Starting phenix.real_space_refine on Sat Apr 13 01:34:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/04_2024/8jo0_36451_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/04_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_36451/04_2024/8jo0_36451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/04_2024/8jo0_36451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/04_2024/8jo0_36451_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo0_36451/04_2024/8jo0_36451_updated.pdb" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 14.30, per 1000 atoms: 0.52 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: 10.82 Conformation dependent library (CDL) restraints added in 4.6 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... running ksdssp... Secondary structure from input PDB file: 172 helices and 10 sheets defined 50.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 31.56 Creating SS restraints... Processing helix chain 'H' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU H 10 " --> pdb=" O GLU H 6 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 32 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 40 through 45 Processing helix chain 'H' and resid 50 through 64 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) Processing helix chain 'H' and resid 72 through 75 No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 81 through 95 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) Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'I' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU I 10 " --> pdb=" O GLU I 6 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR I 15 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG I 16 " --> pdb=" O THR I 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 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 40 through 45 Processing helix chain 'I' and resid 50 through 64 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) Processing helix chain 'I' and resid 72 through 75 No H-bonds generated for 'chain 'I' and resid 72 through 75' Processing helix chain 'I' and resid 81 through 95 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) Processing helix chain 'I' and resid 100 through 104 Processing helix chain 'I' and resid 107 through 109 No H-bonds generated for 'chain 'I' and resid 107 through 109' Processing helix chain 'J' and resid 4 through 17 removed outlier: 3.629A pdb=" N LEU J 10 " --> pdb=" O GLU J 6 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG J 16 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 32 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 40 through 45 Processing helix chain 'J' and resid 50 through 64 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) Processing helix chain 'J' and resid 72 through 75 No H-bonds generated for 'chain 'J' and resid 72 through 75' Processing helix chain 'J' and resid 81 through 95 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) Processing helix chain 'J' and resid 100 through 104 Processing helix chain 'J' and resid 107 through 109 No H-bonds generated for 'chain 'J' and resid 107 through 109' Processing helix chain 'K' and resid 4 through 17 removed outlier: 3.631A pdb=" N LEU K 10 " --> pdb=" O GLU K 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG K 16 " --> pdb=" O THR K 12 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 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 40 through 45 Processing helix chain 'K' and resid 50 through 64 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) Processing helix chain 'K' and resid 72 through 75 No H-bonds generated for 'chain 'K' and resid 72 through 75' Processing helix chain 'K' and resid 81 through 95 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 4 through 17 removed outlier: 3.629A pdb=" N LEU L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR L 15 " --> pdb=" O SER L 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG L 16 " --> pdb=" O THR L 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 32 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 40 through 45 Processing helix chain 'L' and resid 50 through 64 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) Processing helix chain 'L' and resid 72 through 75 No H-bonds generated for 'chain 'L' and resid 72 through 75' Processing helix chain 'L' and resid 81 through 95 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 4 through 17 removed outlier: 3.629A pdb=" N LEU M 10 " --> pdb=" O GLU M 6 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG M 16 " --> pdb=" O THR M 12 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 32 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 40 through 45 Processing helix chain 'M' and resid 50 through 63 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) Processing helix chain 'M' and resid 72 through 75 No H-bonds generated for 'chain 'M' and resid 72 through 75' Processing helix chain 'M' and resid 81 through 95 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 114 through 121 Processing helix chain 'A' and resid 134 through 145 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 165 through 172 Processing helix chain 'A' and resid 199 through 211 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 228 through 238 removed outlier: 3.509A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 295 through 305 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 313 through 326 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 330 through 334 Processing helix chain 'A' and resid 345 through 363 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 375 through 383 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) Processing helix chain 'A' and resid 387 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 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 458 through 465 removed outlier: 4.193A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 485 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) Processing helix chain 'A' and resid 537 through 540 No H-bonds generated for 'chain 'A' and resid 537 through 540' Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 134 through 147 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) removed outlier: 3.578A pdb=" N MET B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.516A pdb=" N SER B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 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 228 through 241 removed outlier: 3.511A pdb=" N ALA B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE B 240 " --> pdb=" O CYS B 236 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 295 through 305 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 313 through 325 Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.610A pdb=" N CYS B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 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 359 through 363 removed outlier: 4.302A pdb=" N VAL B 363 " --> pdb=" O GLY B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 363' Processing helix chain 'B' and resid 375 through 383 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) Processing helix chain 'B' and resid 387 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 411 Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.565A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 437 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.954A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 486 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 534 through 541 removed outlier: 5.072A pdb=" N LYS B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 541 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 134 through 145 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 165 through 172 Processing helix chain 'C' and resid 199 through 211 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 228 through 241 removed outlier: 3.511A pdb=" N ALA C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE C 240 " --> pdb=" O CYS C 236 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 263 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 295 through 305 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 313 through 325 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 330 through 340 Processing helix chain 'C' and resid 345 through 363 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 375 through 383 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) Processing helix chain 'C' and resid 387 through 398 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) removed outlier: 5.156A pdb=" N VAL C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 428 through 439 removed outlier: 3.564A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 437 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 465 removed outlier: 4.147A pdb=" N LEU C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 