Starting phenix.real_space_refine on Wed Jul 24 23:51:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/07_2024/8jo0_36451_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/07_2024/8jo0_36451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/07_2024/8jo0_36451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/07_2024/8jo0_36451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/07_2024/8jo0_36451_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/07_2024/8jo0_36451_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 21 5.49 5 Mg 7 5.21 5 S 199 5.16 5 C 17375 2.51 5 N 4579 2.21 5 O 5181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 4": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J GLU 38": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "L GLU 4": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "M GLU 4": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 440": "NH1" <-> "NH2" Residue "C ARG 448": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 424": "OE1" <-> "OE2" Residue "D ARG 436": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D ARG 448": "NH1" <-> "NH2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 424": "OE1" <-> "OE2" Residue "E ARG 436": "NH1" <-> "NH2" Residue "E ARG 440": "NH1" <-> "NH2" Residue "E ARG 448": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F ARG 436": "NH1" <-> "NH2" Residue "F ARG 440": "NH1" <-> "NH2" Residue "F ARG 448": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F GLU 486": "OE1" <-> "OE2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "G GLU 255": "OE1" <-> "OE2" Residue "G GLU 263": "OE1" <-> "OE2" Residue "G GLU 289": "OE1" <-> "OE2" Residue "G GLU 324": "OE1" <-> "OE2" Residue "G GLU 341": "OE1" <-> "OE2" Residue "G GLU 364": "OE1" <-> "OE2" Residue "G GLU 383": "OE1" <-> "OE2" Residue "G ARG 436": "NH1" <-> "NH2" Residue "G ARG 440": "NH1" <-> "NH2" Residue "G ARG 448": "NH1" <-> "NH2" Residue "G ARG 483": "NH1" <-> "NH2" Residue "G GLU 486": "OE1" <-> "OE2" Residue "G GLU 527": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27362 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 910 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 870 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "C" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 374} Chain breaks: 2 Chain: "D" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "E" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "F" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "G" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3114 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.72, per 1000 atoms: 0.54 Number of scatterers: 27362 At special positions: 0 Unit cell: (161.04, 165, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 199 16.00 P 21 15.00 Mg 7 11.99 O 5181 8.00 N 4579 7.00 C 17375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 11.59 Conformation dependent library (CDL) restraints added in 5.0 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6530 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 14 sheets defined 59.9% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 33 removed outlier: 3.757A pdb=" N ALA H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 49 through 65 removed outlier: 3.557A pdb=" N ARG H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 65 " --> pdb=" O TYR H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.524A pdb=" N PHE H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE H 86 " --> pdb=" O HIS H 82 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA H 94 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.978A pdb=" N GLN H 109 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 18 removed outlier: 3.562A pdb=" N LEU I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 33 removed outlier: 3.756A pdb=" N ALA I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR I 28 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 46 Processing helix chain 'I' and resid 49 through 65 removed outlier: 3.558A pdb=" N ARG I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 65 " --> pdb=" O TYR I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.524A pdb=" N PHE I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA I 94 " --> pdb=" O TYR I 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE I 95 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN I 96 " --> pdb=" O ASP I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 106 through 110 removed outlier: 3.979A pdb=" N GLN I 109 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU J 10 " --> pdb=" O GLU J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 removed outlier: 3.563A pdb=" N LEU J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 33 removed outlier: 3.756A pdb=" N ALA J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR J 28 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 46 Processing helix chain 'J' and resid 49 through 65 removed outlier: 3.558A pdb=" N ARG J 53 " --> pdb=" O THR J 49 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA J 65 " --> pdb=" O TYR J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 removed outlier: 3.524A pdb=" N PHE J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 96 removed outlier: 3.621A pdb=" N ALA J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA J 94 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE J 95 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN J 96 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 106 through 110 removed outlier: 3.978A pdb=" N GLN J 109 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 13 removed outlier: 3.631A pdb=" N LEU K 10 " --> pdb=" O GLU K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 20 removed outlier: 3.561A pdb=" N LEU K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 33 removed outlier: 3.774A pdb=" N ALA K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 46 Processing helix chain 'K' and resid 49 through 65 removed outlier: 3.554A pdb=" N ARG K 53 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG K 62 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG K 63 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA K 94 " --> pdb=" O TYR K 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR L 28 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 46 Processing helix chain 'L' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG L 53 " --> pdb=" O THR L 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG L 62 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN L 64 " --> pdb=" O ILE L 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 65 " --> pdb=" O TYR L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 76 Processing helix chain 'L' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE L 86 " --> pdb=" O HIS L 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA L 94 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 13 removed outlier: 3.629A pdb=" N LEU M 10 " --> pdb=" O GLU M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 20 removed outlier: 3.559A pdb=" N LEU M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA M 26 " --> pdb=" O GLU M 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 46 Processing helix chain 'M' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG M 53 " --> pdb=" O THR M 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG M 62 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG M 63 " --> pdb=" O ARG M 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN M 64 " --> pdb=" O ILE M 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 Processing helix chain 'M' and resid 80 through 96 removed outlier: 3.617A pdb=" N ALA M 84 " --> pdb=" O GLN M 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE M 86 " --> pdb=" O HIS M 82 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA M 94 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.809A pdb=" N LYS A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.520A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.509A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.977A pdb=" N ILE A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.538A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.698A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 344 through 364 removed outlier: 3.567A pdb=" N LEU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 