Starting phenix.real_space_refine on Wed Sep 25 11:09:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/09_2024/8rmn_19365.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/09_2024/8rmn_19365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/09_2024/8rmn_19365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/09_2024/8rmn_19365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/09_2024/8rmn_19365.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/09_2024/8rmn_19365.cif" } resolution = 3.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 460 5.16 5 C 35480 2.51 5 N 9480 2.21 5 O 10020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 55440 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "U" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "B" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "E" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "F" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "G" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "H" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "I" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "J" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "K" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "L" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "M" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "N" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "O" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "P" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "Q" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "R" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "S" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "T" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "V" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "W" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "X" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "Y" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "Z" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "a" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "b" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "c" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "d" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "e" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "f" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "g" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "h" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "i" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "j" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "k" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "l" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "m" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "n" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Time building chain proxies: 22.90, per 1000 atoms: 0.41 Number of scatterers: 55440 At special positions: 0 Unit cell: (138.012, 143.871, 254.541, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 460 16.00 O 10020 8.00 N 9480 7.00 C 35480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.02 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.02 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.02 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.02 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.02 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.02 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.02 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.02 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=2.02 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.02 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.02 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.02 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.02 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 10.45 Conformation dependent library (CDL) restraints added in 5.3 seconds 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13320 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 40 sheets defined 63.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Proline residue: A 115 - end of helix removed outlier: 4.322A pdb=" N TRP A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP A 146 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 170 through 211 Processing helix chain 'A' and resid 214 through 253 Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Proline residue: B 115 - end of helix removed outlier: 4.323A pdb=" N TRP B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 170 through 211 Processing helix chain 'B' and resid 214 through 253 Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 15 through 39 removed outlier: 4.004A pdb=" N ILE C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) Proline residue: C 115 - end of helix removed outlier: 4.323A pdb=" N TRP C 118 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 170 through 211 Processing helix chain 'C' and resid 214 through 253 Processing helix chain 'C' and resid 268 through 276 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) Proline residue: D 115 - end of helix removed outlier: 4.322A pdb=" N TRP D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 170 through 211 Processing helix chain 'D' and resid 214 through 253 Processing helix chain 'D' and resid 268 through 276 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Proline residue: E 115 - end of helix removed outlier: 4.323A pdb=" N TRP E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.592A pdb=" N ASP E 146 " --> pdb=" O PRO E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 160 Processing helix chain 'E' and resid 170 through 211 Processing helix chain 'E' and resid 214 through 253 Processing helix chain 'E' and resid 268 through 276 Processing helix chain 'F' and resid 6 through 14 Processing helix chain 'F' and resid 15 through 39 removed outlier: 4.004A pdb=" N ILE F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) Proline residue: F 115 - end of helix removed outlier: 4.322A pdb=" N TRP F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP F 146 " --> pdb=" O PRO F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 160 Processing helix chain 'F' and resid 170 through 211 Processing helix chain 'F' and resid 214 through 253 Processing helix chain 'F' and resid 268 through 276 Processing helix chain 'G' and resid 6 through 14 Processing helix chain 'G' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) Proline residue: G 115 - end of helix removed outlier: 4.322A pdb=" N TRP G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 134 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP G 146 " --> pdb=" O PRO G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 160 Processing helix chain 'G' and resid 170 through 211 Processing helix chain 'G' and resid 214 through 253 Processing helix chain 'G' and resid 268 through 276 Processing helix chain 'H' and resid 6 through 14 Processing helix chain 'H' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Proline residue: H 115 - end of helix removed outlier: 4.322A pdb=" N TRP H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 134 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP H 146 " --> pdb=" O PRO H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 160 Processing helix chain 'H' and resid 170 through 211 Processing helix chain 'H' and resid 214 through 253 Processing helix chain 'H' and resid 268 through 276 Processing helix chain 'I' and resid 6 through 14 Processing helix chain 'I' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) Proline residue: I 115 - end of helix removed outlier: 4.322A pdb=" N TRP I 118 " --> pdb=" O ALA I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 134 Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP I 146 " --> pdb=" O PRO I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 160 Processing helix chain 'I' and resid 170 through 211 Processing helix chain 'I' and resid 214 through 253 Processing helix chain 'I' and resid 268 through 276 Processing helix chain 'J' and resid 6 through 14 Processing helix chain 'J' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE J 19 " --> pdb=" O ASN J 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.632A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) Proline residue: J 115 - end of helix removed outlier: 4.322A pdb=" N TRP J 118 " --> pdb=" O ALA J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 134 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP J 146 " --> pdb=" O PRO J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 160 Processing helix chain 'J' and resid 170 through 211 Processing helix chain 'J' and resid 214 through 253 Processing helix chain 'J' and resid 268 through 276 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) Proline residue: K 115 - end of helix removed outlier: 4.322A pdb=" N TRP K 118 " --> pdb=" O ALA K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 134 Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP K 146 " --> pdb=" O PRO K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 160 Processing helix chain 'K' and resid 170 through 211 Processing helix chain 'K' and resid 214 through 253 Processing helix chain 'K' and resid 268 through 276 Processing helix chain 'L' and resid 6 through 14 Processing helix chain 'L' and resid 15 through 39 removed outlier: 4.004A pdb=" N ILE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 Proline residue: L 59 - end of helix Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.632A pdb=" N TRP L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 126 removed outlier: 4.349A pdb=" N ARG L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Proline residue: L 115 - end of helix removed outlier: 4.322A pdb=" N TRP L 118 " --> pdb=" O ALA L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 134 Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP L 146 " --> pdb=" O PRO L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 160 Processing helix chain 'L' and resid 170 through 211 Processing helix chain 'L' and resid 214 through 253 Processing helix chain 'L' and resid 268 through 276 Processing helix chain 'M' and resid 6 through 14 Processing helix chain 'M' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 70 Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG M 110 " --> pdb=" O SER M 106 " (cutoff:3.500A) Proline residue: M 115 - end of helix removed outlier: 4.322A pdb=" N TRP M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 134 Processing helix chain 'M' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP M 146 " --> pdb=" O PRO M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 160 Processing helix chain 'M' and resid 170 through 211 Processing helix chain 'M' and resid 214 through 253 Processing helix chain 'M' and resid 268 through 276 Processing helix chain 'N' and resid 6 through 14 Processing helix chain 'N' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE N 19 " --> pdb=" O ASN N 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG N 110 " --> pdb=" O SER N 106 " (cutoff:3.500A) Proline residue: N 115 - end of helix removed outlier: 4.322A pdb=" N TRP N 118 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 134 Processing helix chain 'N' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP N 146 " --> pdb=" O PRO N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 160 Processing helix chain 'N' and resid 170 through 211 Processing helix chain 'N' and resid 214 through 253 Processing helix chain 'N' and resid 268 through 276 Processing helix chain 'O' and resid 6 through 14 Processing helix chain 'O' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 70 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG O 110 " --> pdb=" O SER O 106 " (cutoff:3.500A) Proline residue: O 115 - end of helix removed outlier: 4.322A pdb=" N TRP O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 134 Processing helix chain 'O' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP O 146 " --> pdb=" O PRO O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 160 Processing helix chain 'O' and resid 170 through 211 Processing helix chain 'O' and resid 214 through 253 Processing helix chain 'O' and resid 268 through 276 Processing helix chain 'P' and resid 6 through 14 Processing helix chain 'P' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE P 19 " --> pdb=" O ASN P 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 Proline residue: P 59 - end of helix Processing helix chain 'P' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP P 75 " --> pdb=" O ARG P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG P 110 " --> pdb=" O SER P 106 " (cutoff:3.500A) Proline residue: P 115 - end of helix removed outlier: 4.323A pdb=" N TRP P 118 " --> pdb=" O ALA P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 134 Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP P 146 " --> pdb=" O PRO P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 160 Processing helix chain 'P' and resid 170 through 211 Processing helix chain 'P' and resid 214 through 253 Processing helix chain 'P' and resid 268 through 276 Processing helix chain 'Q' and resid 6 through 14 Processing helix chain 'Q' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 70 Proline residue: Q 59 - end of helix Processing helix chain 'Q' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP Q 75 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG Q 110 " --> pdb=" O SER Q 106 " (cutoff:3.500A) Proline residue: Q 115 - end of helix removed outlier: 4.323A pdb=" N TRP Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 134 Processing helix chain 'Q' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP Q 146 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 160 Processing helix chain 'Q' and resid 170 through 211 Processing helix chain 'Q' and resid 214 through 253 Processing helix chain 'Q' and resid 268 through 276 Processing helix chain 'R' and resid 6 through 14 Processing helix chain 'R' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE R 19 " --> pdb=" O ASN R 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 Proline residue: R 59 - end of helix Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) Proline residue: R 115 - end of helix removed outlier: 4.322A pdb=" N TRP R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 134 Processing helix chain 'R' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP R 146 " --> pdb=" O PRO R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 160 Processing helix chain 'R' and resid 170 through 211 Processing helix chain 'R' and resid 214 through 253 Processing helix chain 'R' and resid 268 through 276 Processing helix chain 'S' and resid 6 through 14 Processing helix chain 'S' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE S 19 " --> pdb=" O ASN S 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 70 Proline residue: S 59 - end of helix Processing helix chain 'S' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG S 110 " --> pdb=" O SER S 106 " (cutoff:3.500A) Proline residue: S 115 - end of helix removed outlier: 4.321A pdb=" N TRP S 118 " --> pdb=" O ALA S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 134 Processing helix chain 'S' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP S 146 " --> pdb=" O PRO S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 160 Processing helix chain 'S' and resid 170 through 211 Processing helix chain 'S' and resid 214 through 253 Processing helix chain 'S' and resid 268 through 276 Processing helix chain 'T' and resid 6 through 14 Processing helix chain 'T' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE T 19 " --> pdb=" O ASN T 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 Proline residue: T 59 - end of helix Processing helix chain 'T' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP T 75 " --> pdb=" O ARG T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG T 110 " --> pdb=" O SER T 106 " (cutoff:3.500A) Proline residue: T 115 - end of helix removed outlier: 4.322A pdb=" N TRP T 118 " --> pdb=" O ALA T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 134 Processing helix chain 'T' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP T 146 " --> pdb=" O PRO T 143 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 160 Processing helix chain 'T' and resid 170 through 211 Processing helix chain 'T' and resid 214 through 253 Processing helix chain 'T' and resid 268 through 276 Processing helix chain 'V' and resid 62 through 65 Processing helix chain 'V' and resid 87 through 91 Processing helix chain 'W' and resid 62 through 65 Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'Y' and resid 62 through 65 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'a' and resid 62 through 65 Processing helix chain 'a' and resid 87 through 91 Processing helix chain 'b' and resid 62 through 65 Processing helix chain 'b' and resid 87 through 91 Processing helix chain 'c' and resid 62 through 65 Processing helix chain 'c' and resid 87 through 91 Processing helix chain 'd' and resid 62 through 65 Processing helix chain 'd' and resid 87 through 91 Processing helix chain 'e' and resid 62 through 65 Processing helix chain 'e' and resid 87 through 91 Processing helix chain 'f' and resid 62 through 65 Processing helix chain 'f' and resid 87 through 91 Processing helix chain 'g' and resid 62 through 65 Processing helix chain 'g' and resid 87 through 91 Processing helix chain 'h' and resid 62 through 65 Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'i' and resid 62 through 65 Processing helix chain 'i' and resid 87 through 91 Processing helix chain 'j' and resid 62 through 65 Processing helix chain 'j' and resid 87 through 91 Processing helix chain 'k' and resid 62 through 65 Processing helix chain 'k' and resid 87 through 91 Processing helix chain 'l' and resid 62 through 65 Processing helix chain 'l' and resid 87 through 91 Processing helix chain 'm' and