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 537 through 540 No H-bonds generated for 'chain 'C' and resid 537 through 540' Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 134 through 145 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 165 through 172 Processing helix chain 'D' and resid 199 through 211 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 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 228 through 238 removed outlier: 3.511A pdb=" N ALA D 238 " --> pdb=" O MET D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 Processing helix chain 'D' and resid 295 through 305 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 313 through 325 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 330 through 337 Processing helix chain 'D' and resid 345 through 356 removed outlier: 4.086A pdb=" N GLN D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 356 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 4.306A pdb=" N VAL D 363 " --> pdb=" O GLY D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 363' Processing helix chain 'D' and resid 374 through 383 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) Processing helix chain 'D' and resid 387 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 411 Processing helix chain 'D' and resid 425 through 439 removed outlier: 4.054A pdb=" N ASP D 428 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 437 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 465 removed outlier: 4.170A pdb=" N LEU D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 485 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) Processing helix chain 'D' and resid 534 through 540 removed outlier: 5.562A pdb=" N LYS D 538 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 121 Processing helix chain 'E' and resid 134 through 145 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 165 through 175 removed outlier: 3.639A pdb=" N SER E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 211 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 228 through 241 removed outlier: 3.511A pdb=" N ALA E 238 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE E 240 " --> pdb=" O CYS E 236 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP E 241 " --> pdb=" O ASN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 295 through 305 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 313 through 325 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 330 through 334 Processing helix chain 'E' and resid 345 through 363 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 374 through 383 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) Processing helix chain 'E' and resid 387 through 397 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) removed outlier: 3.533A pdb=" N VAL E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 411 Processing helix chain 'E' and resid 425 through 427 No H-bonds generated for 'chain 'E' and resid 425 through 427' Processing helix chain 'E' and resid 429 through 439 Processing helix chain 'E' and resid 458 through 467 Processing helix chain 'E' and resid 470 through 484 removed outlier: 4.275A pdb=" N ALA E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'F' and resid 114 through 121 Processing helix chain 'F' and resid 137 through 147 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) removed outlier: 3.584A pdb=" N MET F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 172 Processing helix chain 'F' and resid 199 through 211 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 228 through 241 removed outlier: 3.508A pdb=" N ALA F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE F 240 " --> pdb=" O CYS F 236 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASP F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 295 through 304 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 313 through 326 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 339 Processing helix chain 'F' and resid 345 through 363 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 375 through 383 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) Processing helix chain 'F' and resid 387 through 394 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 426 through 439 removed outlier: 3.946A pdb=" N LEU F 437 " --> pdb=" O LEU F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 467 Processing helix chain 'F' and resid 470 through 482 removed outlier: 3.961A pdb=" N ALA F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'G' and resid 114 through 121 Processing helix chain 'G' and resid 134 through 145 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 165 through 172 Processing helix chain 'G' and resid 199 through 211 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 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'G' and resid 228 through 238 removed outlier: 3.511A pdb=" N ALA G 238 " --> pdb=" O MET G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 263 Processing helix chain 'G' and resid 276 through 280 Processing helix chain 'G' and resid 295 through 305 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 313 through 326 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 330 through 339 removed outlier: 3.641A pdb=" N PHE G 336 " --> pdb=" O THR G 332 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER G 339 " --> pdb=" O MET G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 Processing helix chain 'G' and resid 360 through 363 No H-bonds generated for 'chain 'G' and resid 360 through 363' Processing helix chain 'G' and resid 374 through 383 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) Processing helix chain 'G' and resid 387 through 394 Processing helix chain 'G' and resid 407 through 411 Processing helix chain 'G' and resid 427 through 442 removed outlier: 3.565A pdb=" N LYS G 435 " --> pdb=" O ASP G 432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU G 437 " --> pdb=" O LEU G 434 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 440 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY G 441 " --> pdb=" O SER G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 467 removed outlier: 4.262A pdb=" N LEU G 464 " --> pdb=" O ILE G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 485 Processing helix chain 'G' and resid 534 through 542 removed outlier: 5.540A pdb=" N LYS G 538 " --> pdb=" O LEU G 535 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP G 541 " --> pdb=" O LYS G 538 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 285 through 290 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) removed outlier: 6.876A pdb=" N CYS A 268 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU A 157 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 270 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY A 159 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR A 272 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 444 through 447 Processing sheet with id= C, first strand: chain 'B' and resid 285 through 290 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) removed outlier: 6.876A pdb=" N CYS B 268 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU B 157 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 270 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY B 159 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR B 272 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.482A pdb=" N PHE C 154 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS C 268 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU C 157 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 270 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU C 269 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE C 247 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR C 271 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE C 249 " --> pdb=" O THR C 271 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 285 through 290 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) removed outlier: 6.876A pdb=" N CYS D 268 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU D 157 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 270 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY D 159 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR D 272 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU D 269 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE D 247 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR D 271 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE D 249 " --> pdb=" O THR D 271 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'E' and resid 285 through 290 removed outlier: 6.481A pdb=" N PHE E 154 " --> pdb=" O GLU E 286 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 288 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE E 156 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 290 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N HIS E 158 