4.419A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.653A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 457 through 466 removed outlier: 4.193A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 removed outlier: 3.812A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.808A pdb=" N LYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.516A pdb=" N SER B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.270A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.537A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.549A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.552A pdb=" N GLY B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 363 " --> pdb=" O GLY B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 removed outlier: 4.420A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 3.657A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 427 through 439 removed outlier: 4.041A pdb=" N ALA B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.954A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 487 removed outlier: 4.005A pdb=" N GLU B 481 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.955A pdb=" N SER B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.809A pdb=" N LYS C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 173 Processing helix chain 'C' and resid 198 through 212 removed outlier: 4.270A pdb=" N PHE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 254 through 264 removed outlier: 4.190A pdb=" N ILE C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 294 through 306 removed outlier: 3.538A pdb=" N TYR C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 300 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 326 removed outlier: 3.935A pdb=" N LYS C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 344 through 364 removed outlier: 3.570A pdb=" N LEU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 363 " --> pdb=" O GLY C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 removed outlier: 4.420A pdb=" N ARG C 380 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.663A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 428 through 439 removed outlier: 3.524A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 466 removed outlier: 4.147A pdb=" N LEU C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.812A pdb=" N ALA C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 535 removed outlier: 3.904A pdb=" N LEU C 535 " --> pdb=" O PHE C 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 535' Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'D' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 146 removed outlier: 3.810A pdb=" N LYS D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA D 238 " --> pdb=" O MET D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 removed outlier: 4.326A pdb=" N ILE D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 306 removed outlier: 3.537A pdb=" N TYR D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 300 " --> pdb=" O ASP D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 326 removed outlier: 3.789A pdb=" N LYS D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 338 Processing helix chain 'D' and resid 344 through 355 removed outlier: 4.086A pdb=" N GLN D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 364 removed outlier: 3.572A pdb=" N GLY D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 363 " --> pdb=" O GLY D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 removed outlier: 4.420A pdb=" N ARG D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 395 removed outlier: 3.665A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 392 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 424 through 427 removed outlier: 3.735A pdb=" N ASP D 427 " --> pdb=" O GLU D 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 424 through 427' Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'D' and resid 457 through 466 removed outlier: 4.170A pdb=" N LEU D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 486 removed outlier: 3.814A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 481 " --> pdb=" O ILE D 477 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 482 " --> pdb=" O SER D 478 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 541 Processing helix chain 'E' and resid 113 through 122 removed outlier: 3.598A pdb=" N ARG E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 removed outlier: 3.809A pdb=" N LYS E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 176 removed outlier: 3.528A pdb=" N ILE E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET E 210 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 211 " --> pdb=" O ILE E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA E 238 " --> pdb=" O MET E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 254 through 264 removed outlier: 3.984A pdb=" N ILE E 258 " --> pdb=" O GLN E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 294 through 306 removed outlier: 3.536A pdb=" N TYR E 299 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP E 300 " --> pdb=" O ASP E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.960A pdb=" N LYS E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 323 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 344 through 364 removed outlier: 4.146A pdb=" N GLN E 350 " --> pdb=" O GLU E 346 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU E 360 " --> pdb=" O GLU E 356 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 362 " --> pdb=" O ARG E 358 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 363 " --> pdb=" O GLY E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 384 removed outlier: 3.765A pdb=" N ALA E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 396 removed outlier: 3.666A pdb=" N SER E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 424 through 427 Processing helix chain 'E' and resid 428 through 439 Processing helix chain 'E' and resid 457 through 468 Processing helix chain 'E' and resid 469 through 485 removed outlier: 3.506A pdb=" N ILE E 473 " --> pdb=" O ASP E 469 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.599A pdb=" N ARG F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 removed outlier: 3.809A pdb=" N LYS F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 143 " --> pdb=" O ARG F 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 173 removed outlier: 3.522A pdb=" N ILE F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 212 removed outlier: 4.270A pdb=" N PHE F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET F 210 " --> pdb=" O ASP F 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.508A pdb=" N ALA F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 255 through 265 Processing helix chain 'F' and resid 274 through 281 removed outlier: 4.203A pdb=" N ILE F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER F 278 " --> pdb=" O VAL F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.536A pdb=" N TYR F 299 " --> pdb=" O ILE F 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 300 " --> pdb=" O ASP F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 327 removed outlier: 3.811A pdb=" N ASN F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 321 " --> pdb=" O ASP F 317 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 340 Processing helix chain 'F' and resid 344 through 364 removed outlier: 8.820A pdb=" N LEU F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 384 removed outlier: 4.419A pdb=" N ARG F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 395 removed outlier: 3.665A pdb=" N SER F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 removed outlier: 3.586A pdb=" N CYS F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 439 removed outlier: 3.703A pdb=" N ALA F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 468 Processing helix chain 'F' and resid 469 through 483 removed outlier: 3.961A pdb=" N ALA F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.597A pdb=" N ARG G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.810A pdb=" N LYS G 142 " --> pdb=" O ASP G 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS G 143 " --> pdb=" O ARG G 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 173 removed outlier: 3.521A pdb=" N ILE G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 212 removed outlier: 4.271A pdb=" N PHE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET G 210 " --> pdb=" O ASP G 