resid 62 through 65 Processing helix chain 'm' and resid 87 through 91 Processing helix chain 'n' and resid 62 through 65 Processing helix chain 'n' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'U' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL U 5 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY U 10 " --> pdb=" O GLN U 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER U 114 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET U 34 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL V 5 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR V 78 " --> pdb=" O ASP V 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY V 10 " --> pdb=" O GLN V 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER V 114 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET V 34 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'W' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL W 5 " --> pdb=" O ALA W 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR W 78 " --> pdb=" O ASP W 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY W 10 " --> pdb=" O GLN W 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER W 114 " --> pdb=" O VAL W 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET W 34 " --> pdb=" O ALA W 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL X 5 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR X 78 " --> pdb=" O ASP X 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY X 10 " --> pdb=" O GLN X 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER X 114 " --> pdb=" O VAL X 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET X 34 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL Y 5 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR Y 78 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY Y 10 " --> pdb=" O GLN Y 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER Y 114 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET Y 34 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL Z 5 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR Z 78 " --> pdb=" O ASP Z 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY Z 10 " --> pdb=" O GLN Z 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER Z 114 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET Z 34 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP Z 36 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL a 5 " --> pdb=" O ALA a 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR a 78 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY a 10 " --> pdb=" O GLN a 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER a 114 " --> pdb=" O VAL a 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET a 34 " --> pdb=" O ALA a 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP a 36 " --> pdb=" O VAL a 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL b 5 " --> pdb=" O ALA b 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR b 78 " --> pdb=" O ASP b 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY b 10 " --> pdb=" O GLN b 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER b 114 " --> pdb=" O VAL b 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET b 34 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA b 50 " --> pdb=" O MET b 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP b 36 " --> pdb=" O VAL b 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL c 5 " --> pdb=" O ALA c 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR c 78 " --> pdb=" O ASP c 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY c 10 " --> pdb=" O GLN c 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER c 114 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET c 34 " --> pdb=" O ALA c 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP c 36 " --> pdb=" O VAL c 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL d 5 " --> pdb=" O ALA d 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR d 78 " --> pdb=" O ASP d 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY d 10 " --> pdb=" O GLN d 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER d 114 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET d 34 " --> pdb=" O ALA d 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA d 50 " --> pdb=" O MET d 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP d 36 " --> pdb=" O VAL d 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 4 through 7 removed outlier: 3.723A pdb=" N VAL e 5 " --> pdb=" O ALA e 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR e 78 " --> pdb=" O ASP e 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY e 10 " --> pdb=" O GLN e 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER e 114 " --> pdb=" O VAL e 12 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET e 34 " --> pdb=" O ALA e 50 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA e 50 " --> pdb=" O MET e 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP e 36 " --> pdb=" O VAL e 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL f 5 " --> pdb=" O ALA f 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR f 78 " --> pdb=" O ASP f 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY f 10 " --> pdb=" O GLN f 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER f 114 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET f 34 " --> pdb=" O ALA f 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA f 50 " --> pdb=" O MET f 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP f 36 " --> pdb=" O VAL f 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL g 5 " --> pdb=" O ALA g 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR g 78 " --> pdb=" O ASP g 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY g 10 " --> pdb=" O GLN g 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER g 114 " --> pdb=" O VAL g 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET g 34 " --> pdb=" O ALA g 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA g 50 " --> pdb=" O MET g 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP g 36 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL h 5 " --> pdb=" O ALA h 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'h' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY h 10 " --> pdb=" O GLN h 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER h 114 " --> pdb=" O VAL h 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET h 34 " --> pdb=" O ALA h 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'i' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL i 5 " --> pdb=" O ALA i 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR i 78 " --> pdb=" O ASP i 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'i' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY i 10 " --> pdb=" O GLN i 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER i 114 " --> pdb=" O VAL i 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET i 34 " --> pdb=" O ALA i 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA i 50 " --> pdb=" O MET i 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP i 36 " --> pdb=" O VAL i 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 4 through 7 removed outlier: 3.725A pdb=" N VAL j 5 " --> pdb=" O ALA j 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR j 78 " --> pdb=" O ASP j 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'j' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY j 10 " --> pdb=" O GLN j 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER j 114 " --> pdb=" O VAL j 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET j 34 " --> pdb=" O ALA j 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA j 50 " --> pdb=" O MET j 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP j 36 " --> pdb=" O VAL j 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL k 5 " --> pdb=" O ALA k 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR k 78 " --> pdb=" O ASP k 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY k 10 " --> pdb=" O GLN k 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER k 114 " --> pdb=" O VAL k 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET k 34 " --> pdb=" O ALA k 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA k 50 " --> pdb=" O MET k 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP k 36 " --> pdb=" O VAL k 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL l 5 " --> pdb=" O ALA l 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR l 78 " --> pdb=" O ASP l 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY l 10 " --> pdb=" O GLN l 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER l 114 " --> pdb=" O VAL l 12 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET l 34 " --> pdb=" O ALA l 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA l 50 " --> pdb=" O MET l 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP l 36 " --> pdb=" O VAL l 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'm' and resid 4 through 7 removed outlier: 3.723A pdb=" N VAL m 5 " --> pdb=" O ALA m 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR m 78 " --> pdb=" O ASP m 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'm' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY m 10 " --> pdb=" O GLN m 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER m 114 " --> pdb=" O VAL m 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET m 34 " --> pdb=" O ALA m 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA m 50 " --> pdb=" O MET m 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP m 36 " --> pdb=" O VAL m 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'n' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL n 5 " --> pdb=" O ALA n 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR n 78 " --> pdb=" O ASP n 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'n' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY n 10 " --> pdb=" O GLN n 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER n 114 " --> pdb=" O VAL n 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET n 34 " --> pdb=" O ALA n 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA n 50 " --> pdb=" O MET n 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP n 36 " --> pdb=" O VAL n 48 " (cutoff:3.500A) 3901 hydrogen bonds defined for protein. 