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS E 268 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU E 157 " --> pdb=" O CYS E 268 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL E 270 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY E 159 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR E 272 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU E 269 " --> pdb=" O THR E 245 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE E 247 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR E 271 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE E 249 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER E 186 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL E 248 " --> pdb=" O SER E 186 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 445 through 447 Processing sheet with id= H, first strand: chain 'F' and resid 284 through 287 removed outlier: 6.875A pdb=" N CYS F 268 " --> pdb=" O LEU F 155 " (cutoff:3.500A) 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= I, first strand: chain 'F' and resid 445 through 447 Processing sheet with id= J, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.659A pdb=" N PHE G 154 " --> pdb=" O GLU G 286 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS G 268 " --> pdb=" O LEU G 155 " (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) 804 hydrogen bonds defined for protein. 2226 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: 6.56 Time building geometry restraints manager: 11.74 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: 151 2.43 - 3.05: 20259 3.05 - 3.67: 42056 3.67 - 4.28: 64789 4.28 - 4.90: 99332 Nonbonded interactions: 226587 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 226582 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.020 Check model and map are aligned: 0.360 Set scattering table: 0.260 Process input model: 67.110 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.150 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.350 ------------------------------------------------------------------------------- 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= 0.601 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 : 2.597 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: 0.3961 time to fit residues: 645.1849 Evaluate side-chains 482 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 229 time to evaluate : 3.570 ------------------------------------------------------------------------------- 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: 0.9980 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 171 optimal weight: 0.0050 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 20.0000 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 244 ASN B 353 ASN B 471 GLN B 482 GLN C 123 ASN C 237 ASN C 244 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 482 GLN C 534 GLN 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 123 ASN E 225 HIS E 237 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 ASN G 283 GLN G 329 ASN G 350 GLN G 458 HIS G 466 HIS G 471 GLN G 475 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27854 Z= 0.250 Angle : 0.810 14.071 37676 Z= 0.403 Chirality : 0.045 0.188 4337 Planarity : 0.007 0.101 4780 Dihedral : 15.984 116.896 4408 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.11 % Favored : 94.44 % Rotamer: Outliers : 9.29 % Allowed : 23.86 % Favored : 66.85 % 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: -3.00 (0.13), residues: 3328 helix: -1.98 (0.11), residues: 1743 sheet: -0.84 (0.30), residues: 259 loop : -2.03 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 410 HIS 0.015 0.002 HIS F 466 PHE 0.021 0.002 PHE I 93 TYR 0.032 0.002 TYR D 305 ARG 0.012 0.001 ARG A 525 *********************** 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 541 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 255 time to evaluate : 3.208 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: I 17 LEU cc_start: 0.8406 (tt) cc_final: 0.8197 (mm) REVERT: I 106 ILE cc_start: 0.4377 (mm) cc_final: 0.4045 (mm) REVERT: K 46 LYS cc_start: 0.5542 (OUTLIER) cc_final: 0.4428 (pttm) REVERT: K 64 GLN cc_start: 0.3506 (OUTLIER) cc_final: 0.1475 (pp30) REVERT: K 71 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4726 (tm) REVERT: L 68 LEU cc_start: -0.1049 (OUTLIER) cc_final: -0.1282 (pp) REVERT: M 47 MET cc_start: 0.4227 (mmm) cc_final: 0.2533 (tmm) REVERT: A 203 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9415 (tt) REVERT: A 218 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.7767 (pt) REVERT: A 228 SER cc_start: 0.9305 (m) cc_final: 0.9004 (p) REVERT: A 296 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8971 (p0) REVERT: A 410 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.8553 (m-90) REVERT: A 437 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8958 (mt) REVERT: B 128 MET cc_start: 0.8479 (mmp) cc_final: 0.8188 (tpp) REVERT: B 218 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.7896 (pt) REVERT: B 307 MET cc_start: 0.7867 (tpt) cc_final: 0.7622 (mmm) REVERT: B 398 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 410 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.8574 (m-90) REVERT: C 317 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: C 335 MET cc_start: 0.9344 (mtt) cc_final: 0.9039 (mtt) REVERT: C 350 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: C 410 TRP cc_start: 0.9184 (OUTLIER) cc_final: 0.8862 (m-90) REVERT: C 443 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8527 (pt) REVERT: C 444 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8543 (mm) REVERT: C 445 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7623 (t) REVERT: C 455 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9004 (ptmm) REVERT: C 531 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7561 (mmmt) REVERT: C 533 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8781 (tpp) REVERT: D 218 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7499 (pt) REVERT: D 351 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9161 (mt) REVERT: D 355 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9277 (mm) REVERT: D 410 TRP cc_start: 0.8932 (OUTLIER) cc_final: 0.8645 (m-90) REVERT: F 210 MET cc_start: 0.8914 (tpp) cc_final: 0.8702 (tpp) REVERT: F 269 LEU cc_start: 0.9030 (tp) cc_final: 0.8791 (tp) REVERT: F 399 MET cc_start: 0.8470 (tpp) cc_final: 0.8223 (mmm) REVERT: G 116 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8496 (p0) REVERT: G 128 MET cc_start: 0.8774 (mmm) cc_final: 0.8420 (mmm) REVERT: G 210 MET cc_start: 0.8910 (tpp) cc_final: 0.8629 (tpp) REVERT: G 218 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8264 (pt) REVERT: G 315 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: G 410 TRP cc_start: 0.9140 (OUTLIER) cc_final: 0.8933 (m-90) REVERT: G 531 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.7167 (tptt) outliers start: 286 outliers final: 114 residues processed: 514 average time/residue: 0.3715 time to fit residues: 307.7589 Evaluate side-chains 340 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 196 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 35 ILE 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 77 TYR 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 68 LEU 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 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 71 LEU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 381 CYS 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 426 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 524 ILE 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 295 ILE Chi-restraints excluded: chain B residue 316 GLU 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 410 TRP 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 157 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 303 GLU 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 350 GLN 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 410 TRP 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 485 LEU 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 533 MET Chi-restraints excluded: chain D residue 149 ASP 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 351 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 381 CYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 486 GLU 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 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 248 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 285 CYS Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 381 CYS 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 485 LEU Chi-restraints excluded: chain E residue 522 THR 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 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 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 397 VAL Chi-restraints excluded: chain G residue 398 VAL 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 