206 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 211 " --> pdb=" O ILE G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 226 Processing helix chain 'G' and resid 227 through 239 removed outlier: 3.511A pdb=" N ALA G 238 " --> pdb=" O MET G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 294 through 306 removed outlier: 3.537A pdb=" N TYR G 299 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 327 removed outlier: 3.696A pdb=" N LYS G 321 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR G 322 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER G 326 " --> pdb=" O THR G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 338 removed outlier: 3.641A pdb=" N PHE G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 356 Processing helix chain 'G' and resid 359 through 364 removed outlier: 3.737A pdb=" N VAL G 363 " --> pdb=" O GLY G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 384 removed outlier: 3.518A pdb=" N ALA G 377 " --> pdb=" O SER G 373 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG G 380 " --> pdb=" O MET G 376 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS G 381 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 407 through 412 Processing helix chain 'G' and resid 427 through 440 removed outlier: 4.213A pdb=" N ALA G 431 " --> pdb=" O ASP G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 443 No H-bonds generated for 'chain 'G' and resid 441 through 443' Processing helix chain 'G' and resid 457 through 468 removed outlier: 4.262A pdb=" N LEU G 464 " --> pdb=" O ILE G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 486 Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 541 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 191 removed outlier: 3.676A pdb=" N THR A 272 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.557A pdb=" N SER B 186 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 248 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 188 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP B 250 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 190 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 252 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG B 267 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 191 removed outlier: 6.554A pdb=" N SER C 186 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL C 248 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 188 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP C 250 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 190 " --> pdb=" O ASP C 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 252 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG C 267 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR C 272 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AA7, first strand: chain 'D' and resid 186 through 191 removed outlier: 6.528A pdb=" N SER D 186 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL D 248 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 188 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP D 250 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 190 " --> pdb=" O ASP D 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL D 252 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 272 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE D 154 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE D 288 " --> pdb=" O PHE D 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE D 156 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL D 290 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N HIS D 158 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AA9, first strand: chain 'E' and resid 187 through 191 removed outlier: 6.535A pdb=" N VAL E 188 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP E 250 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 190 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 252 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 272 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AB2, first strand: chain 'F' and resid 186 through 191 removed outlier: 6.508A pdb=" N SER F 186 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL F 248 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL F 188 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP F 250 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU F 190 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 252 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 405 through 406 Processing sheet with id=AB4, first strand: chain 'G' and resid 187 through 191 removed outlier: 6.535A pdb=" N VAL G 188 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP G 250 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU G 190 " --> pdb=" O ASP G 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL G 252 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE G 247 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR G 271 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE G 249 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 155 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR G 272 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE G 154 " --> pdb=" O GLU G 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 405 through 406 1085 hydrogen bonds defined for protein. 3153 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: 8.14 Time building geometry restraints manager: 12.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7938 1.33 - 1.46: 5781 1.46 - 1.59: 13798 1.59 - 1.72: 21 1.72 - 1.85: 316 Bond restraints: 27854 Sorted by residual: bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.31e+01 bond pdb=" C4 ATP G 602 " pdb=" C5 ATP G 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.24e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.13e+01 bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.10e+01 bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 9.04e+01 ... (remaining 27849 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.47: 529 104.47 - 112.15: 13258 112.15 - 119.83: 10976 119.83 - 127.51: 12743 127.51 - 135.19: 170 Bond angle restraints: 37676 Sorted by residual: angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 114.18 25.69 1.00e+00 1.00e+00 6.60e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 114.20 25.67 1.00e+00 1.00e+00 6.59e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 114.21 25.66 1.00e+00 1.00e+00 6.58e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.23 25.64 1.00e+00 1.00e+00 6.57e+02 ... (remaining 37671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 15155 25.73 - 51.46: 1581 51.46 - 77.20: 457 77.20 - 102.93: 39 102.93 - 128.66: 6 Dihedral angle restraints: 17238 sinusoidal: 7273 harmonic: 9965 Sorted by residual: dihedral pdb=" CA MET A 449 " pdb=" C MET A 449 " pdb=" N PRO A 450 " pdb=" CA PRO A 450 " ideal model delta harmonic sigma weight residual -180.00 -51.34 -128.66 0 5.00e+00 4.00e-02 6.62e+02 dihedral pdb=" CA MET G 449 " pdb=" C MET G 449 " pdb=" N PRO G 450 " pdb=" CA PRO G 450 " ideal model delta harmonic sigma weight residual -180.00 -51.39 -128.61 0 5.00e+00 4.00e-02 6.62e+02 dihedral pdb=" CA MET B 449 " pdb=" C MET B 449 " pdb=" N PRO B 450 " pdb=" CA PRO B 450 " ideal model delta harmonic sigma weight residual -180.00 -51.40 -128.60 0 5.00e+00 4.00e-02 6.61e+02 ... (remaining 17235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2916 0.070 - 0.139: 1088 0.139 - 0.209: 263 0.209 - 0.279: 58 0.279 - 0.348: 12 Chirality restraints: 4337 Sorted by residual: chirality pdb=" CA PHE E 204 " pdb=" N PHE E 204 " pdb=" C PHE E 204 " pdb=" CB PHE E 204 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA PHE C 532 " pdb=" N PHE C 532 " pdb=" C PHE C 532 " pdb=" CB PHE C 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 4334 not shown) Planarity restraints: 4780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 443 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C LEU B 443 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU B 443 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 444 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 148 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C CYS C 148 " -0.061 2.00e-02 2.50e+03 pdb=" O CYS C 148 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP C 149 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 336 " 0.016 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PHE