11223 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: 23.45 Time building geometry restraints manager: 12.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17616 1.34 - 1.46: 12250 1.46 - 1.58: 26134 1.58 - 1.69: 0 1.69 - 1.81: 600 Bond restraints: 56600 Sorted by residual: bond pdb=" N ARG e 35 " pdb=" CA ARG e 35 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.16e+00 bond pdb=" N MET e 34 " pdb=" CA MET e 34 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.25e-02 6.40e+03 6.71e+00 bond pdb=" N TRP e 36 " pdb=" CA TRP e 36 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.23e-02 6.61e+03 6.36e+00 bond pdb=" N TYR A 51 " pdb=" CA TYR A 51 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.43e+00 bond pdb=" N TYR D 51 " pdb=" CA TYR D 51 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 5.07e+00 ... (remaining 56595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 74156 1.65 - 3.30: 1865 3.30 - 4.95: 373 4.95 - 6.60: 183 6.60 - 8.25: 43 Bond angle restraints: 76620 Sorted by residual: angle pdb=" CA GLN T 270 " pdb=" CB GLN T 270 " pdb=" CG GLN T 270 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.34e+00 angle pdb=" CA GLN I 270 " pdb=" CB GLN I 270 " pdb=" CG GLN I 270 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.34e+00 angle pdb=" CA GLN S 270 " pdb=" CB GLN S 270 " pdb=" CG GLN S 270 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 angle pdb=" CA GLN B 270 " pdb=" CB GLN B 270 " pdb=" CG GLN B 270 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 angle pdb=" CA GLN G 270 " pdb=" CB GLN G 270 " pdb=" CG GLN G 270 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.29e+00 ... (remaining 76615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 30565 17.96 - 35.91: 2275 35.91 - 53.87: 500 53.87 - 71.83: 99 71.83 - 89.79: 41 Dihedral angle restraints: 33480 sinusoidal: 12900 harmonic: 20580 Sorted by residual: dihedral pdb=" CD ARG e 35 " pdb=" NE ARG e 35 " pdb=" CZ ARG e 35 " pdb=" NH1 ARG e 35 " ideal model delta sinusoidal sigma weight residual 0.00 79.35 -79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB GLU I 259 " pdb=" CG GLU I 259 " pdb=" CD GLU I 259 " pdb=" OE1 GLU I 259 " ideal model delta sinusoidal sigma weight residual 0.00 89.23 -89.23 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU M 259 " pdb=" CG GLU M 259 " pdb=" CD GLU M 259 " pdb=" OE1 GLU M 259 " ideal model delta sinusoidal sigma weight residual 0.00 89.20 -89.20 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 33477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7680 0.058 - 0.117: 991 0.117 - 0.175: 49 0.175 - 0.234: 0 0.234 - 0.292: 20 Chirality restraints: 8740 Sorted by residual: chirality pdb=" CG LEU Y 81 " pdb=" CB LEU Y 81 " pdb=" CD1 LEU Y 81 " pdb=" CD2 LEU Y 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU d 81 " pdb=" CB LEU d 81 " pdb=" CD1 LEU d 81 " pdb=" CD2 LEU d 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU Z 81 " pdb=" CB LEU Z 81 " pdb=" CD1 LEU Z 81 " pdb=" CD2 LEU Z 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 8737 not shown) Planarity restraints: 9540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG e 35 " 1.083 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG e 35 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG e 35 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG e 35 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG e 35 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 14 " -0.238 9.50e-02 1.11e+02 1.07e-01 7.15e+00 pdb=" NE ARG H 14 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 14 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 14 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 14 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 14 " 0.238 9.50e-02 1.11e+02 1.07e-01 7.15e+00 pdb=" NE ARG F 14 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG F 14 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 14 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 14 " 0.006 2.00e-02 2.50e+03 ... (remaining 9537 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1018 2.69 - 3.24: 56565 3.24 - 3.79: 86419 3.79 - 4.35: 104153 4.35 - 4.90: 177265 Nonbonded interactions: 425420 Sorted by model distance: nonbonded pdb=" OH TYR I 142 " pdb=" OE1 GLU I 176 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR N 142 " pdb=" OE1 GLU N 176 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR D 142 " pdb=" OE1 GLU D 176 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR E 142 " pdb=" OE1 GLU E 176 " model vdw 2.133 3.040 nonbonded pdb=" OH TYR K 142 " pdb=" OE1 GLU K 176 " model vdw 2.133 3.040 ... (remaining 425415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.190 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: 0.060 Extract box with map and model: 1.900 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 98.350 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.004 0.042 56600 Z= 0.268 Angle : 0.710 8.247 76620 Z= 0.373 Chirality : 0.041 0.292 8740 Planarity : 0.008 0.485 9540 Dihedral : 13.550 89.787 20040 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.16 % Allowed : 20.43 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.10), residues: 6820 helix: 2.56 (0.08), residues: 3920 sheet: 2.02 (0.15), residues: 880 loop : -0.26 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 221 HIS 0.005 0.001 HIS Q 263 PHE 0.031 0.002 PHE T 160 TYR 0.013 0.002 TYR M 51 ARG 0.008 0.001 ARG O 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1013 time to evaluate : 4.568 Fit side-chains REVERT: B 105 PHE cc_start: 0.8086 (t80) cc_final: 0.7748 (t80) REVERT: B 238 GLN cc_start: 0.7850 (tt0) cc_final: 0.7598 (tt0) REVERT: C 96 GLU cc_start: 0.6054 (mp0) cc_final: 0.5072 (mt-10) REVERT: C 244 MET cc_start: 0.7719 (tpt) cc_final: 0.6995 (tpp) REVERT: D 244 MET cc_start: 0.8183 (tpt) cc_final: 0.7938 (tpt) REVERT: E 187 MET cc_start: 0.7573 (mmm) cc_final: 0.6416 (ttp) REVERT: F 47 LYS cc_start: 0.6651 (ptpt) cc_final: 0.6376 (pttt) REVERT: F 238 GLN cc_start: 0.7619 (tt0) cc_final: 0.6945 (tt0) REVERT: G 244 MET cc_start: 0.7886 (tpt) cc_final: 0.7616 (tpp) REVERT: H 244 MET cc_start: 0.8187 (tpt) cc_final: 0.7943 (tpp) REVERT: I 244 MET cc_start: 0.7925 (tpt) cc_final: 0.7500 (tpp) REVERT: J 244 MET cc_start: 0.7996 (tpt) cc_final: 0.7498 (tpp) REVERT: L 105 PHE cc_start: 0.8136 (t80) cc_final: 0.7913 (t80) REVERT: M 274 ASP cc_start: 0.7394 (m-30) cc_final: 0.7048 (m-30) REVERT: R 273 LYS cc_start: 0.8073 (tptp) cc_final: 0.7843 (mttp) REVERT: S 187 MET cc_start: 0.7165 (mmm) cc_final: 0.6049 (ttp) REVERT: S 244 MET cc_start: 0.7624 (tpt) cc_final: 0.7113 (tpt) REVERT: T 244 MET cc_start: 0.7550 (tpt) cc_final: 0.7292 (tpt) REVERT: W 107 GLN cc_start: 0.4224 (mm-40) cc_final: 0.3771 (mm110) REVERT: l 58 THR cc_start: 0.4915 (t) cc_final: 0.4685 (p) REVERT: m 58 THR cc_start: 0.4850 (t) cc_final: 0.4649 (p) outliers start: 70 outliers final: 38 residues processed: 1082 average time/residue: 0.5242 time to fit residues: 976.1876 Evaluate side-chains 822 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 784 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 271 ASP Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 271 ASP Chi-restraints excluded: chain O residue 154 GLU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 271 ASP Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain Q residue 154 GLU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain S residue 154 GLU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain h residue 70 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 591 optimal weight: 10.0000 chunk 530 optimal weight: 0.9980 chunk 294 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 357 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 548 optimal weight: 0.3980 chunk 212 optimal weight: 1.9990 chunk 333 optimal weight: 0.0570 chunk 408 optimal weight: 0.9990 chunk 635 optimal weight: 6.