410 TRP 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: 0.5980 chunk 94 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 84 optimal weight: 0.0770 chunk 305 optimal weight: 0.4980 chunk 330 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN I 56 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN B 123 ASN B 283 GLN B 353 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 HIS E 113 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 GLN ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 ASN ** F 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27854 Z= 0.207 Angle : 0.694 18.703 37676 Z= 0.339 Chirality : 0.041 0.193 4337 Planarity : 0.006 0.066 4780 Dihedral : 13.002 121.624 4069 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.41 % Favored : 94.29 % Rotamer: Outliers : 6.43 % Allowed : 23.90 % Favored : 69.68 % 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: -1.82 (0.14), residues: 3328 helix: -1.03 (0.12), residues: 1811 sheet: -0.58 (0.30), residues: 259 loop : -1.38 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 410 HIS 0.010 0.001 HIS E 536 PHE 0.012 0.001 PHE B 156 TYR 0.026 0.001 TYR D 305 ARG 0.008 0.000 ARG F 133 *********************** 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 419 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 221 time to evaluate : 3.017 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: I 42 GLU cc_start: 0.6565 (tm-30) cc_final: 0.5711 (pt0) REVERT: K 46 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4369 (pttm) REVERT: K 71 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4764 (tm) REVERT: L 1 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.4788 (tpt) REVERT: L 35 ILE cc_start: 0.3206 (OUTLIER) cc_final: 0.2547 (mt) REVERT: L 68 LEU cc_start: -0.1153 (OUTLIER) cc_final: -0.1398 (pp) REVERT: M 46 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4313 (pttm) REVERT: M 47 MET cc_start: 0.4089 (mmm) cc_final: 0.2442 (tmm) REVERT: A 218 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7891 (pt) REVERT: A 228 SER cc_start: 0.9319 (m) cc_final: 0.9057 (p) REVERT: A 296 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8942 (p0) REVERT: A 410 TRP cc_start: 0.9014 (OUTLIER) cc_final: 0.8623 (m-90) REVERT: A 449 MET cc_start: 0.9007 (pmm) cc_final: 0.8777 (pmm) REVERT: A 462 MET cc_start: 0.9056 (mtp) cc_final: 0.8214 (ttm) REVERT: B 128 MET cc_start: 0.8750 (mmp) cc_final: 0.8478 (tpp) REVERT: B 218 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8219 (pt) REVERT: B 410 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.8572 (m-90) REVERT: B 449 MET cc_start: 0.9095 (pmm) cc_final: 0.8891 (pmm) REVERT: C 218 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8047 (pt) REVERT: C 262 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.9067 (tt0) REVERT: C 444 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8569 (mm) REVERT: C 455 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9141 (ptmm) REVERT: C 533 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8782 (tpp) REVERT: D 218 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (pt) REVERT: D 351 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9277 (mt) REVERT: D 355 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9269 (mm) REVERT: D 410 TRP cc_start: 0.8937 (OUTLIER) cc_final: 0.8620 (m-90) REVERT: D 449 MET cc_start: 0.9119 (pmm) cc_final: 0.8811 (pmm) REVERT: E 218 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8295 (pt) REVERT: E 228 SER cc_start: 0.9476 (OUTLIER) cc_final: 0.9139 (p) REVERT: F 269 LEU cc_start: 0.9023 (tp) cc_final: 0.8796 (tp) REVERT: F 399 MET cc_start: 0.8574 (tpp) cc_final: 0.8353 (mmm) REVERT: G 116 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8471 (p0) REVERT: G 128 MET cc_start: 0.8695 (mmm) cc_final: 0.8448 (mmm) REVERT: G 210 MET cc_start: 0.8993 (tpp) cc_final: 0.8709 (tpp) REVERT: G 218 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8112 (pt) REVERT: G 410 TRP cc_start: 0.9131 (OUTLIER) cc_final: 0.8843 (m-90) REVERT: G 449 MET cc_start: 0.9003 (pmm) cc_final: 0.8762 (pmm) REVERT: G 531 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.7376 (tptt) outliers start: 198 outliers final: 98 residues processed: 403 average time/residue: 0.4102 time to fit residues: 268.9544 Evaluate side-chains 323 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 199 time to evaluate : 3.220 ------------------------------------------------------------------------------- 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 95 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 2 LEU 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 77 TYR 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 1 MET Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 150 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 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 410 TRP Chi-restraints excluded: chain B residue 524 ILE 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 262 GLN 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 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 460 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 D residue 218 LEU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 381 CYS 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 485 LEU Chi-restraints excluded: chain E residue 524 ILE 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 319 LEU 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 381 CYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 416 VAL 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 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 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 393 LEU 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 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: 0.5980 chunk 229 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 33 optimal weight: 80.0000 chunk 145 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 56 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN ** 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 352 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27854 Z= 0.182 Angle : 0.649 15.912 37676 Z= 0.314 Chirality : 0.040 0.219 4337 Planarity : 0.005 0.062 4780 Dihedral : 11.995 124.151 4015 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.69 % Favored : 95.07 % Rotamer: Outliers : 5.58 % Allowed : 24.19 % Favored : 70.23 % 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: -1.17 (0.15), residues: 3328 helix: -0.48 (0.12), residues: 1818 sheet: -0.20 (0.31), residues: 259 loop : -1.14 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 410 HIS 0.012 0.001 HIS B 225 PHE 0.012 0.001 PHE H 74 TYR 0.020 0.001 TYR D 305 ARG 0.004 0.000 ARG I 59 *********************** 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 382 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 210 time to evaluate : 3.449 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: H 2 LEU cc_start: 0.6608 (mp) cc_final: 0.6174 (tp) REVERT: H 63 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6766 (mpp80) REVERT: I 8 ARG cc_start: 0.2268 (tpt170) cc_final: 0.1381 (tpt170) REVERT: K 46 LYS cc_start: 0.5365 (OUTLIER) cc_final: 0.4454 (pttm) REVERT: K 71 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4496 (tp) REVERT: L 1 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.4609 (tpt) REVERT: L 47 MET cc_start: 0.0866 (mmt) cc_final: -0.0787 (tmm) REVERT: M 46 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4465 (pttm) REVERT: A 212 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8803 (ttpt) REVERT: A 218 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8203 (pt) REVERT: A 228 SER cc_start: 0.9332 (m) cc_final: 0.9087 (p) REVERT: A 296 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8977 (p0) REVERT: A 410 TRP cc_start: 0.8977 (OUTLIER) cc_final: 0.8620 (m-90) REVERT: A 462 MET cc_start: 0.9111 (mtp) cc_final: 0.8364 (ttp) REVERT: B 128 MET cc_start: 0.8824 (mmp) cc_final: 0.8608 (tpp) REVERT: B 218 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8351 (pt) REVERT: B 410 TRP cc_start: 0.8938 (OUTLIER) cc_final: 0.8655 (m-90) REVERT: B 449 MET cc_start: 0.9165 (pmm) cc_final: 0.8825 (pmm) REVERT: C 218 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8429 (pt) REVERT: C 262 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8917 (tp-100) REVERT: C 307 MET cc_start: 0.9019 (tpp) cc_final: 0.8549 (tpp) REVERT: C 444 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8751 (mm) REVERT: C 523 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8935 (p) REVERT: C 533 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8713 (tpp) REVERT: D 218 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8192 (pt) REVERT: D 269 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8839 (tp) REVERT: D 348 MET cc_start: 0.9405 (ppp) cc_final: 0.9179 (ppp) REVERT: D 