E 336 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE E 336 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE E 337 " 0.019 2.00e-02 2.50e+03 ... (remaining 4777 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 148 2.43 - 3.05: 20077 3.05 - 3.67: 41817 3.67 - 4.28: 64208 4.28 - 4.90: 99213 Nonbonded interactions: 225463 Sorted by model distance: nonbonded pdb=" OG1 THR A 367 " pdb=" CD PRO A 368 " model vdw 1.813 3.440 nonbonded pdb=" CD PRO A 530 " pdb=" NZ LYS A 531 " model vdw 1.994 3.520 nonbonded pdb=" CD PRO B 530 " pdb=" NZ LYS B 531 " model vdw 1.995 3.520 nonbonded pdb=" CD PRO E 530 " pdb=" NZ LYS E 531 " model vdw 1.995 3.520 nonbonded pdb=" CD PRO C 530 " pdb=" NZ LYS C 531 " model vdw 1.995 3.520 ... (remaining 225458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'H' and resid 1 through 105) selection = (chain 'I' and resid 1 through 105) selection = (chain 'J' and resid 1 through 105) selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 71.030 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 27854 Z= 0.597 Angle : 1.485 25.727 37676 Z= 1.071 Chirality : 0.076 0.348 4337 Planarity : 0.006 0.059 4780 Dihedral : 21.290 128.660 10708 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 62.06 Ramachandran Plot: Outliers : 1.32 % Allowed : 13.79 % Favored : 84.89 % Rotamer: Outliers : 27.27 % Allowed : 15.78 % Favored : 56.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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: -4.82 (0.12), residues: 3328 helix: -3.40 (0.09), residues: 1803 sheet: -1.88 (0.31), residues: 259 loop : -2.89 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP F 189 HIS 0.004 0.001 HIS A 536 PHE 0.020 0.002 PHE F 345 TYR 0.022 0.003 TYR C 371 ARG 0.004 0.000 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 840 poor density : 329 time to evaluate : 3.043 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 64 GLN cc_start: 0.2185 (OUTLIER) cc_final: 0.1945 (mm110) REVERT: I 56 ASN cc_start: 0.3494 (m-40) cc_final: 0.3228 (m-40) REVERT: I 106 ILE cc_start: 0.4356 (mm) cc_final: 0.3714 (mm) REVERT: J 77 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: K 35 ILE cc_start: -0.4836 (OUTLIER) cc_final: -0.5143 (mt) REVERT: L 35 ILE cc_start: 0.4156 (OUTLIER) cc_final: 0.3588 (mp) REVERT: L 68 LEU cc_start: -0.0908 (OUTLIER) cc_final: -0.1853 (pp) REVERT: M 43 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6560 (mp) REVERT: M 68 LEU cc_start: -0.0093 (OUTLIER) cc_final: -0.1984 (tp) REVERT: M 77 TYR cc_start: 0.4656 (OUTLIER) cc_final: 0.3907 (p90) REVERT: A 126 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8911 (tptp) REVERT: A 290 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 296 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8681 (p0) REVERT: A 336 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.9027 (t80) REVERT: A 350 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: A 393 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 410 TRP cc_start: 0.9224 (OUTLIER) cc_final: 0.8429 (m-90) REVERT: A 426 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7799 (tp) REVERT: A 536 HIS cc_start: 0.7470 (m-70) cc_final: 0.6846 (m170) REVERT: B 203 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9363 (tp) REVERT: B 228 SER cc_start: 0.9446 (OUTLIER) cc_final: 0.9235 (p) REVERT: B 296 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8794 (p0) REVERT: B 369 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8390 (t80) REVERT: B 445 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 540 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: C 290 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8276 (t) REVERT: C 316 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: C 350 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8382 (tm-30) REVERT: C 369 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8247 (t80) REVERT: C 439 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9045 (mmtm) REVERT: D 117 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.9024 (mmp80) REVERT: D 135 TYR cc_start: 0.8766 (t80) cc_final: 0.8537 (t80) REVERT: D 351 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9152 (mt) REVERT: D 439 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.9136 (mmtm) REVERT: E 244 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8612 (t0) REVERT: E 259 ARG cc_start: 0.9448 (OUTLIER) cc_final: 0.9247 (tpp-160) REVERT: E 290 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8402 (t) REVERT: F 117 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8738 (mmt90) REVERT: F 203 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9374 (tp) REVERT: F 221 PRO cc_start: 0.7510 (Cg_endo) cc_final: 0.7039 (Cg_exo) REVERT: F 296 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8885 (p0) REVERT: F 369 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8300 (t80) REVERT: G 264 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9085 (mt) REVERT: G 296 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8937 (p0) REVERT: G 316 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: G 397 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8523 (p) REVERT: G 410 TRP cc_start: 0.8764 (OUTLIER) cc_final: 0.8389 (m-90) REVERT: G 531 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.6717 (tptt) outliers start: 840 outliers final: 210 residues processed: 1066 average time/residue: 0.4247 time to fit residues: 697.2526 Evaluate side-chains 482 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 229 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 ARG Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 77 TYR Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 8 ARG Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 52 GLU Chi-restraints excluded: chain L residue 64 GLN Chi-restraints excluded: chain L residue 67 GLU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 8 ARG Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 447 LYS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 534 GLN Chi-restraints excluded: chain C residue 540 TYR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 220 PHE Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 424 GLU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 486 GLU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 533 MET Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 220 PHE Chi-restraints excluded: chain E residue 244 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 259 ARG Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 285 CYS Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 410 TRP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 527 GLU Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 381 CYS Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 435 LYS Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 381 CYS Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 305 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 34 ASN I 34 ASN J 34 ASN J 56 ASN K 34 ASN L 34 ASN M 34 ASN A 123 ASN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS A 237 ASN A 244 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN A 283 GLN A 471 GLN B 123 ASN B 237 ASN B 244 ASN B 471 GLN B 482 GLN C 123 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN C 283 GLN C 471 GLN C 482 GLN ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN D 123 ASN D 225 HIS ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 471 GLN D 537 GLN E 113 GLN E 123 ASN E 225 HIS E 237 ASN E 350 GLN E 471 GLN E 482 GLN F 123 ASN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 ASN F 244 ASN F 262 GLN F 329 ASN F 352 ASN F 471 GLN F 475 ASN F 536 HIS G 123 ASN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 ASN G 283 GLN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 466 HIS G 471 GLN G 475 ASN G 482 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27854 Z= 0.274 Angle : 0.807 15.317 37676 Z= 0.407 Chirality : 0.044 0.204 4337 Planarity : 0.007 0.103 4780 Dihedral : 15.727 117.662 4408 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.23 % Favored : 94.35 % Rotamer: Outliers : 9.16 % Allowed : 24.09 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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: -3.01 (0.13), residues: 3328 helix: -1.94 (0.10), residues: 1909 sheet: -1.23 (0.31), residues: 224 loop : -1.95 