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN U 110 GLN ** B 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN ** C 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 270 GLN ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 GLN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN ** K 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** L 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 238 GLN ** M 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 GLN N 238 GLN ** O 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 GLN O 238 GLN ** P 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 186 GLN Q 6 ASN Q 186 GLN ** R 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 GLN S 186 GLN ** T 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 186 GLN V 110 GLN W 110 GLN X 110 GLN Y 110 GLN Z 110 GLN a 110 GLN b 110 GLN c 110 GLN d 110 GLN e 110 GLN f 110 GLN g 110 GLN h 110 GLN i 110 GLN j 110 GLN k 110 GLN l 110 GLN m 110 GLN n 110 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 56600 Z= 0.181 Angle : 0.602 7.142 76620 Z= 0.314 Chirality : 0.038 0.261 8740 Planarity : 0.004 0.084 9540 Dihedral : 4.757 56.166 7704 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.91 % Allowed : 17.94 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.10), residues: 6820 helix: 2.63 (0.07), residues: 3940 sheet: 1.71 (0.14), residues: 980 loop : -0.25 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 221 HIS 0.005 0.001 HIS e 33 PHE 0.024 0.002 PHE F 105 TYR 0.014 0.001 TYR g 52 ARG 0.007 0.001 ARG H 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 883 time to evaluate : 4.494 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8036 (tt0) cc_final: 0.7777 (tt0) REVERT: B 230 GLU cc_start: 0.7908 (tt0) cc_final: 0.7662 (tm-30) REVERT: B 231 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (mm) REVERT: B 244 MET cc_start: 0.8275 (tpt) cc_final: 0.7656 (tpp) REVERT: C 96 GLU cc_start: 0.5814 (mp0) cc_final: 0.5160 (mt-10) REVERT: C 244 MET cc_start: 0.7471 (tpt) cc_final: 0.7170 (tpp) REVERT: C 273 LYS cc_start: 0.8455 (ptmt) cc_final: 0.8220 (mttt) REVERT: D 238 GLN cc_start: 0.7969 (tt0) cc_final: 0.7621 (tt0) REVERT: D 244 MET cc_start: 0.8183 (tpt) cc_final: 0.7939 (tpt) REVERT: E 187 MET cc_start: 0.7454 (mmm) cc_final: 0.6277 (ttp) REVERT: G 244 MET cc_start: 0.7844 (tpt) cc_final: 0.7381 (tpp) REVERT: H 244 MET cc_start: 0.8109 (tpt) cc_final: 0.7837 (tpp) REVERT: I 244 MET cc_start: 0.7862 (tpt) cc_final: 0.7415 (tpp) REVERT: J 238 GLN cc_start: 0.7987 (tt0) cc_final: 0.7621 (tt0) REVERT: J 244 MET cc_start: 0.7937 (tpt) cc_final: 0.7477 (tpp) REVERT: K 238 GLN cc_start: 0.8072 (tt0) cc_final: 0.7838 (tt0) REVERT: L 229 ARG cc_start: 0.8654 (tpp80) cc_final: 0.7420 (mtm110) REVERT: M 270 GLN cc_start: 0.6147 (tp-100) cc_final: 0.5908 (tp-100) REVERT: N 244 MET cc_start: 0.8309 (tpt) cc_final: 0.8101 (tpp) REVERT: O 230 GLU cc_start: 0.7954 (tt0) cc_final: 0.7646 (tm-30) REVERT: O 238 GLN cc_start: 0.7921 (tt0) cc_final: 0.7490 (tt0) REVERT: P 7 ASN cc_start: 0.6938 (p0) cc_final: 0.6629 (p0) REVERT: Q 238 GLN cc_start: 0.7735 (tt0) cc_final: 0.7303 (tt0) REVERT: R 244 MET cc_start: 0.7115 (tpp) cc_final: 0.6709 (tpp) REVERT: R 251 LEU cc_start: 0.8586 (tp) cc_final: 0.8367 (tp) REVERT: S 187 MET cc_start: 0.7193 (mmm) cc_final: 0.6076 (ttp) REVERT: S 244 MET cc_start: 0.7406 (tpt) cc_final: 0.6830 (tpp) REVERT: T 6 ASN cc_start: 0.4552 (t0) cc_final: 0.4219 (p0) REVERT: T 238 GLN cc_start: 0.7696 (tt0) cc_final: 0.7463 (tt0) REVERT: T 244 MET cc_start: 0.7441 (tpt) cc_final: 0.7035 (tpp) REVERT: a 19 ARG cc_start: 0.5504 (tpt90) cc_final: 0.5092 (mmm-85) REVERT: g 82 GLN cc_start: 0.6511 (tm-30) cc_final: 0.6274 (tm-30) REVERT: h 107 GLN cc_start: 0.5610 (tm-30) cc_final: 0.5174 (mm-40) REVERT: i 107 GLN cc_start: 0.6088 (tm-30) cc_final: 0.5402 (pm20) REVERT: l 58 THR cc_start: 0.5150 (t) cc_final: 0.4870 (p) REVERT: m 58 THR cc_start: 0.5538 (t) cc_final: 0.5289 (p) REVERT: n 68 PHE cc_start: 0.5572 (m-80) cc_final: 0.5340 (m-80) outliers start: 175 outliers final: 98 residues processed: 987 average time/residue: 0.4821 time to fit residues: 820.0059 Evaluate side-chains 845 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 746 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 224 HIS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 224 HIS Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 250 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain a residue 70 ILE Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 70 ILE Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 70 ILE Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 70 ILE Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 70 ILE Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 70 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 70 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 0.0870 chunk 197 optimal weight: 4.9990 chunk 529 optimal weight: 40.0000 chunk 432 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 636 optimal weight: 0.5980 chunk 687 optimal weight: 30.0000 chunk 567 optimal weight: 40.0000 chunk 631 optimal weight: 30.0000 chunk 217 optimal weight: 20.0000 chunk 510 optimal weight: 5.9990 overall best weight: 1.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN B 6 ASN C 6 ASN D 6 ASN E 6 ASN F 6 ASN F 238 GLN G 6 ASN G 238 GLN H 6 ASN I 6 ASN J 6 ASN K 6 ASN L 6 ASN M 6 ASN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 270 GLN N 6 ASN O 6 ASN P 6 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 ASN S 181 HIS S 238 GLN T 6 ASN Z 59 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 56600 Z= 0.181 Angle : 0.567 6.866 76620 Z= 0.296 Chirality : 0.037 0.186 8740 Planarity : 0.003 0.035 9540 Dihedral : 3.945 29.358 7624 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.89 % Allowed : 17.34 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.10), residues: 6820 helix: 2.50 (0.07), residues: 4000 sheet: 1.61 (0.14), residues: 980 loop : -0.38 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP e 36 HIS 0.002 0.001 HIS F 263 PHE 0.026 0.002 PHE F 105 TYR 0.018 0.001 TYR J 142 ARG 0.007 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 828 time to evaluate : 4.589 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7870 (mmm) cc_final: 0.7607 (mmm) REVERT: A 238 GLN cc_start: 0.8014 (tt0) cc_final: 0.7796 (tt0) REVERT: B 231 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 244 MET cc_start: 0.8253 (tpt) cc_final: 0.7775 (tpp) REVERT: C 96 GLU cc_start: 0.5757 (mp0) cc_final: 0.5138 (mt-10) REVERT: C 244 MET cc_start: 0.7557 (tpt) cc_final: 0.7101 (tpp) REVERT: D 238 GLN cc_start: 0.7992 (tt0) cc_final: 0.7660 (tt0) REVERT: D 244 MET cc_start: 0.8290 (tpt) cc_final: 0.7729 (tpp) REVERT: E 187 MET cc_start: 0.7485 (mmm) cc_final: 0.6308 (ttp) REVERT: G 244 MET cc_start: 0.7876 (tpt) cc_final: 0.7257 (tpp) REVERT: H 238 GLN cc_start: 0.8077 (tt0) cc_final: 0.7840 (tt0) REVERT: H 244 MET cc_start: 0.8144 (tpt) cc_final: 0.7844 (tpp) REVERT: I 238 GLN cc_start: 0.8051 (tt0) cc_final: 0.7828 (tt0) REVERT: I 244 MET cc_start: 0.7979 (tpt) cc_final: 0.7495 (tpp) REVERT: J 105 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7825 (t80) REVERT: J 238 GLN cc_start: 0.8030 (tt0) cc_final: 0.7761 (tt0) REVERT: J 244 MET cc_start: 0.7836 (tpt) cc_final: 0.7290 (tpp) REVERT: K 238 GLN cc_start: 0.8064 (tt0) cc_final: 0.7778 (tt0) REVERT: M 238 GLN cc_start: 0.7937 (tt0) cc_final: 0.7598 (tt0) REVERT: O 230 GLU cc_start: 0.8023 (tt0) cc_final: 0.7647 (tm-30) REVERT: P 7 ASN cc_start: 0.7104 (p0) cc_final: 0.6800 (p0) REVERT: P 238 GLN cc_start: 0.8017 (tt0) cc_final: 0.7804 (tt0) REVERT: Q 238 GLN cc_start: 0.7769 (tt0) cc_final: 0.7426 (tt0) REVERT: R 244 MET cc_start: 0.7245 (tpp) cc_final: 0.6521 (tpp) REVERT: S 187 MET cc_start: 0.7257 (mmm) cc_final: 0.6126 (ttp) REVERT: S 244 MET cc_start: 0.7361 (tpt) cc_final: 0.6627 (tpp) REVERT: T 244 MET cc_start: 0.7498 (tpt) cc_final: 0.7050 (tpp) REVERT: f 18 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4214 (mp) REVERT: f 22 CYS cc_start: 0.6366 (t) cc_final: 0.6092 (t) REVERT: g 82 GLN cc_start: 0.6369 (tm-30) cc_final: 0.6092 (tm-30) REVERT: k 34 MET cc_start: 0.2359 (mmm) cc_final: 0.1873 (mmm) REVERT: k 107 GLN cc_start: 0.5700 (tm-30) cc_final: 0.5128 (pm20) REVERT: m 58 THR cc_start: 0.5822 (t) cc_final: 0.5566 (p) outliers start: 234 outliers final: 150 residues processed: 960 average time/residue: 0.4897 time to fit residues: 814.7473 Evaluate side-chains 890 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 737 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 18 LEU Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 70 