351 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9296 (mt) REVERT: D 355 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9177 (mm) REVERT: D 410 TRP cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (m-90) REVERT: E 128 MET cc_start: 0.8007 (mtm) cc_final: 0.7739 (mtm) REVERT: E 150 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8911 (tm) REVERT: E 218 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8477 (pt) REVERT: E 228 SER cc_start: 0.9492 (OUTLIER) cc_final: 0.9150 (p) REVERT: E 309 MET cc_start: 0.8377 (tpp) cc_final: 0.7826 (tpp) REVERT: F 399 MET cc_start: 0.8492 (tpp) cc_final: 0.8159 (mmm) REVERT: F 533 MET cc_start: 0.8256 (ppp) cc_final: 0.7321 (ppp) REVERT: G 210 MET cc_start: 0.9030 (tpp) cc_final: 0.8763 (tpp) REVERT: G 218 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8060 (pt) REVERT: G 531 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.7747 (tptt) outliers start: 172 outliers final: 101 residues processed: 361 average time/residue: 0.3811 time to fit residues: 222.4370 Evaluate side-chains 321 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 194 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU 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 71 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 381 CYS 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 426 LEU 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 218 LEU Chi-restraints excluded: chain B residue 246 LEU 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 410 TRP 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 262 GLN 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 381 CYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 456 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 269 LEU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 351 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 376 MET Chi-restraints excluded: chain D residue 381 CYS 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 532 PHE 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 218 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 229 VAL 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 485 LEU 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 234 MET 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 319 LEU 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 393 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 529 PHE 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 229 VAL Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 393 LEU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 524 ILE 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: 0.0370 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 165 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 40 HIS J 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 262 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 536 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.6081 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= 0.242 Angle : 0.653 14.107 37676 Z= 0.318 Chirality : 0.040 0.208 4337 Planarity : 0.005 0.065 4780 Dihedral : 11.638 124.747 3992 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 5.39 % Allowed : 24.81 % Favored : 69.81 % 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: -0.73 (0.15), residues: 3328 helix: -0.05 (0.13), residues: 1799 sheet: 0.06 (0.32), residues: 259 loop : -1.09 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 410 HIS 0.012 0.001 HIS B 225 PHE 0.013 0.001 PHE F 532 TYR 0.018 0.001 TYR D 305 ARG 0.012 0.000 ARG J 53 *********************** 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 368 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 202 time to evaluate : 3.162 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: H 2 LEU cc_start: 0.6345 (mp) cc_final: 0.5859 (tp) REVERT: H 36 PHE cc_start: 0.5361 (m-80) cc_final: 0.5139 (m-80) REVERT: H 106 ILE cc_start: 0.6308 (pt) cc_final: 0.5149 (pt) REVERT: I 8 ARG cc_start: 0.1988 (tpt170) cc_final: 0.0941 (tpt170) REVERT: J 16 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8222 (ptp90) REVERT: K 46 LYS cc_start: 0.5403 (OUTLIER) cc_final: 0.4396 (pttm) REVERT: K 71 LEU cc_start: 0.5090 (OUTLIER) cc_final: 0.4470 (tp) REVERT: L 1 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.4647 (tpt) REVERT: L 35 ILE cc_start: 0.2596 (OUTLIER) cc_final: 0.2149 (mt) REVERT: L 47 MET cc_start: 0.0865 (mmt) cc_final: -0.0715 (tmm) REVERT: A 141 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8945 (mm) REVERT: A 212 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8915 (ttpt) REVERT: A 218 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8205 (pt) REVERT: A 410 TRP cc_start: 0.9004 (OUTLIER) cc_final: 0.8602 (m-90) REVERT: B 147 MET cc_start: 0.9413 (mmp) cc_final: 0.9203 (mmm) REVERT: B 218 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8523 (pt) REVERT: B 307 MET cc_start: 0.8705 (mmm) cc_final: 0.7669 (mmm) REVERT: B 410 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8588 (m-90) REVERT: C 218 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8413 (pt) REVERT: C 262 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8972 (tp-100) REVERT: C 307 MET cc_start: 0.9104 (tpp) cc_final: 0.8462 (tpp) REVERT: C 444 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8746 (mm) REVERT: C 533 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8773 (tpp) REVERT: D 218 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8395 (pt) REVERT: D 269 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8789 (tp) REVERT: D 351 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9368 (mt) REVERT: D 355 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9177 (mm) REVERT: D 410 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.8601 (m-90) REVERT: E 128 MET cc_start: 0.8412 (mtm) cc_final: 0.8203 (mtm) REVERT: E 150 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8991 (tm) REVERT: E 309 MET cc_start: 0.8678 (tpp) cc_final: 0.8123 (tpp) REVERT: E 410 TRP cc_start: 0.9056 (OUTLIER) cc_final: 0.8850 (m-90) REVERT: E 533 MET cc_start: 0.8207 (pmm) cc_final: 0.7952 (pmm) REVERT: F 533 MET cc_start: 0.8233 (ppp) cc_final: 0.7371 (ppp) REVERT: G 128 MET cc_start: 0.8668 (mmm) cc_final: 0.8273 (mtt) REVERT: G 210 MET cc_start: 0.9081 (tpp) cc_final: 0.8817 (tpp) REVERT: G 218 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8300 (pt) REVERT: G 234 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8518 (mpp) REVERT: G 410 TRP cc_start: 0.9235 (OUTLIER) cc_final: 0.8687 (m-90) REVERT: G 531 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.7756 (tptt) outliers start: 166 outliers final: 103 residues processed: 341 average time/residue: 0.3819 time to fit residues: 208.4170 Evaluate side-chains 315 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 186 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 16 ARG Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain L residue 1 MET 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 M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 97 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 LEU 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 258 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 373 SER 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 426 LEU 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 218 LEU Chi-restraints excluded: chain B residue 246 LEU 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 393 LEU Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 TRP 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 229 VAL Chi-restraints excluded: chain C residue 234 MET 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 262 GLN 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 381 CYS Chi-restraints excluded: chain C residue 405 ILE 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 533 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 381 CYS 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 376 MET Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 410 TRP 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 234 MET 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 376 MET 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 F residue 529 PHE 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 272 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 6.9990 chunk 292 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 269 optimal weight: 0.0070 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 64 GLN J 19 HIS ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 HIS F 254 GLN G 225 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27854 Z= 0.171 Angle : 0.643 11.788 37676 Z= 0.305 Chirality : 0.039 0.178 4337 Planarity : 0.005 0.067 4780 Dihedral : 11.259 123.811 3981 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 4.64 % Allowed : 25.58 % Favored : 69.77 % 