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 410 HIS 0.011 0.002 HIS D 225 PHE 0.020 0.002 PHE A 395 TYR 0.033 0.002 TYR D 305 ARG 0.005 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 247 time to evaluate : 3.145 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: symmetry clash REVERT: H 58 LEU cc_start: 0.8936 (mt) cc_final: 0.8615 (pp) REVERT: H 64 GLN cc_start: 0.2065 (OUTLIER) cc_final: 0.1450 (mt0) REVERT: I 46 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.5314 (pttm) REVERT: I 106 ILE cc_start: 0.4629 (mm) cc_final: 0.4280 (mm) REVERT: J 1 MET cc_start: 0.4866 (ptm) cc_final: 0.4658 (ptm) REVERT: J 16 ARG cc_start: 0.8361 (ptp90) cc_final: 0.8134 (ptp90) REVERT: J 62 ARG cc_start: 0.7183 (tmm160) cc_final: 0.5528 (ttt-90) REVERT: K 71 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5917 (tm) REVERT: M 46 LYS cc_start: 0.5290 (OUTLIER) cc_final: 0.4589 (pttm) REVERT: M 47 MET cc_start: 0.4159 (mmm) cc_final: 0.2431 (tmm) REVERT: A 203 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9498 (tt) REVERT: A 218 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7762 (pt) REVERT: A 437 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8979 (mt) REVERT: B 218 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7955 (pt) REVERT: B 307 MET cc_start: 0.8247 (tpt) cc_final: 0.7951 (mmm) REVERT: B 398 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8806 (p) REVERT: C 228 SER cc_start: 0.9506 (m) cc_final: 0.9294 (p) REVERT: C 317 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8507 (m-30) REVERT: C 399 MET cc_start: 0.8464 (mmm) cc_final: 0.8149 (mmp) REVERT: C 439 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9165 (mmtm) REVERT: C 443 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8322 (pt) REVERT: C 444 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8575 (mm) REVERT: C 445 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7676 (t) REVERT: C 455 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9069 (ptmm) REVERT: C 533 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8811 (tpp) REVERT: C 540 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8297 (m-10) REVERT: D 135 TYR cc_start: 0.8761 (t80) cc_final: 0.8503 (t80) REVERT: D 218 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7537 (pt) REVERT: D 355 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9354 (mm) REVERT: E 206 ASP cc_start: 0.8727 (m-30) cc_final: 0.8470 (m-30) REVERT: E 228 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.9115 (p) REVERT: E 399 MET cc_start: 0.7742 (mpp) cc_final: 0.7389 (mmp) REVERT: F 269 LEU cc_start: 0.9147 (tp) cc_final: 0.8925 (tp) REVERT: F 399 MET cc_start: 0.8394 (tpp) cc_final: 0.8129 (mmm) REVERT: G 116 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8384 (p0) REVERT: G 128 MET cc_start: 0.8716 (mmm) cc_final: 0.8466 (mmm) REVERT: G 210 MET cc_start: 0.8967 (tpp) cc_final: 0.8746 (tpp) REVERT: G 218 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8274 (pt) REVERT: G 296 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8888 (p0) REVERT: G 315 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7508 (tm-30) outliers start: 282 outliers final: 113 residues processed: 506 average time/residue: 0.3596 time to fit residues: 296.1683 Evaluate side-chains 327 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 190 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 52 GLU Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 540 TYR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 381 CYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 374 LEU Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 0.0010 chunk 305 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 overall best weight: 3.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 40 HIS I 56 ASN M 64 GLN A 113 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN B 113 GLN B 283 GLN C 113 GLN C 237 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 283 GLN ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN G 237 ASN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27854 Z= 0.311 Angle : 0.739 17.612 37676 Z= 0.369 Chirality : 0.043 0.308 4337 Planarity : 0.006 0.068 4780 Dihedral : 12.831 121.816 4052 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.98 % Favored : 93.75 % Rotamer: Outliers : 6.82 % Allowed : 24.71 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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: -1.83 (0.14), residues: 3328 helix: -0.85 (0.12), residues: 1911 sheet: -0.94 (0.28), residues: 259 loop : -1.67 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 410 HIS 0.012 0.001 HIS A 536 PHE 0.019 0.002 PHE D 454 TYR 0.032 0.002 TYR D 305 ARG 0.004 0.000 ARG E 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 196 time to evaluate : 3.399 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: H 2 LEU cc_start: 0.6695 (mp) cc_final: 0.6179 (tp) REVERT: H 58 LEU cc_start: 0.8976 (mt) cc_final: 0.8672 (pp) REVERT: H 64 GLN cc_start: 0.2629 (OUTLIER) cc_final: 0.2095 (mm110) REVERT: I 8 ARG cc_start: 0.2104 (tpt170) cc_final: 0.1225 (tpt170) REVERT: I 46 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.5439 (pttm) REVERT: K 71 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5810 (tm) REVERT: L 1 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.4678 (tpt) REVERT: L 35 ILE cc_start: 0.2712 (OUTLIER) cc_final: 0.2290 (mt) REVERT: L 47 MET cc_start: 0.0968 (mmt) cc_final: 0.0354 (tpp) REVERT: M 46 LYS cc_start: 0.5089 (OUTLIER) cc_final: 0.4663 (pttm) REVERT: M 47 MET cc_start: 0.4446 (mmm) cc_final: 0.2720 (tmm) REVERT: A 218 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8102 (pt) REVERT: A 348 MET cc_start: 0.9351 (ppp) cc_final: 0.9145 (ppp) REVERT: A 449 MET cc_start: 0.9084 (pmm) cc_final: 0.8853 (pmm) REVERT: B 218 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8254 (pt) REVERT: B 307 MET cc_start: 0.8452 (tpt) cc_final: 0.8217 (mmm) REVERT: C 218 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8207 (pt) REVERT: C 309 MET cc_start: 0.9141 (mmm) cc_final: 0.8870 (mmm) REVERT: C 439 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9050 (mmtm) REVERT: C 444 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8840 (mm) REVERT: C 455 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9080 (ptmm) REVERT: C 533 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8471 (tpp) REVERT: C 540 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: D 218 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8239 (pt) REVERT: D 355 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9318 (mm) REVERT: D 449 MET cc_start: 0.9172 (pmm) cc_final: 0.8862 (pmm) REVERT: E 206 ASP cc_start: 0.8866 (m-30) cc_final: 0.8614 (m-30) REVERT: E 218 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8215 (pt) REVERT: E 403 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8494 (m) REVERT: F 399 MET cc_start: 0.8666 (tpp) cc_final: 0.8158 (mmm) REVERT: G 115 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8338 (mm) REVERT: G 116 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8393 (p0) REVERT: G 210 MET cc_start: 0.9059 (tpp) cc_final: 0.8769 (tpp) REVERT: G 218 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8270 (pt) REVERT: G 296 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8937 (p0) REVERT: G 315 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7647 (tm-30) outliers start: 210 outliers final: 124 residues processed: 390 average time/residue: 0.3609 time to fit residues: 228.3370 Evaluate side-chains 322 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 175 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 64 GLN Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 4 GLU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 540 TYR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 374 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 524 ILE Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 4.9990 chunk 229 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 33 optimal weight: 70.0000 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 306 optimal weight: 0.8980 chunk 324 optimal weight: 5.9990 chunk 160 optimal weight: 0.0870 chunk 290 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 64 GLN J 56 ASN K 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 353 ASN E 534 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 536 