ILE Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 70 ILE Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 10.0000 chunk 478 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 427 optimal weight: 4.9990 chunk 639 optimal weight: 30.0000 chunk 676 optimal weight: 0.4980 chunk 333 optimal weight: 9.9990 chunk 605 optimal weight: 30.0000 chunk 182 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS ** U 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS K 6 ASN M 227 ASN N 6 ASN O 238 GLN P 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 181 HIS Z 59 HIS c 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 56600 Z= 0.193 Angle : 0.571 8.460 76620 Z= 0.297 Chirality : 0.038 0.183 8740 Planarity : 0.003 0.036 9540 Dihedral : 3.959 18.039 7620 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.42 % Allowed : 18.17 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.10), residues: 6820 helix: 2.46 (0.08), residues: 4000 sheet: 1.54 (0.14), residues: 980 loop : -0.47 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Z 47 HIS 0.005 0.001 HIS Z 33 PHE 0.029 0.002 PHE F 105 TYR 0.013 0.001 TYR c 95 ARG 0.008 0.000 ARG H 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 811 time to evaluate : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7819 (mmm) cc_final: 0.7536 (mmm) REVERT: U 52 TYR cc_start: 0.3597 (OUTLIER) cc_final: 0.3028 (m-80) REVERT: B 244 MET cc_start: 0.8296 (tpt) cc_final: 0.7807 (tpp) REVERT: C 244 MET cc_start: 0.7550 (tpt) cc_final: 0.7103 (tpp) REVERT: C 273 LYS cc_start: 0.8489 (ptmt) cc_final: 0.8212 (mttm) REVERT: D 238 GLN cc_start: 0.8003 (tt0) cc_final: 0.7654 (tt0) REVERT: D 244 MET cc_start: 0.8278 (tpt) cc_final: 0.7725 (tpp) REVERT: E 244 MET cc_start: 0.7757 (tpp) cc_final: 0.7379 (tpp) REVERT: F 238 GLN cc_start: 0.8012 (tt0) cc_final: 0.7585 (tt0) REVERT: G 244 MET cc_start: 0.7834 (tpt) cc_final: 0.7231 (tpp) REVERT: H 244 MET cc_start: 0.8151 (tpt) cc_final: 0.7891 (tpp) REVERT: I 238 GLN cc_start: 0.8064 (tt0) cc_final: 0.7813 (tt0) REVERT: I 244 MET cc_start: 0.8099 (tpt) cc_final: 0.7609 (tpp) REVERT: J 104 PHE cc_start: 0.6599 (t80) cc_final: 0.6344 (t80) REVERT: J 105 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7831 (t80) REVERT: J 238 GLN cc_start: 0.8061 (tt0) cc_final: 0.7740 (tt0) REVERT: J 244 MET cc_start: 0.7797 (tpt) cc_final: 0.7254 (tpp) REVERT: K 238 GLN cc_start: 0.8061 (tt0) cc_final: 0.7757 (tt0) REVERT: K 251 LEU cc_start: 0.8216 (tp) cc_final: 0.8007 (tp) REVERT: L 187 MET cc_start: 0.7796 (mmm) cc_final: 0.7447 (mmm) REVERT: M 227 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7582 (t0) REVERT: M 238 GLN cc_start: 0.7963 (tt0) cc_final: 0.7668 (tt0) REVERT: O 230 GLU cc_start: 0.8118 (tt0) cc_final: 0.7707 (tm-30) REVERT: P 7 ASN cc_start: 0.7168 (p0) cc_final: 0.6920 (p0) REVERT: P 238 GLN cc_start: 0.8061 (tt0) cc_final: 0.7820 (tt0) REVERT: Q 238 GLN cc_start: 0.7843 (tt0) cc_final: 0.7531 (tt0) REVERT: R 6 ASN cc_start: 0.4584 (t160) cc_final: 0.4123 (p0) REVERT: R 96 GLU cc_start: 0.5957 (mp0) cc_final: 0.5648 (mt-10) REVERT: R 135 GLU cc_start: 0.7606 (tt0) cc_final: 0.7124 (tt0) REVERT: R 244 MET cc_start: 0.7396 (tpp) cc_final: 0.6664 (tpp) REVERT: S 105 PHE cc_start: 0.8267 (t80) cc_final: 0.7976 (t80) REVERT: S 187 MET cc_start: 0.7393 (mmm) cc_final: 0.6356 (ttp) REVERT: S 244 MET cc_start: 0.7392 (tpt) cc_final: 0.7096 (tpp) REVERT: T 105 PHE cc_start: 0.8161 (t80) cc_final: 0.7916 (t80) REVERT: T 244 MET cc_start: 0.7521 (tpt) cc_final: 0.7051 (tpp) REVERT: Z 35 ARG cc_start: 0.5537 (mtm-85) cc_final: 0.5118 (mtm-85) REVERT: b 35 ARG cc_start: 0.5389 (mtt-85) cc_final: 0.4445 (mtt-85) REVERT: g 35 ARG cc_start: 0.5494 (mmt90) cc_final: 0.5129 (mtt-85) REVERT: g 82 GLN cc_start: 0.6420 (tm-30) cc_final: 0.6111 (tm-30) REVERT: h 35 ARG cc_start: 0.5500 (mtt90) cc_final: 0.5112 (mtt-85) REVERT: h 107 GLN cc_start: 0.5603 (tm-30) cc_final: 0.5038 (pm20) REVERT: i 107 GLN cc_start: 0.5816 (tm-30) cc_final: 0.5058 (pm20) REVERT: j 35 ARG cc_start: 0.5321 (mmt90) cc_final: 0.5021 (mtt-85) REVERT: k 34 MET cc_start: 0.2824 (mmm) cc_final: 0.2406 (mmm) REVERT: k 107 GLN cc_start: 0.5711 (tm-30) cc_final: 0.5115 (pm20) outliers start: 266 outliers final: 190 residues processed: 985 average time/residue: 0.4726 time to fit residues: 813.8204 Evaluate side-chains 891 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 698 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 12 VAL Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 20.0000 chunk 384 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 503 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 577 optimal weight: 30.0000 chunk 467 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 345 optimal weight: 0.0570 chunk 607 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 147 ASN ** U 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN D 147 ASN E 147 ASN F 6 ASN G 6 ASN G 147 ASN H 238 GLN I 6 ASN I 147 ASN J 6 ASN K 147 ASN L 147 ASN N 147 ASN O 147 ASN P 6 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 ASN S 234 GLN S 238 GLN T 6 ASN T 147 ASN ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56600 Z= 0.208 Angle : 0.577 9.428 76620 Z= 0.301 Chirality : 0.038 0.181 8740 Planarity : 0.003 0.047 9540 Dihedral : 4.064 17.429 7620 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.22 % Allowed : 17.74 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.10), residues: 6820 helix: 2.40 (0.08), residues: 4000 sheet: 1.53 (0.14), residues: 980 loop : -0.47 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 47 HIS 0.004 0.001 HIS c 33 PHE 0.029 0.002 PHE F 105 TYR 0.011 0.001 TYR c 95 ARG 0.008 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 752 time to evaluate : 4.603 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7795 (mmm) cc_final: 0.7580 (mmm) REVERT: B 22 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8701 (tm) REVERT: B 244 MET cc_start: 0.8306 (tpt) cc_final: 0.7838 (tpp) REVERT: C 6 ASN cc_start: 0.4952 (t160) cc_final: 0.4229 (p0) REVERT: C 244 MET cc_start: 0.7624 (tpt) cc_final: 0.7132 (tpp) REVERT: C 273 LYS cc_start: 0.8449 (ptmt) cc_final: 0.8171 (mttm) REVERT: D 187 MET cc_start: 0.7918 (mmm) cc_final: 0.7628 (mmm) REVERT: D 238 GLN cc_start: 0.7965 (tt0) cc_final: 0.7659 (tt0) REVERT: D 244 MET cc_start: 0.8286 (tpt) cc_final: 0.7734 (tpp) REVERT: E 22 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8679 (tm) REVERT: E 244 MET cc_start: 0.7803 (tpp) cc_final: 0.7427 (tpp) REVERT: G 22 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8714 (tm) REVERT: G 244 MET cc_start: 0.7792 (tpt) cc_final: 0.7236 (tpp) REVERT: H 244 MET cc_start: 0.8178 (tpt) cc_final: 0.7914 (tpp) REVERT: I 238 GLN cc_start: 0.8032 (tt0) cc_final: 0.7777 (tt0) REVERT: I 244 MET cc_start: 0.8161 (tpt) cc_final: 0.7626 (tpp) REVERT: J 22 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8706 (tm) REVERT: J 104 PHE cc_start: 0.6635 (t80) cc_final: 0.6388 (t80) REVERT: J 105 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7835 (t80) REVERT: J 238 GLN cc_start: 0.8031 (tt0) cc_final: 0.7760 (tt0) REVERT: J 244 MET cc_start: 0.7792 (tpt) cc_final: 0.7224 (tpp) REVERT: K 238 GLN cc_start: 0.8052 (tt0) cc_final: 0.7732 (tt0) REVERT: L 22 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8714 (tm) REVERT: L 244 MET cc_start: 0.8063 (tpt) cc_final: 0.7500 (tpp) REVERT: M 238 GLN cc_start: 0.7994 (tt0) cc_final: 0.7700 (tt0) REVERT: O 22 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8731 (tm) REVERT: P 7 ASN cc_start: 0.7212 (p0) cc_final: 0.6975 (p0) REVERT: P 238 GLN cc_start: 0.8032 (tt0) cc_final: 0.7817 (tt0) REVERT: Q 22 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8689 (tm) REVERT: Q 238 GLN cc_start: 0.7872 (tt0) cc_final: 0.7546 (tt0) REVERT: R 6 ASN cc_start: 0.4469 (t160) cc_final: 0.4112 (p0) REVERT: R 244 MET cc_start: 0.7531 (tpp) cc_final: 0.7284 (tpp) REVERT: S 105 PHE cc_start: 0.8258 (t80) cc_final: 0.8020 (t80) REVERT: S 244 MET cc_start: 0.7407 (tpt) cc_final: 0.7040 (tpp) REVERT: T 22 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8753 (tm) REVERT: T 105 PHE cc_start: 0.8137 (t80) cc_final: 0.7865 (t80) REVERT: T 244 MET cc_start: 0.7613 (tpt) cc_final: 0.7128 (tpp) REVERT: V 34 MET cc_start: 0.3481 (OUTLIER) cc_final: 0.3105 (mmm) REVERT: X 52 TYR cc_start: 0.4008 (OUTLIER) cc_final: 0.2931 (m-10) REVERT: i 107 GLN cc_start: 0.5710 (tm-30) cc_final: 0.4869 (pm20) REVERT: j 34 MET cc_start: 0.3374 (OUTLIER) cc_final: 0.3001 (mmm) REVERT: k 34 MET cc_start: 0.3118 (mmm) cc_final: 0.2718 (mmm) REVERT: k 107 GLN cc_start: 0.5820 (tm-30) cc_final: 0.5197 (pm20) REVERT: n 34 MET cc_start: 0.3359 (OUTLIER) cc_final: 0.3055 (mmm) outliers start: 314 outliers final: 211 residues processed: 978 average time/residue: 0.4591 time to fit residues: 796.3709 Evaluate side-chains 898 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 674 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 213 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 