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: -0.48 (0.15), residues: 3328 helix: 0.16 (0.13), residues: 1802 sheet: 0.21 (0.32), residues: 259 loop : -1.00 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 410 HIS 0.011 0.001 HIS D 225 PHE 0.011 0.001 PHE F 532 TYR 0.016 0.001 TYR D 305 ARG 0.003 0.000 ARG J 62 *********************** 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 334 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 191 time to evaluate : 2.965 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: H 106 ILE cc_start: 0.6003 (pt) cc_final: 0.5175 (pt) REVERT: I 8 ARG cc_start: 0.1962 (tpt170) cc_final: 0.0854 (tpt170) REVERT: I 64 GLN cc_start: 0.2282 (OUTLIER) cc_final: 0.0015 (tm-30) REVERT: K 46 LYS cc_start: 0.5328 (OUTLIER) cc_final: 0.4424 (pttm) REVERT: K 71 LEU cc_start: 0.4990 (OUTLIER) cc_final: 0.4371 (tp) REVERT: L 35 ILE cc_start: 0.2512 (OUTLIER) cc_final: 0.2055 (mt) REVERT: L 47 MET cc_start: 0.0853 (mmt) cc_final: -0.0757 (tmm) REVERT: M 46 LYS cc_start: 0.5316 (OUTLIER) cc_final: 0.4719 (pttm) REVERT: A 212 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8935 (ttpt) REVERT: A 218 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8520 (pt) REVERT: A 426 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9018 (tm) REVERT: A 462 MET cc_start: 0.8977 (mtp) cc_final: 0.8547 (ttp) REVERT: B 307 MET cc_start: 0.8634 (mmm) cc_final: 0.8013 (mmm) REVERT: B 410 TRP cc_start: 0.8974 (OUTLIER) cc_final: 0.8589 (m-90) REVERT: C 218 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8591 (pt) REVERT: C 262 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8868 (tp-100) REVERT: C 307 MET cc_start: 0.9117 (tpp) cc_final: 0.8385 (tpp) REVERT: C 444 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8673 (mm) REVERT: C 533 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8702 (tpp) REVERT: D 266 LEU cc_start: 0.9204 (mp) cc_final: 0.8990 (mp) REVERT: D 269 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8735 (tp) REVERT: D 351 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9369 (mt) REVERT: D 355 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9152 (mm) REVERT: D 410 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.8583 (m-90) REVERT: D 533 MET cc_start: 0.7052 (mmm) cc_final: 0.6690 (mmm) REVERT: E 150 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9053 (pt) REVERT: E 309 MET cc_start: 0.8720 (tpp) cc_final: 0.8129 (tpp) REVERT: F 399 MET cc_start: 0.8812 (tpp) cc_final: 0.8540 (mmm) REVERT: F 410 TRP cc_start: 0.9002 (OUTLIER) cc_final: 0.8779 (m-90) REVERT: F 533 MET cc_start: 0.8011 (ppp) cc_final: 0.7306 (ppp) REVERT: G 128 MET cc_start: 0.8731 (mmm) cc_final: 0.8430 (mtt) REVERT: G 210 MET cc_start: 0.9036 (tpp) cc_final: 0.8780 (tpp) REVERT: G 218 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8262 (pt) REVERT: G 379 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9271 (tm-30) REVERT: G 410 TRP cc_start: 0.9051 (OUTLIER) cc_final: 0.8697 (m-90) REVERT: G 531 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.7848 (tptt) outliers start: 143 outliers final: 88 residues processed: 311 average time/residue: 0.3797 time to fit residues: 191.3510 Evaluate side-chains 291 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 180 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 88 GLU 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 15 THR Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 71 LEU 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 M residue 1 MET Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 398 VAL 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 524 ILE Chi-restraints excluded: chain B residue 167 VAL 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 410 TRP 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 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 262 GLN 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 405 ILE 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 533 MET Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 351 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 150 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 229 VAL 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 524 ILE Chi-restraints excluded: chain E residue 536 HIS 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 234 MET 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 376 MET Chi-restraints excluded: chain F residue 393 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 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 241 ASP Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 393 LEU 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 531 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 323 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN I 64 GLN J 40 HIS J 96 ASN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 350 GLN ** 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 482 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27854 Z= 0.295 Angle : 0.693 12.536 37676 Z= 0.336 Chirality : 0.040 0.201 4337 Planarity : 0.005 0.066 4780 Dihedral : 10.982 122.517 3963 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 5.32 % Allowed : 25.16 % Favored : 69.51 % 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: -0.44 (0.15), residues: 3328 helix: 0.21 (0.13), residues: 1796 sheet: 0.42 (0.33), residues: 259 loop : -1.05 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 410 HIS 0.020 0.001 HIS A 225 PHE 0.016 0.001 PHE I 36 TYR 0.018 0.001 TYR D 305 ARG 0.010 0.000 ARG I 62 *********************** 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 347 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 183 time to evaluate : 3.336 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: H 68 LEU cc_start: 0.6987 (pp) cc_final: 0.6777 (pt) REVERT: H 106 ILE cc_start: 0.6206 (pt) cc_final: 0.5609 (pt) REVERT: I 8 ARG cc_start: 0.2457 (tpt170) cc_final: 0.1340 (tpt170) REVERT: J 47 MET cc_start: 0.4973 (ptp) cc_final: 0.4488 (ptp) REVERT: K 1 MET cc_start: 0.6432 (tpt) cc_final: 0.6181 (tpt) REVERT: K 46 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.4677 (pttm) REVERT: K 71 LEU cc_start: 0.5064 (OUTLIER) cc_final: 0.4442 (tp) REVERT: K 97 GLU cc_start: -0.1562 (OUTLIER) cc_final: -0.1900 (tp30) REVERT: L 1 MET cc_start: 0.5970 (mmp) cc_final: 0.4927 (tpp) REVERT: L 35 ILE cc_start: 0.2750 (OUTLIER) cc_final: 0.2316 (mt) REVERT: L 47 MET cc_start: 0.0962 (mmt) cc_final: -0.0597 (tmm) REVERT: A 212 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9022 (ttpt) REVERT: B 128 MET cc_start: 0.8980 (mmm) cc_final: 0.8103 (mtp) REVERT: B 410 TRP cc_start: 0.9103 (OUTLIER) cc_final: 0.8627 (m-90) REVERT: B 543 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6734 (pp) REVERT: C 218 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8555 (pt) REVERT: C 262 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8986 (tp-100) REVERT: C 307 MET cc_start: 0.9167 (tpp) cc_final: 0.8418 (tpp) REVERT: C 410 TRP cc_start: 0.9138 (OUTLIER) cc_final: 0.8592 (m-90) REVERT: C 444 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8856 (mm) REVERT: C 533 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8816 (tpp) REVERT: D 150 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8909 (mp) REVERT: D 351 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9379 (mt) REVERT: D 355 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9323 (mm) REVERT: D 410 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.8426 (m-90) REVERT: D 533 MET cc_start: 0.7473 (mmm) cc_final: 0.7261 (mmm) REVERT: E 128 MET cc_start: 0.8264 (mtm) cc_final: 0.7926 (mtm) REVERT: E 150 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9004 (tm) REVERT: E 228 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9183 (p) REVERT: E 533 MET cc_start: 0.8258 (pmm) cc_final: 0.8044 (pmm) REVERT: F 147 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7967 (ptp) REVERT: F 399 MET cc_start: 0.8744 (tpp) cc_final: 0.8511 (mmm) REVERT: F 410 TRP cc_start: 0.9073 (OUTLIER) cc_final: 0.8658 (m-90) REVERT: G 116 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8521 (p0) REVERT: G 128 MET cc_start: 0.8993 (mmm) cc_final: 0.8783 (mtt) REVERT: G 210 MET cc_start: 0.9061 (tpp) cc_final: 0.8834 (tpp) REVERT: G 234 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8557 (mpp) REVERT: G 379 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9213 (tm-30) REVERT: G 410 TRP cc_start: 0.9185 (OUTLIER) cc_final: 0.8608 (m-90) REVERT: G 531 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.7610 (tptt) outliers start: 164 outliers final: 101 residues processed: 323 average time/residue: 0.3866 time to fit residues: 202.5809 Evaluate side-chains 304 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 178 time to evaluate : 3.604 ------------------------------------------------------------------------------- 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 