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27854 Z= 0.191 Angle : 0.665 15.454 37676 Z= 0.323 Chirality : 0.040 0.164 4337 Planarity : 0.005 0.062 4780 Dihedral : 12.036 121.680 4020 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.84 % Favored : 94.98 % Rotamer: Outliers : 5.75 % Allowed : 24.38 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % 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: -1.02 (0.15), residues: 3328 helix: -0.18 (0.12), residues: 1923 sheet: -0.70 (0.28), residues: 259 loop : -1.34 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 410 HIS 0.011 0.001 HIS B 225 PHE 0.014 0.001 PHE I 93 TYR 0.024 0.001 TYR D 305 ARG 0.015 0.000 ARG J 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 192 time to evaluate : 3.774 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: H 2 LEU cc_start: 0.6412 (mp) cc_final: 0.5969 (tp) REVERT: H 58 LEU cc_start: 0.8995 (mt) cc_final: 0.8708 (pp) REVERT: H 64 GLN cc_start: 0.2722 (OUTLIER) cc_final: 0.2307 (mm110) REVERT: H 106 ILE cc_start: 0.6583 (pt) cc_final: 0.5724 (pt) REVERT: I 8 ARG cc_start: 0.2143 (tpt170) cc_final: 0.1212 (tpt170) REVERT: I 46 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.5532 (pttm) REVERT: I 64 GLN cc_start: 0.2856 (OUTLIER) cc_final: 0.0523 (tm-30) REVERT: J 1 MET cc_start: 0.4748 (ptm) cc_final: 0.4448 (ptt) REVERT: K 1 MET cc_start: 0.6204 (tpt) cc_final: 0.5956 (tpt) REVERT: K 47 MET cc_start: 0.0571 (mmm) cc_final: -0.0686 (ttt) REVERT: K 71 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5746 (tm) REVERT: L 1 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.4711 (tpt) REVERT: L 47 MET cc_start: 0.1065 (mmt) cc_final: -0.0497 (tmm) REVERT: M 46 LYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4560 (pttm) REVERT: A 218 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8291 (pt) REVERT: A 462 MET cc_start: 0.9150 (mtp) cc_final: 0.8449 (ttm) REVERT: B 128 MET cc_start: 0.8841 (mmm) cc_final: 0.8143 (mtt) REVERT: B 218 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8525 (pt) REVERT: C 218 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8416 (pt) REVERT: C 309 MET cc_start: 0.9092 (mmm) cc_final: 0.8814 (mmm) REVERT: C 439 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.8976 (mmtm) REVERT: C 444 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8761 (mm) REVERT: C 455 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8984 (ptmm) REVERT: C 523 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8910 (p) REVERT: C 533 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8893 (tpp) REVERT: D 218 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8299 (pt) REVERT: D 355 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9300 (mm) REVERT: E 150 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9037 (pt) REVERT: E 206 ASP cc_start: 0.8883 (m-30) cc_final: 0.8592 (m-30) REVERT: E 218 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8725 (pt) REVERT: E 309 MET cc_start: 0.8545 (tpp) cc_final: 0.7951 (tpp) REVERT: F 399 MET cc_start: 0.8490 (tpp) cc_final: 0.8132 (mmm) REVERT: G 115 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8359 (mm) REVERT: G 116 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8433 (p0) REVERT: G 128 MET cc_start: 0.8672 (mmm) cc_final: 0.8389 (mtt) REVERT: G 210 MET cc_start: 0.9032 (tpp) cc_final: 0.8770 (tpp) REVERT: G 218 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8473 (pt) REVERT: G 296 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.9023 (p0) REVERT: G 371 TYR cc_start: 0.8946 (m-80) cc_final: 0.8558 (m-80) REVERT: G 531 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.7691 (tptt) outliers start: 177 outliers final: 99 residues processed: 348 average time/residue: 0.3927 time to fit residues: 220.2390 Evaluate side-chains 302 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 180 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 374 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 437 LEU Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 224 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 165 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 64 GLN J 40 HIS J 56 ASN J 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN B 225 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 27854 Z= 0.357 Angle : 0.730 11.634 37676 Z= 0.362 Chirality : 0.041 0.172 4337 Planarity : 0.006 0.067 4780 Dihedral : 11.591 125.755 3985 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.31 % Favored : 93.63 % Rotamer: Outliers : 6.07 % Allowed : 24.61 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3328 helix: -0.00 (0.12), residues: 1922 sheet: -0.56 (0.32), residues: 224 loop : -1.32 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 410 HIS 0.011 0.002 HIS G 158 PHE 0.023 0.002 PHE F 532 TYR 0.023 0.002 TYR D 305 ARG 0.021 0.001 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 184 time to evaluate : 3.502 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: H 54 ILE cc_start: 0.4918 (mt) cc_final: 0.4628 (mt) REVERT: H 64 GLN cc_start: 0.3215 (OUTLIER) cc_final: 0.2942 (mt0) REVERT: H 106 ILE cc_start: 0.6634 (pt) cc_final: 0.6290 (pt) REVERT: I 8 ARG cc_start: 0.2671 (tpt170) cc_final: 0.1810 (tpt170) REVERT: I 64 GLN cc_start: 0.4167 (OUTLIER) cc_final: 0.3493 (tt0) REVERT: K 1 MET cc_start: 0.6236 (tpt) cc_final: 0.6018 (tpt) REVERT: L 35 ILE cc_start: 0.2821 (OUTLIER) cc_final: 0.2390 (mt) REVERT: M 46 LYS cc_start: 0.4818 (OUTLIER) cc_final: 0.4593 (pttm) REVERT: A 212 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8997 (ttpt) REVERT: B 218 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8652 (pt) REVERT: B 262 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.8977 (pp30) REVERT: B 533 MET cc_start: 0.7111 (ppp) cc_final: 0.6883 (ppp) REVERT: B 543 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6550 (pp) REVERT: C 218 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8696 (pt) REVERT: C 234 MET cc_start: 0.9097 (mtm) cc_final: 0.8875 (mtm) REVERT: C 307 MET cc_start: 0.8817 (tpp) cc_final: 0.8526 (tpp) REVERT: C 309 MET cc_start: 0.9184 (mmm) cc_final: 0.8925 (mmm) REVERT: C 399 MET cc_start: 0.8506 (mmp) cc_final: 0.8254 (mmp) REVERT: C 439 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8976 (mmtm) REVERT: C 444 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8992 (mm) REVERT: C 455 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.9026 (ptmm) REVERT: C 533 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8942 (tpp) REVERT: D 218 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8739 (pt) REVERT: D 355 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9299 (mm) REVERT: D 444 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8910 (mm) REVERT: E 150 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8947 (tm) REVERT: F 198 LYS cc_start: 0.9035 (tppt) cc_final: 0.8802 (tppt) REVERT: F 348 MET cc_start: 0.9251 (mtt) cc_final: 0.9030 (ptp) REVERT: F 410 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8590 (m-90) REVERT: G 115 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8566 (mm) REVERT: G 116 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8498 (p0) REVERT: G 210 MET cc_start: 0.9094 (tpp) cc_final: 0.8854 (tpp) REVERT: G 218 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8460 (pt) REVERT: G 234 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8653 (mpp) REVERT: G 316 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8593 (mt-10) REVERT: G 399 MET cc_start: 0.8181 (mpp) cc_final: 0.7906 (mpp) REVERT: G 410 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8419 (m-90) REVERT: G 531 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.7276 (tptt) outliers start: 187 outliers final: 109 residues processed: 356 average time/residue: 0.3771 time to fit residues: 216.8325 Evaluate side-chains 313 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 179 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 64 GLN Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 543 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 96 ASN I 64 GLN J 56 ASN J 96 ASN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27854 Z= 0.189 Angle : 0.673 15.864 37676 Z= 0.320 Chirality : 0.040 0.176 4337 Planarity : 0.005 0.068 4780 Dihedral : 11.268 124.373 3975 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 4.61 % Allowed : 25.75 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3328 