83 MET Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 7 SER Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 1.9990 chunk 609 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 397 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 677 optimal weight: 20.0000 chunk 562 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 181 HIS E 147 ASN H 6 ASN L 147 ASN M 6 ASN O 6 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 56600 Z= 0.172 Angle : 0.568 8.866 76620 Z= 0.292 Chirality : 0.037 0.169 8740 Planarity : 0.003 0.040 9540 Dihedral : 4.002 17.088 7620 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.99 % Allowed : 19.44 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.10), residues: 6820 helix: 2.43 (0.08), residues: 4020 sheet: 1.51 (0.13), residues: 1100 loop : -0.68 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Z 47 HIS 0.004 0.000 HIS b 33 PHE 0.029 0.002 PHE F 105 TYR 0.011 0.001 TYR f 95 ARG 0.009 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 746 time to evaluate : 4.659 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8696 (tm) REVERT: B 244 MET cc_start: 0.8279 (tpt) cc_final: 0.7824 (tpp) REVERT: C 6 ASN cc_start: 0.4946 (t160) cc_final: 0.4145 (p0) REVERT: C 244 MET cc_start: 0.7619 (tpt) cc_final: 0.7151 (tpp) REVERT: C 273 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8178 (mttt) REVERT: D 238 GLN cc_start: 0.7942 (tt0) cc_final: 0.7624 (tt0) REVERT: D 244 MET cc_start: 0.8291 (tpt) cc_final: 0.7742 (tpp) REVERT: E 22 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8663 (tm) REVERT: E 244 MET cc_start: 0.7768 (tpp) cc_final: 0.7456 (tpp) REVERT: G 22 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8697 (tm) REVERT: G 244 MET cc_start: 0.7776 (tpt) cc_final: 0.7250 (tpp) REVERT: H 244 MET cc_start: 0.8154 (tpt) cc_final: 0.7880 (tpp) REVERT: I 238 GLN cc_start: 0.8000 (tt0) cc_final: 0.7754 (tt0) REVERT: I 244 MET cc_start: 0.8176 (tpt) cc_final: 0.7622 (tpp) REVERT: J 22 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8693 (tm) REVERT: J 105 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7643 (t80) REVERT: J 238 GLN cc_start: 0.7999 (tt0) cc_final: 0.7677 (tt0) REVERT: J 244 MET cc_start: 0.7765 (tpt) cc_final: 0.7271 (tpp) REVERT: K 238 GLN cc_start: 0.8031 (tt0) cc_final: 0.7708 (tt0) REVERT: K 244 MET cc_start: 0.8149 (tpt) cc_final: 0.7603 (tpp) REVERT: L 22 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8718 (tm) REVERT: L 187 MET cc_start: 0.7703 (mmm) cc_final: 0.7386 (mmm) REVERT: L 244 MET cc_start: 0.8039 (tpt) cc_final: 0.7516 (tpp) REVERT: M 238 GLN cc_start: 0.7894 (tt0) cc_final: 0.7607 (tt0) REVERT: O 22 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8707 (tm) REVERT: P 7 ASN cc_start: 0.7245 (p0) cc_final: 0.6992 (p0) REVERT: P 187 MET cc_start: 0.7811 (mmm) cc_final: 0.7529 (mmm) REVERT: Q 22 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8683 (tm) REVERT: Q 238 GLN cc_start: 0.7789 (tt0) cc_final: 0.7534 (tt0) REVERT: Q 274 ASP cc_start: 0.8073 (p0) cc_final: 0.7842 (p0) REVERT: R 6 ASN cc_start: 0.4574 (t160) cc_final: 0.4202 (p0) REVERT: R 104 PHE cc_start: 0.6402 (t80) cc_final: 0.6145 (t80) REVERT: R 244 MET cc_start: 0.7535 (tpp) cc_final: 0.7312 (tpp) REVERT: S 244 MET cc_start: 0.7372 (tpt) cc_final: 0.6997 (tpp) REVERT: T 22 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8715 (tm) REVERT: T 244 MET cc_start: 0.7562 (tpt) cc_final: 0.7161 (tpp) REVERT: V 34 MET cc_start: 0.3572 (mmm) cc_final: 0.3216 (mmm) REVERT: c 34 MET cc_start: 0.6240 (tpp) cc_final: 0.5808 (tpp) REVERT: e 83 MET cc_start: 0.7066 (ptp) cc_final: 0.6844 (ptt) REVERT: h 107 GLN cc_start: 0.5386 (tm-30) cc_final: 0.4828 (pm20) REVERT: i 107 GLN cc_start: 0.5735 (tm-30) cc_final: 0.4954 (pm20) REVERT: j 34 MET cc_start: 0.3497 (OUTLIER) cc_final: 0.3163 (mmm) REVERT: k 107 GLN cc_start: 0.5838 (tm-30) cc_final: 0.5246 (pm20) REVERT: n 34 MET cc_start: 0.3711 (OUTLIER) cc_final: 0.3401 (mmm) outliers start: 240 outliers final: 186 residues processed: 933 average time/residue: 0.4690 time to fit residues: 768.3003 Evaluate side-chains 865 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 668 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 147 ASN Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 213 LEU Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 188 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 5 VAL Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 494 optimal weight: 1.9990 chunk 383 optimal weight: 0.6980 chunk 570 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 chunk 674 optimal weight: 20.0000 chunk 422 optimal weight: 3.9990 chunk 411 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN L 6 ASN N 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 ASN S 238 GLN T 238 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 56600 Z= 0.234 Angle : 0.608 8.467 76620 Z= 0.316 Chirality : 0.039 0.189 8740 Planarity : 0.004 0.040 9540 Dihedral : 4.177 18.212 7620 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.47 % Allowed : 19.62 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.10), residues: 6820 helix: 2.28 (0.08), residues: 4020 sheet: 1.45 (0.14), residues: 1100 loop : -0.74 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 47 HIS 0.004 0.001 HIS Q 239 PHE 0.030 0.002 PHE S 105 TYR 0.015 0.001 TYR R 220 ARG 0.009 0.000 ARG Q 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 738 time to evaluate : 4.763 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8698 (tm) REVERT: C 6 ASN cc_start: 0.4949 (t160) cc_final: 0.4130 (p0) REVERT: C 244 MET cc_start: 0.7749 (tpt) cc_final: 0.7154 (tpp) REVERT: C 273 LYS cc_start: 0.8441 (ptmt) cc_final: 0.8199 (mttt) REVERT: D 238 GLN cc_start: 0.7983 (tt0) cc_final: 0.7705 (tt0) REVERT: D 244 MET cc_start: 0.8301 (tpt) cc_final: 0.7764 (tpp) REVERT: E 22 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8651 (tm) REVERT: E 244 MET cc_start: 0.7792 (tpp) cc_final: 0.7483 (tpp) REVERT: F 238 GLN cc_start: 0.8114 (tt0) cc_final: 0.7828 (tt0) REVERT: G 22 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8705 (tm) REVERT: G 244 MET cc_start: 0.7888 (tpt) cc_final: 0.7294 (tpp) REVERT: H 244 MET cc_start: 0.8196 (tpt) cc_final: 0.7937 (tpp) REVERT: I 238 GLN cc_start: 0.8026 (tt0) cc_final: 0.7785 (tt0) REVERT: I 244 MET cc_start: 0.8251 (tpt) cc_final: 0.7948 (tpp) REVERT: J 22 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8700 (tm) REVERT: J 238 GLN cc_start: 0.8004 (tt0) cc_final: 0.7696 (tt0) REVERT: J 244 MET cc_start: 0.7826 (tpt) cc_final: 0.7264 (tpp) REVERT: K 238 GLN cc_start: 0.8054 (tt0) cc_final: 0.7741 (tt0) REVERT: K 244 MET cc_start: 0.8174 (tpt) cc_final: 0.7649 (tpp) REVERT: L 22 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8704 (tm) REVERT: L 244 MET cc_start: 0.8112 (tpt) cc_final: 0.7627 (tpp) REVERT: M 238 GLN cc_start: 0.7942 (tt0) cc_final: 0.7644 (tt0) REVERT: O 22 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8729 (tm) REVERT: P 7 ASN cc_start: 0.7254 (p0) cc_final: 0.6991 (p0) REVERT: Q 22 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8705 (tm) REVERT: Q 238 GLN cc_start: 0.7833 (tt0) cc_final: 0.7582 (tt0) REVERT: Q 274 ASP cc_start: 0.8112 (p0) cc_final: 0.7854 (p0) REVERT: R 244 MET cc_start: 0.7633 (tpp) cc_final: 0.7420 (tpp) REVERT: S 104 PHE cc_start: 0.6689 (t80) cc_final: 0.6480 (t80) REVERT: S 244 MET cc_start: 0.7538 (tpt) cc_final: 0.7136 (tpp) REVERT: T 22 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8709 (tm) REVERT: T 244 MET cc_start: 0.7708 (tpt) cc_final: 0.7236 (tpp) REVERT: V 34 MET cc_start: 0.3937 (OUTLIER) cc_final: 0.3511 (mmm) REVERT: W 34 MET cc_start: 0.3843 (mtm) cc_final: 0.3583 (mtt) REVERT: a 11 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5208 (pt) REVERT: h 107 GLN cc_start: 0.5679 (tm-30) cc_final: 0.4917 (pm20) REVERT: i 107 GLN cc_start: 0.5928 (tm-30) cc_final: 0.5010 (pm20) REVERT: k 107 GLN cc_start: 0.5905 (tm-30) cc_final: 0.5189 (pm20) REVERT: n 34 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.3825 (mmm) outliers start: 269 outliers final: 210 residues processed: 949 average time/residue: 0.4802 time to fit residues: 805.7116 Evaluate side-chains 891 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 670 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 5 VAL Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain i residue 81 LEU Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 7 SER Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 0.9980 chunk 269 optimal weight: 20.0000 chunk 402 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 428 optimal weight: 1.9990 chunk 459 optimal weight: 2.9990 chunk 333 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 530 optimal weight: 9.