I residue 2 LEU Chi-restraints excluded: chain I residue 64 GLN Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 97 GLU 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 M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 225 HIS 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 258 ILE 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 398 VAL Chi-restraints excluded: chain A residue 405 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 155 LEU 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 376 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 410 TRP 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 234 MET 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 262 GLN 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 405 ILE Chi-restraints excluded: chain C residue 410 TRP 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 533 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 351 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 376 MET 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 228 SER Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 403 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 485 LEU 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 147 MET 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 234 MET 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 374 LEU Chi-restraints excluded: chain F residue 376 MET 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 116 ASP Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 234 MET Chi-restraints excluded: chain G residue 241 ASP 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 379 GLN 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 437 LEU Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 254 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN I 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** 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 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN E 353 ASN F 254 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27854 Z= 0.227 Angle : 0.687 12.811 37676 Z= 0.324 Chirality : 0.040 0.195 4337 Planarity : 0.005 0.067 4780 Dihedral : 10.616 117.530 3953 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 4.22 % Allowed : 26.27 % Favored : 69.51 % 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: -0.29 (0.15), residues: 3328 helix: 0.35 (0.13), residues: 1786 sheet: 0.51 (0.33), residues: 259 loop : -1.02 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 410 HIS 0.015 0.001 HIS A 225 PHE 0.031 0.001 PHE I 36 TYR 0.037 0.001 TYR C 305 ARG 0.008 0.000 ARG I 63 *********************** 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 316 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 186 time to evaluate : 3.402 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: H 36 PHE cc_start: 0.6180 (m-80) cc_final: 0.5723 (m-10) REVERT: H 106 ILE cc_start: 0.6462 (pt) cc_final: 0.5840 (pt) REVERT: I 8 ARG cc_start: 0.2477 (tpt170) cc_final: 0.1339 (tpt170) REVERT: J 47 MET cc_start: 0.4936 (ptp) cc_final: 0.4346 (ptp) REVERT: K 1 MET cc_start: 0.6446 (tpt) cc_final: 0.6189 (tpt) REVERT: K 46 LYS cc_start: 0.5763 (OUTLIER) cc_final: 0.4774 (pttm) REVERT: K 71 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4390 (tp) REVERT: K 97 GLU cc_start: -0.1536 (OUTLIER) cc_final: -0.1870 (tp30) REVERT: L 35 ILE cc_start: 0.2705 (OUTLIER) cc_final: 0.2272 (mt) REVERT: L 47 MET cc_start: 0.0985 (mmt) cc_final: -0.0593 (tmm) REVERT: A 212 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8935 (ttpt) REVERT: A 399 MET cc_start: 0.8392 (tpp) cc_final: 0.8056 (mmm) REVERT: A 462 MET cc_start: 0.9079 (mtp) cc_final: 0.8707 (ttp) REVERT: B 128 MET cc_start: 0.8994 (mmm) cc_final: 0.8161 (mtp) REVERT: B 307 MET cc_start: 0.8667 (mmm) cc_final: 0.8361 (mmm) REVERT: B 410 TRP cc_start: 0.9032 (OUTLIER) cc_final: 0.8610 (m-90) REVERT: C 262 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8812 (tp-100) REVERT: C 307 MET cc_start: 0.9224 (tpp) cc_final: 0.8564 (tpp) REVERT: C 410 TRP cc_start: 0.9079 (OUTLIER) cc_final: 0.8628 (m-90) REVERT: C 444 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8831 (mm) REVERT: C 533 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8888 (tpp) REVERT: D 150 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8892 (mp) REVERT: D 355 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9327 (mm) REVERT: D 410 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.8524 (m-90) REVERT: D 533 MET cc_start: 0.7433 (mmm) cc_final: 0.7216 (mmm) REVERT: E 150 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8970 (pt) REVERT: E 228 SER cc_start: 0.9397 (OUTLIER) cc_final: 0.9153 (p) REVERT: E 234 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8894 (mtm) REVERT: F 307 MET cc_start: 0.8628 (mmm) cc_final: 0.8254 (mmm) REVERT: F 410 TRP cc_start: 0.9033 (OUTLIER) cc_final: 0.8729 (m-90) REVERT: G 116 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8554 (p0) REVERT: G 410 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.8506 (m-90) REVERT: G 531 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.7699 (tptt) outliers start: 130 outliers final: 93 residues processed: 297 average time/residue: 0.3836 time to fit residues: 185.4846 Evaluate side-chains 295 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 182 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 56 ASN 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 15 THR Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 97 GLU 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 M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 225 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 LEU 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 410 TRP 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 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN 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 405 ILE Chi-restraints excluded: chain C residue 410 TRP 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 486 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 229 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 376 MET 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 228 SER Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 234 MET 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 179 LEU Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 234 MET 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 116 ASP Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 241 ASP 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 405 ILE Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain G residue 410 TRP Chi-restraints excluded: chain G residue 531 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 6.9990 chunk 310 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 chunk 301 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 236 optimal weight: 0.1980 chunk 92 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN I 64 GLN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 225 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN F 254 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27854 Z= 0.184 Angle : 0.691 13.032 37676 Z= 0.322 Chirality : 0.040 0.177 4337 Planarity : 0.005 0.067 4780 Dihedral : 10.272 112.783 3946 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 3.90 % Allowed : 26.56 % Favored : 69.55 % 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: -0.07 (0.15), residues: 3328 helix: 0.48 (0.13), residues: 1743 sheet: 0.52 (0.33), residues: 259 loop : -0.77 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 410 HIS 0.017 0.001 HIS D 225 PHE 0.014 0.001 PHE H 110 TYR 0.035 0.001 TYR C 305 ARG 0.002 0.000 ARG I 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: 120 poor density : 188 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 PHE cc_start: 0.5929 (m-80) cc_final: 0.5449 (m-10) REVERT: H 106 ILE cc_start: 0.6301 (pt) cc_final: 0.5786 (pt) REVERT: I 8 ARG cc_start: 0.2667 (tpt170) cc_final: 0.1549 (tpt170) REVERT: I 42 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6944 (pt0) REVERT: J 47 MET cc_start: 0.4891 (ptp) cc_final: 0.4307 (ptp) REVERT: K 1 MET cc_start: 0.6426 (tpt) cc_final: 0.6133 (tpt) REVERT: K 71 LEU cc_start: 0.4972 (OUTLIER) cc_final: 0.4356 (tp) REVERT: K 97 GLU cc_start: -0.1501 (OUTLIER) cc_final: -0.1814 (tp30) REVERT: L 35 ILE cc_start: 0.3042 (OUTLIER) cc_final: 0.2619 (mt) REVERT: L 47 MET cc_start: 0.0883 (mmt) cc_final: -0.0605 (tmm) REVERT: A 212 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8918 (ttpt) REVERT: A 399 MET cc_start: 0.8294 (tpp) cc_final: 0.8060 (mmm) REVERT: A 462 MET cc_start: 0.9047 (mtp) cc_final: 0.8708 (ttp) REVERT: B 128 MET cc_start: 0.9070 (mmm) cc_final: 0.8211 (mtp) REVERT: B 216 ASP cc_start: 0.9290 (m-30) cc_final: 0.8721 (t0) REVERT: B 307 MET cc_start: 0.8601 (mmm) cc_final: 0.8322 (mmm) REVERT: B 410 