helix: 0.42 (0.13), residues: 1909 sheet: -0.51 (0.31), residues: 224 loop : -1.08 (0.19), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 410 HIS 0.005 0.001 HIS I 40 PHE 0.013 0.001 PHE B 204 TYR 0.031 0.001 TYR C 305 ARG 0.009 0.000 ARG I 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 191 time to evaluate : 3.431 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: H 54 ILE cc_start: 0.4582 (mt) cc_final: 0.4367 (mt) REVERT: I 8 ARG cc_start: 0.2428 (tpt170) cc_final: 0.1611 (tpt170) REVERT: K 1 MET cc_start: 0.6194 (tpt) cc_final: 0.5958 (tpt) REVERT: K 97 GLU cc_start: -0.1323 (OUTLIER) cc_final: -0.1664 (tp30) REVERT: L 35 ILE cc_start: 0.2939 (OUTLIER) cc_final: 0.2500 (mt) REVERT: L 47 MET cc_start: 0.1278 (mmt) cc_final: 0.0520 (tpp) REVERT: A 212 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8932 (ttpt) REVERT: A 462 MET cc_start: 0.9091 (mtp) cc_final: 0.8716 (ttm) REVERT: B 262 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.8940 (pp30) REVERT: B 533 MET cc_start: 0.7226 (ppp) cc_final: 0.6981 (ppp) REVERT: C 234 MET cc_start: 0.9032 (mtm) cc_final: 0.8817 (mtm) REVERT: C 307 MET cc_start: 0.8975 (tpp) cc_final: 0.8620 (tpp) REVERT: C 309 MET cc_start: 0.9229 (mmm) cc_final: 0.8932 (mmm) REVERT: C 444 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8833 (mm) REVERT: C 531 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8318 (mmmt) REVERT: D 150 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8820 (mp) REVERT: D 355 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9209 (mm) REVERT: D 410 TRP cc_start: 0.8715 (OUTLIER) cc_final: 0.8346 (m-90) REVERT: E 136 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.8119 (m90) REVERT: E 150 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8943 (tm) REVERT: E 198 LYS cc_start: 0.8615 (tppt) cc_final: 0.8343 (tppt) REVERT: E 234 MET cc_start: 0.9068 (mtm) cc_final: 0.8799 (mtm) REVERT: E 309 MET cc_start: 0.8717 (tpp) cc_final: 0.8216 (tpp) REVERT: F 198 LYS cc_start: 0.8984 (tppt) cc_final: 0.8711 (tppt) REVERT: F 399 MET cc_start: 0.8662 (tpp) cc_final: 0.8362 (mmm) REVERT: F 410 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.8707 (m-90) REVERT: G 116 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8520 (p0) REVERT: G 210 MET cc_start: 0.9023 (tpp) cc_final: 0.8807 (tpp) REVERT: G 234 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8412 (mpp) REVERT: G 410 TRP cc_start: 0.8678 (OUTLIER) cc_final: 0.8449 (m-90) REVERT: G 531 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.7463 (tptt) outliers start: 142 outliers final: 98 residues processed: 318 average time/residue: 0.3733 time to fit residues: 194.0607 Evaluate side-chains 297 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 183 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 462 MET Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27854 Z= 0.277 Angle : 0.704 13.243 37676 Z= 0.337 Chirality : 0.040 0.178 4337 Planarity : 0.005 0.069 4780 Dihedral : 10.700 126.056 3942 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.95 % Favored : 93.99 % Rotamer: Outliers : 4.74 % Allowed : 26.30 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3328 helix: 0.46 (0.12), residues: 1941 sheet: -0.43 (0.32), residues: 224 loop : -1.17 (0.19), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 410 HIS 0.007 0.001 HIS G 158 PHE 0.018 0.001 PHE F 532 TYR 0.029 0.002 TYR C 305 ARG 0.004 0.000 ARG E 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 189 time to evaluate : 3.139 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: H 68 LEU cc_start: 0.7741 (pt) cc_final: 0.7334 (mt) REVERT: K 1 MET cc_start: 0.6228 (tpt) cc_final: 0.5999 (tpt) REVERT: K 47 MET cc_start: 0.0902 (mmm) cc_final: -0.0253 (ptm) REVERT: K 97 GLU cc_start: -0.1260 (OUTLIER) cc_final: -0.1577 (tp30) REVERT: L 35 ILE cc_start: 0.2875 (OUTLIER) cc_final: 0.2446 (mt) REVERT: L 47 MET cc_start: 0.1383 (mmt) cc_final: 0.0576 (tpp) REVERT: A 212 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8966 (ttpt) REVERT: A 462 MET cc_start: 0.9184 (mtp) cc_final: 0.8772 (ttm) REVERT: B 262 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.8982 (pp30) REVERT: B 533 MET cc_start: 0.7175 (ppp) cc_final: 0.6726 (ppp) REVERT: C 234 MET cc_start: 0.9097 (mtm) cc_final: 0.8823 (mtm) REVERT: C 309 MET cc_start: 0.9235 (mmm) cc_final: 0.8944 (mmm) REVERT: C 444 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8960 (mm) REVERT: C 531 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8326 (mmmm) REVERT: D 150 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8955 (mm) REVERT: D 355 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9283 (mm) REVERT: D 410 TRP cc_start: 0.8754 (OUTLIER) cc_final: 0.8371 (m-90) REVERT: E 150 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8953 (pt) REVERT: E 198 LYS cc_start: 0.8629 (tppt) cc_final: 0.8251 (tppt) REVERT: E 234 MET cc_start: 0.9103 (mtm) cc_final: 0.8842 (mtm) REVERT: E 335 MET cc_start: 0.9179 (mtm) cc_final: 0.8967 (mtt) REVERT: E 533 MET cc_start: 0.7962 (pmm) cc_final: 0.7701 (pmm) REVERT: F 198 LYS cc_start: 0.8944 (tppt) cc_final: 0.8675 (tppt) REVERT: F 348 MET cc_start: 0.9341 (mtt) cc_final: 0.9118 (ptp) REVERT: F 399 MET cc_start: 0.8791 (tpp) cc_final: 0.8502 (mmm) REVERT: F 410 TRP cc_start: 0.9026 (OUTLIER) cc_final: 0.8716 (m-90) REVERT: G 210 MET cc_start: 0.9059 (tpp) cc_final: 0.8846 (tpp) REVERT: G 234 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8480 (mpp) REVERT: G 379 GLN cc_start: 0.9533 (OUTLIER) cc_final: 0.9302 (tm-30) REVERT: G 531 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.7300 (tptt) outliers start: 146 outliers final: 106 residues processed: 322 average time/residue: 0.3600 time to fit residues: 188.7937 Evaluate side-chains 303 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 183 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 77 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 373 SER Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 374 LEU Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 0.5980 chunk 220 optimal weight: 0.9990 chunk 160 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 HIS H 64 GLN I 56 ASN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27854 Z= 0.181 Angle : 0.687 13.480 37676 Z= 0.321 Chirality : 0.040 0.180 4337 Planarity : 0.005 0.068 4780 Dihedral : 10.006 87.049 3932 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.74 % Rotamer: Outliers : 3.80 % Allowed : 26.82 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3328 helix: 0.65 (0.13), residues: 1944 sheet: -0.36 (0.32), residues: 224 loop : -1.03 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 410 HIS 0.004 0.001 HIS E 536 PHE 0.034 0.001 PHE I 36 TYR 0.030 0.001 TYR C 305 ARG 0.005 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 192 time to evaluate : 3.168 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: H 58 LEU cc_start: 0.9069 (mp) cc_final: 0.8650 (pt) REVERT: K 1 MET cc_start: 0.6200 (tpt) cc_final: 0.5968 (tpt) REVERT: K 47 MET cc_start: 0.0849 (mmm) cc_final: -0.0265 (ptm) REVERT: K 97 GLU cc_start: -0.1235 (OUTLIER) cc_final: -0.1506 (tp30) REVERT: L 35 ILE cc_start: 0.2873 (OUTLIER) cc_final: 0.2451 (mt) REVERT: L 47 MET cc_start: 0.1024 (mmt) cc_final: 0.0248 (tpp) REVERT: A 212 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8852 (ttpt) REVERT: A 462 MET cc_start: 0.9104 (mtp) cc_final: 0.8745 (ttm) REVERT: B 262 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8961 (pp30) REVERT: B 348 MET cc_start: 0.9616 (ppp) cc_final: 0.9301 (ppp) REVERT: B 449 MET cc_start: 0.9236 (pmm) cc_final: 0.8963 (ppp) REVERT: B 533 MET cc_start: 0.6993 (ppp) cc_final: 0.6614 (ppp) REVERT: C 234 MET cc_start: 0.9077 (mtm) cc_final: 0.8813 (mtm) REVERT: C 444 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8827 (mm) REVERT: C 531 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8113 (mmmt) REVERT: D 150 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9026 (mm) REVERT: D 355 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9259 (mm) REVERT: D 410 TRP cc_start: 0.8635 (OUTLIER) cc_final: 0.8400 (m-90) REVERT: E 198 LYS cc_start: 0.8590 (tppt) cc_final: 0.8270 (tppt) REVERT: E 234 MET cc_start: 0.9035 (mtm) cc_final: 0.8777 (mtm) REVERT: F 198 LYS cc_start: 0.8901 (tppt) cc_final: 0.8658 (tppt) REVERT: F 348 MET cc_start: 0.9290 (mtt) cc_final: 0.9053 (ptp) REVERT: F 399 MET cc_start: 