 0.7578 (m) cc_final: 0.7245 (t) REVERT: E 75 ILE cc_start: 0.7912 (mm) cc_final: 0.7698 (mt) REVERT: G 108 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7724 (mtp) REVERT: G 162 TRP cc_start: 0.7833 (m100) cc_final: 0.7553 (m100) REVERT: G 222 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5876 (mptt) REVERT: J 67 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7363 (mtp180) REVERT: K 123 GLU cc_start: 0.8365 (tp30) cc_final: 0.7496 (pp20) outliers start: 138 outliers final: 97 residues processed: 547 average time/residue: 1.0182 time to fit residues: 712.8510 Evaluate side-chains 514 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 410 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 1.9990 chunk 407 optimal weight: 20.0000 chunk 248 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 283 optimal weight: 0.9980 chunk 427 optimal weight: 0.9980 chunk 393 optimal weight: 0.8980 chunk 340 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 360 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1106 GLN D 163 ASN H 53 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 1.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.386 34951 Z= 0.418 Angle : 0.981 59.200 47530 Z= 0.527 Chirality : 0.051 0.696 5561 Planarity : 0.006 0.166 6072 Dihedral : 6.529 58.257 5759 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.76 % Favored : 92.22 % Rotamer: Outliers : 3.26 % Allowed : 33.11 % Favored : 63.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4265 helix: 0.90 (0.20), residues: 676 sheet: -0.74 (0.15), residues: 1215 loop : -2.01 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 162 HIS 0.026 0.001 HIS B 207 PHE 0.342 0.002 PHE A 562 TYR 0.345 0.002 TYR C 505 ARG 0.019 0.001 ARG J 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 413 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1612 (mmp) cc_final: 0.1060 (ptp) REVERT: A 421 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6272 (p90) REVERT: A 1050 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7493 (pmm) REVERT: B 31 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.8033 (p) REVERT: B 84 LEU cc_start: 0.7604 (mt) cc_final: 0.7287 (mt) REVERT: B 138 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6964 (p0) REVERT: B 421 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.6548 (p90) REVERT: C 153 MET cc_start: 0.2937 (ptm) cc_final: 0.2515 (ptt) REVERT: D 3 GLN cc_start: 0.7481 (pm20) cc_final: 0.7211 (pm20) REVERT: E 10 THR cc_start: 0.7534 (m) cc_final: 0.7213 (t) REVERT: E 75 ILE cc_start: 0.7909 (mm) cc_final: 0.7696 (mt) REVERT: G 3 GLN cc_start: 0.7733 (mp10) cc_final: 0.7510 (mm110) REVERT: G 162 TRP cc_start: 0.7827 (m100) cc_final: 0.7587 (m100) REVERT: G 222 LYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5875 (mptt) REVERT: K 123 GLU cc_start: 0.8349 (tp30) cc_final: 0.7503 (pp20) outliers start: 122 outliers final: 104 residues processed: 511 average time/residue: 1.0189 time to fit residues: 669.5320 Evaluate side-chains 519 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 409 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 222 LYS Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.0030 chunk 362 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 313 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 340 optimal weight: 8.9990 chunk 142 optimal weight: 0.4980 chunk 350 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1005 GLN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN D 163 ASN ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.111623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.085891 restraints weight = 88799.841| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.66 r_work: 0.3349 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 1.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34951 Z= 0.234 Angle : 0.815 15.498 47530 Z= 0.395 Chirality : 0.050 0.610 5561 Planarity : 0.005 0.078 6072 Dihedral : 6.466 57.519 5759 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.60 % Favored : 92.38 % Rotamer: Outliers : 3.20 % Allowed : 32.98 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 4265 helix: 0.89 (0.20), residues: 684 sheet: -0.65 (0.15), residues: 1198 loop : -2.00 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 162 HIS 0.006 0.001 HIS D 172 PHE 0.054 0.002 PHE A 562 TYR 0.048 0.002 TYR C 505 ARG 0.014 0.001 ARG G 87 =============================================================================== Job complete usr+sys time: 15076.24 seconds wall clock time: 266 minutes 13.61 seconds (15973.61 seconds total)