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.8566 (m-90) REVERT: C 150 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8921 (pt) REVERT: C 262 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8841 (tp-100) REVERT: C 307 MET cc_start: 0.9190 (tpp) cc_final: 0.8554 (tpp) REVERT: C 444 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8803 (mm) REVERT: D 150 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8868 (mp) REVERT: D 355 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9319 (mm) REVERT: D 410 TRP cc_start: 0.8910 (OUTLIER) cc_final: 0.8512 (m-90) REVERT: D 533 MET cc_start: 0.7885 (mmm) cc_final: 0.7589 (mmm) REVERT: E 128 MET cc_start: 0.8246 (mtm) cc_final: 0.7813 (mtm) REVERT: E 150 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8981 (tm) REVERT: E 234 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8919 (mtm) REVERT: F 147 MET cc_start: 0.8491 (ptp) cc_final: 0.8011 (ptp) REVERT: F 316 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8360 (mm-30) REVERT: F 410 TRP cc_start: 0.9018 (OUTLIER) cc_final: 0.8718 (m-90) REVERT: G 216 ASP cc_start: 0.8719 (m-30) cc_final: 0.8442 (t0) REVERT: G 234 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8445 (mpp) REVERT: G 379 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.9231 (tm-30) REVERT: G 410 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.8574 (m-90) REVERT: G 531 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.7734 (tptt) outliers start: 120 outliers final: 85 residues processed: 293 average time/residue: 0.3791 time to fit residues: 182.2356 Evaluate side-chains 287 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 183 time to evaluate : 3.455 ------------------------------------------------------------------------------- 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 64 GLN Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 97 GLU 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 M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain A residue 150 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 258 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 155 LEU 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 410 TRP 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 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN 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 405 ILE 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 486 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 229 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 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 234 MET 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 485 LEU 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 234 MET 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 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 379 GLN 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 531 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 10.0000 chunk 319 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 334 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 225 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN F 254 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 534 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27854 Z= 0.180 Angle : 0.701 15.968 37676 Z= 0.323 Chirality : 0.040 0.182 4337 Planarity : 0.005 0.066 4780 Dihedral : 10.092 109.261 3940 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 3.44 % Allowed : 27.05 % Favored : 69.51 % 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: 0.48 (0.13), residues: 1743 sheet: 0.55 (0.33), residues: 259 loop : -0.76 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 410 HIS 0.021 0.001 HIS D 225 PHE 0.015 0.001 PHE H 110 TYR 0.032 0.001 TYR C 305 ARG 0.006 0.000 ARG C 233 ********************** 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 294 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 188 time to evaluate : 3.533 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: H 36 PHE cc_start: 0.6124 (m-80) cc_final: 0.5640 (m-10) REVERT: H 106 ILE cc_start: 0.6322 (pt) cc_final: 0.5810 (pt) REVERT: I 42 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6882 (pt0) REVERT: J 47 MET cc_start: 0.4799 (ptp) cc_final: 0.4214 (ptp) REVERT: K 1 MET cc_start: 0.6419 (tpt) cc_final: 0.6119 (tpt) REVERT: K 71 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.4352 (tp) REVERT: K 97 GLU cc_start: -0.1518 (OUTLIER) cc_final: -0.1832 (tp30) REVERT: L 35 ILE cc_start: 0.2988 (OUTLIER) cc_final: 0.2569 (mt) REVERT: L 47 MET cc_start: 0.0899 (mmt) cc_final: -0.0511 (tmm) REVERT: A 212 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8886 (ttpt) REVERT: A 462 MET cc_start: 0.9047 (mtp) cc_final: 0.8514 (ttt) REVERT: B 128 MET cc_start: 0.9076 (mmm) cc_final: 0.8189 (mtp) REVERT: B 216 ASP cc_start: 0.9277 (m-30) cc_final: 0.8721 (t0) REVERT: B 307 MET cc_start: 0.8614 (mmm) cc_final: 0.8373 (mmm) REVERT: B 410 TRP cc_start: 0.9030 (OUTLIER) cc_final: 0.8605 (m-90) REVERT: B 449 MET cc_start: 0.9335 (pmm) cc_final: 0.9096 (ppp) REVERT: C 262 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8894 (tp-100) REVERT: C 307 MET cc_start: 0.9182 (tpp) cc_final: 0.8544 (tpp) REVERT: C 444 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8915 (mm) REVERT: D 355 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9316 (mm) REVERT: D 410 TRP cc_start: 0.8899 (OUTLIER) cc_final: 0.8550 (m-90) REVERT: D 533 MET cc_start: 0.7886 (mmm) cc_final: 0.7584 (mmm) REVERT: E 128 MET cc_start: 0.8217 (mtm) cc_final: 0.7783 (mtm) REVERT: E 150 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8997 (tm) REVERT: E 234 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8801 (mtm) REVERT: F 147 MET cc_start: 0.8475 (ptp) cc_final: 0.7870 (ptp) REVERT: F 307 MET cc_start: 0.8679 (mmm) cc_final: 0.8247 (mmm) REVERT: F 410 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8702 (m-90) REVERT: G 210 MET cc_start: 0.8915 (tpp) cc_final: 0.8645 (tpp) REVERT: G 216 ASP cc_start: 0.8684 (m-30) cc_final: 0.8417 (t0) REVERT: G 379 GLN cc_start: 0.9481 (OUTLIER) cc_final: 0.9215 (tm-30) REVERT: G 410 TRP cc_start: 0.8844 (OUTLIER) cc_final: 0.8384 (m-90) outliers start: 106 outliers final: 85 residues processed: 281 average time/residue: 0.3751 time to fit residues: 172.1674 Evaluate side-chains 283 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 184 time to evaluate : 3.238 ------------------------------------------------------------------------------- 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 64 GLN Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 97 GLU 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 M residue 1 MET Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 46 LYS Chi-restraints excluded: chain A residue 150 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 258 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 LEU 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 410 TRP 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 155 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 GLN 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 405 ILE 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 486 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 410 TRP 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 234 MET 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 485 LEU 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 234 MET 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 150 LEU 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 379 GLN 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 531 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 245 optimal weight: 1.9990 chunk 39 optimal weight: 0.0270 chunk 74 optimal weight: 0.7980 chunk 266 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 33 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 225 HIS D 482 GLN ** E 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.087657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.052881 restraints weight = 197931.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.052182 restraints weight = 150113.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051778 restraints weight = 117725.637| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27854 Z= 0.166 Angle : 0.700 13.274 37676 Z= 0.321 Chirality : 0.040 0.185 4337 Planarity : 0.005 0.066 4780 Dihedral : 9.956 107.582 3940 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 3.25 % Allowed : 27.37 % 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: 0.46 (0.13), residues: 1753 sheet: 0.53 (0.33), residues: 259 loop : -0.70 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 410 HIS 0.012 0.001 HIS D 225 PHE 0.016 0.001 PHE H 110 TYR 0.029 0.001 TYR C 305 ARG 0.007 0.000 ARG I 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6045.64 seconds wall clock time: 112 minutes 53.92 seconds (6773.92 seconds total)