0.8712 (tpp) cc_final: 0.8508 (mmm) REVERT: F 410 TRP cc_start: 0.9004 (OUTLIER) cc_final: 0.8728 (m-90) REVERT: G 531 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.7541 (tptt) outliers start: 117 outliers final: 89 residues processed: 298 average time/residue: 0.4135 time to fit residues: 202.9454 Evaluate side-chains 290 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 190 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 301 optimal weight: 0.0010 chunk 181 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.7720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27854 Z= 0.215 Angle : 0.705 14.940 37676 Z= 0.328 Chirality : 0.040 0.175 4337 Planarity : 0.005 0.069 4780 Dihedral : 9.666 86.092 3928 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 3.96 % Allowed : 26.85 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3328 helix: 0.69 (0.13), residues: 1944 sheet: -0.29 (0.32), residues: 224 loop : -1.03 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 410 HIS 0.004 0.001 HIS G 158 PHE 0.016 0.001 PHE L 74 TYR 0.031 0.001 TYR C 305 ARG 0.006 0.000 ARG H 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 186 time to evaluate : 3.404 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: H 62 ARG cc_start: 0.6231 (ttt90) cc_final: 0.4560 (ptm-80) REVERT: H 68 LEU cc_start: 0.7545 (pt) cc_final: 0.7190 (mt) REVERT: K 1 MET cc_start: 0.6236 (tpt) cc_final: 0.5994 (tpt) REVERT: K 97 GLU cc_start: -0.1214 (OUTLIER) cc_final: -0.1488 (tp30) REVERT: L 35 ILE cc_start: 0.2709 (OUTLIER) cc_final: 0.2303 (mt) REVERT: L 47 MET cc_start: 0.1049 (mmt) cc_final: 0.0270 (tpp) REVERT: A 212 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8865 (ttpt) REVERT: A 462 MET cc_start: 0.9159 (mtp) cc_final: 0.8769 (ttm) REVERT: B 253 VAL cc_start: 0.9664 (OUTLIER) cc_final: 0.9446 (t) REVERT: B 262 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8974 (pp30) REVERT: B 348 MET cc_start: 0.9593 (ppp) cc_final: 0.9296 (ppp) REVERT: B 449 MET cc_start: 0.9268 (pmm) cc_final: 0.9001 (ppp) REVERT: B 533 MET cc_start: 0.7127 (ppp) cc_final: 0.6637 (ppp) REVERT: C 234 MET cc_start: 0.9085 (mtm) cc_final: 0.8812 (mtm) REVERT: C 444 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8900 (mm) REVERT: C 531 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8436 (mmmm) REVERT: D 150 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9012 (mm) REVERT: D 355 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9268 (mm) REVERT: D 410 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.8434 (m-90) REVERT: E 198 LYS cc_start: 0.8670 (tppt) cc_final: 0.8305 (tppt) REVERT: E 234 MET cc_start: 0.9063 (mtm) cc_final: 0.8765 (mtm) REVERT: F 198 LYS cc_start: 0.8916 (tppt) cc_final: 0.8642 (tppt) REVERT: F 348 MET cc_start: 0.9313 (mtt) cc_final: 0.9049 (ptp) REVERT: F 410 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.8658 (m-90) REVERT: G 379 GLN cc_start: 0.9536 (OUTLIER) cc_final: 0.9302 (tm-30) outliers start: 122 outliers final: 93 residues processed: 299 average time/residue: 0.3832 time to fit residues: 184.6546 Evaluate side-chains 289 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 184 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 410 TRP Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 225 HIS Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 7.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 151 optimal weight: 0.0060 chunk 221 optimal weight: 6.9990 chunk 334 optimal weight: 0.0010 chunk 308 optimal weight: 0.7980 chunk 266 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27854 Z= 0.167 Angle : 0.721 14.464 37676 Z= 0.329 Chirality : 0.040 0.190 4337 Planarity : 0.005 0.067 4780 Dihedral : 9.472 85.908 3928 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 3.08 % Allowed : 27.86 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3328 helix: 0.72 (0.13), residues: 1944 sheet: -0.25 (0.32), residues: 224 loop : -0.86 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 410 HIS 0.004 0.001 HIS B 536 PHE 0.015 0.001 PHE H 110 TYR 0.027 0.001 TYR C 305 ARG 0.011 0.000 ARG I 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 194 time to evaluate : 3.139 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: H 36 PHE cc_start: 0.6529 (m-80) cc_final: 0.5960 (m-80) REVERT: H 62 ARG cc_start: 0.6187 (ttt90) cc_final: 0.4436 (ptm-80) REVERT: H 68 LEU cc_start: 0.7599 (pt) cc_final: 0.7203 (mt) REVERT: K 1 MET cc_start: 0.6199 (tpt) cc_final: 0.5930 (tpt) REVERT: K 47 MET cc_start: 0.0836 (mmm) cc_final: -0.0213 (ptm) REVERT: K 97 GLU cc_start: -0.1354 (OUTLIER) cc_final: -0.1648 (tp30) REVERT: L 35 ILE cc_start: 0.2987 (OUTLIER) cc_final: 0.2591 (mt) REVERT: L 47 MET cc_start: 0.0997 (mmt) cc_final: 0.0244 (tpp) REVERT: A 212 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8790 (ttpt) REVERT: A 462 MET cc_start: 0.9057 (mtp) cc_final: 0.8698 (ttm) REVERT: B 253 VAL cc_start: 0.9633 (OUTLIER) cc_final: 0.9432 (t) REVERT: B 262 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.9080 (tt0) REVERT: B 307 MET cc_start: 0.8625 (mmm) cc_final: 0.8218 (mmm) REVERT: B 348 MET cc_start: 0.9567 (ppp) cc_final: 0.9262 (ppp) REVERT: B 533 MET cc_start: 0.6808 (ppp) cc_final: 0.6452 (ppp) REVERT: C 234 MET cc_start: 0.9010 (mtm) cc_final: 0.8767 (mtm) REVERT: C 307 MET cc_start: 0.8846 (tpp) cc_final: 0.8562 (tpp) REVERT: C 444 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8605 (mm) REVERT: C 462 MET cc_start: 0.9162 (mtp) cc_final: 0.8577 (ttp) REVERT: C 531 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8122 (mmmm) REVERT: D 150 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8756 (mp) REVERT: D 355 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9222 (mm) REVERT: D 393 LEU cc_start: 0.9209 (pp) cc_final: 0.8909 (pp) REVERT: E 198 LYS cc_start: 0.8637 (tppt) cc_final: 0.8305 (tppt) REVERT: E 234 MET cc_start: 0.9018 (mtm) cc_final: 0.8737 (mtm) REVERT: F 198 LYS cc_start: 0.8936 (tppt) cc_final: 0.8667 (tppt) REVERT: F 348 MET cc_start: 0.9309 (mtt) cc_final: 0.9050 (ptp) REVERT: G 210 MET cc_start: 0.8974 (tpp) cc_final: 0.8624 (tpp) REVERT: G 234 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8803 (mtm) REVERT: G 348 MET cc_start: 0.9532 (ptp) cc_final: 0.9239 (ptp) REVERT: G 379 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.9310 (tm-30) outliers start: 95 outliers final: 74 residues processed: 282 average time/residue: 0.3897 time to fit residues: 177.0138 Evaluate side-chains 272 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 187 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 542 SER Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 536 HIS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 316 GLU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 531 LYS Chi-restraints excluded: chain G residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 274 optimal weight: 10.0000 chunk 33 optimal weight: 50.0000 chunk 49 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN A 237 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN B 237 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 534 GLN ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 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 = 0.3600 r_free = 0.3600 target = 0.081802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.045744 restraints weight = 161206.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044132 restraints weight = 135845.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.044358 restraints weight = 110456.184| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.7983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27854 Z= 0.282 Angle : 0.731 13.228 37676 Z= 0.344 Chirality : 0.041 0.220 4337 Planarity : 0.005 0.069 4780 Dihedral : 9.401 80.482 3928 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.71 % Rotamer: Outliers : 3.28 % Allowed : 27.92 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.72 % Cis-general : 0.00 % Twisted Proline : 4.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3328 helix: 0.69 (0.13), residues: 1958 sheet: -0.09 (0.32), residues: 224 loop : -0.96 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 410 HIS 0.007 0.001 HIS G 158 PHE 0.016 0.001 PHE L 74 TYR 0.031 0.002 TYR C 305 ARG 0.019 0.000 ARG I 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5866.95 seconds wall clock time: 106 minutes 47.24 seconds (6407.24 seconds total)