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 HIS Q 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 56600 Z= 0.163 Angle : 0.577 9.183 76620 Z= 0.295 Chirality : 0.037 0.167 8740 Planarity : 0.003 0.042 9540 Dihedral : 4.037 17.825 7620 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.94 % Allowed : 21.78 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.10), residues: 6820 helix: 2.45 (0.08), residues: 4020 sheet: 1.51 (0.14), residues: 1100 loop : -0.65 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 221 HIS 0.003 0.000 HIS h 33 PHE 0.030 0.002 PHE F 105 TYR 0.013 0.001 TYR I 220 ARG 0.012 0.000 ARG M 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 752 time to evaluate : 4.518 Fit side-chains REVERT: B 22 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8714 (tm) REVERT: B 244 MET cc_start: 0.8223 (tpt) cc_final: 0.7796 (tpp) REVERT: C 6 ASN cc_start: 0.4918 (t160) cc_final: 0.4141 (p0) REVERT: C 244 MET cc_start: 0.7659 (tpt) cc_final: 0.7161 (tpp) REVERT: C 273 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8134 (mttt) REVERT: D 238 GLN cc_start: 0.7928 (tt0) cc_final: 0.7682 (tt0) REVERT: D 244 MET cc_start: 0.8284 (tpt) cc_final: 0.7752 (tpp) REVERT: E 22 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8634 (tm) REVERT: E 244 MET cc_start: 0.7704 (tpp) cc_final: 0.7452 (tpp) REVERT: G 22 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8694 (tm) REVERT: G 244 MET cc_start: 0.7785 (tpt) cc_final: 0.7329 (tpp) REVERT: H 244 MET cc_start: 0.8176 (tpt) cc_final: 0.7806 (tpp) REVERT: I 238 GLN cc_start: 0.7972 (tt0) cc_final: 0.7739 (tt0) REVERT: I 244 MET cc_start: 0.8225 (tpt) cc_final: 0.7977 (tpp) REVERT: J 22 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8696 (tm) REVERT: J 238 GLN cc_start: 0.7960 (tt0) cc_final: 0.7696 (tt0) REVERT: J 244 MET cc_start: 0.7759 (tpt) cc_final: 0.7368 (tpp) REVERT: K 244 MET cc_start: 0.8143 (tpt) cc_final: 0.7645 (tpp) REVERT: L 22 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8726 (tm) REVERT: L 244 MET cc_start: 0.8039 (tpt) cc_final: 0.7574 (tpp) REVERT: M 238 GLN cc_start: 0.7838 (tt0) cc_final: 0.7548 (tt0) REVERT: O 22 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8704 (tm) REVERT: O 244 MET cc_start: 0.8327 (tpt) cc_final: 0.7857 (tpp) REVERT: P 7 ASN cc_start: 0.7265 (p0) cc_final: 0.7016 (p0) REVERT: Q 22 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8685 (tm) REVERT: Q 274 ASP cc_start: 0.8038 (p0) cc_final: 0.7776 (p0) REVERT: R 244 MET cc_start: 0.7579 (tpp) cc_final: 0.7354 (tpp) REVERT: S 244 MET cc_start: 0.7446 (tpt) cc_final: 0.7112 (tpp) REVERT: T 22 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8691 (tm) REVERT: T 152 LYS cc_start: 0.7498 (tptp) cc_final: 0.7277 (tptp) REVERT: T 244 MET cc_start: 0.7649 (tpt) cc_final: 0.7267 (tpp) REVERT: W 34 MET cc_start: 0.3777 (mtm) cc_final: 0.3570 (mtt) REVERT: a 11 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5212 (pt) REVERT: h 107 GLN cc_start: 0.5777 (tm-30) cc_final: 0.5037 (pm20) REVERT: i 107 GLN cc_start: 0.6002 (tm-30) cc_final: 0.5066 (pm20) REVERT: j 34 MET cc_start: 0.3812 (OUTLIER) cc_final: 0.3459 (mmm) REVERT: k 107 GLN cc_start: 0.5898 (tm-30) cc_final: 0.5240 (pm20) outliers start: 177 outliers final: 145 residues processed: 899 average time/residue: 0.4641 time to fit residues: 731.5523 Evaluate side-chains 832 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 677 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 255 ILE Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain c residue 81 LEU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 5 VAL Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 20.0000 chunk 646 optimal weight: 9.9990 chunk 589 optimal weight: 7.9990 chunk 628 optimal weight: 0.3980 chunk 378 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 493 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 568 optimal weight: 20.0000 chunk 594 optimal weight: 30.0000 chunk 626 optimal weight: 7.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 56600 Z= 0.267 Angle : 0.636 8.642 76620 Z= 0.329 Chirality : 0.039 0.193 8740 Planarity : 0.004 0.045 9540 Dihedral : 4.229 20.535 7620 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.11 % Allowed : 21.66 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.10), residues: 6820 helix: 2.25 (0.08), residues: 4000 sheet: 1.47 (0.14), residues: 1100 loop : -0.65 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 221 HIS 0.005 0.001 HIS Q 239 PHE 0.033 0.002 PHE F 105 TYR 0.022 0.002 TYR J 220 ARG 0.009 0.000 ARG Q 241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 687 time to evaluate : 4.594 Fit side-chains REVERT: B 22 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8690 (tm) REVERT: C 6 ASN cc_start: 0.5051 (t160) cc_final: 0.4213 (p0) REVERT: C 244 MET cc_start: 0.7853 (tpt) cc_final: 0.7236 (tpp) REVERT: C 273 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8181 (mttt) REVERT: D 238 GLN cc_start: 0.7998 (tt0) cc_final: 0.7721 (tt0) REVERT: D 244 MET cc_start: 0.8329 (tpt) cc_final: 0.7790 (tpp) REVERT: E 22 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8682 (tm) REVERT: E 244 MET cc_start: 0.7809 (tpp) cc_final: 0.7534 (tpp) REVERT: F 238 GLN cc_start: 0.8175 (tt0) cc_final: 0.7897 (tt0) REVERT: G 22 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8722 (tm) REVERT: G 244 MET cc_start: 0.7933 (tpt) cc_final: 0.7368 (tpp) REVERT: H 244 MET cc_start: 0.8146 (tpt) cc_final: 0.7670 (tpp) REVERT: I 238 GLN cc_start: 0.8060 (tt0) cc_final: 0.7828 (tt0) REVERT: I 244 MET cc_start: 0.8300 (tpt) cc_final: 0.8000 (tpp) REVERT: J 22 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8715 (tm) REVERT: J 238 GLN cc_start: 0.8034 (tt0) cc_final: 0.7759 (tt0) REVERT: J 244 MET cc_start: 0.7904 (tpt) cc_final: 0.7317 (tpp) REVERT: K 244 MET cc_start: 0.8208 (tpt) cc_final: 0.7702 (tpp) REVERT: L 22 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8704 (tm) REVERT: L 244 MET cc_start: 0.8159 (tpt) cc_final: 0.7711 (tpp) REVERT: M 238 GLN cc_start: 0.7882 (tt0) cc_final: 0.7637 (tt0) REVERT: M 264 ILE cc_start: 0.8593 (mm) cc_final: 0.8143 (pt) REVERT: N 244 MET cc_start: 0.7913 (tpp) cc_final: 0.7297 (tpp) REVERT: O 22 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8735 (tm) REVERT: O 244 MET cc_start: 0.8256 (tpt) cc_final: 0.7969 (tpp) REVERT: P 7 ASN cc_start: 0.7264 (p0) cc_final: 0.7002 (p0) REVERT: Q 22 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8697 (tm) REVERT: S 244 MET cc_start: 0.7672 (tpt) cc_final: 0.7166 (tpp) REVERT: T 22 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8731 (tm) REVERT: T 230 GLU cc_start: 0.7970 (tt0) cc_final: 0.7725 (tm-30) REVERT: T 237 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8098 (tm-30) REVERT: T 244 MET cc_start: 0.7814 (tpt) cc_final: 0.7314 (tpp) REVERT: a 11 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5251 (pt) REVERT: b 34 MET cc_start: 0.6129 (mmm) cc_final: 0.5815 (mmm) REVERT: c 34 MET cc_start: 0.6306 (mmp) cc_final: 0.5803 (ttt) REVERT: h 107 GLN cc_start: 0.5872 (tm-30) cc_final: 0.4995 (pm20) REVERT: i 107 GLN cc_start: 0.6113 (tm-30) cc_final: 0.5076 (pm20) REVERT: k 107 GLN cc_start: 0.5976 (tm-30) cc_final: 0.5214 (pm20) outliers start: 187 outliers final: 157 residues processed: 842 average time/residue: 0.4690 time to fit residues: 694.0515 Evaluate side-chains 812 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 645 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 52 TYR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain c residue 81 LEU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain e residue 98 VAL Chi-restraints excluded: chain f residue 5 VAL Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 52 TYR Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 0.8980 chunk 664 optimal weight: 40.0000 chunk 405 optimal weight: 6.9990 chunk 315 optimal weight: 8.9990 chunk 462 optimal weight: 0.8980 chunk 697 optimal weight: 5.9990 chunk 641 optimal weight: 20.0000 chunk 555 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 428 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 39 GLN C 6 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN a 59 HIS b 59 HIS b 82 GLN i 59 HIS j 39 GLN m 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 56600 Z= 0.227 Angle : 0.622 9.242 76620 Z= 0.320 Chirality : 0.039 0.190 8740 Planarity : 0.004 0.048 9540 Dihedral : 4.228 22.701 7620 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.84 % Allowed : 21.98 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.10), residues: 6820 helix: 2.21 (0.08), residues: 4020 sheet: 1.47 (0.14), residues: 1100 loop : -0.74 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP S 221 HIS 0.005 0.001 HIS V 33 PHE 0.030 0.002 PHE F 105 TYR 0.018 0.001 TYR J 220 ARG 0.010 0.000 ARG M 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 693 time to evaluate : 4.568 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8716 (tm) REVERT: C 244 MET cc_start: 0.7846 (tpt) cc_final: 0.7243 (tpp) REVERT: C 273 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8164 (mttt) REVERT: D 237 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8224 (tm-30) REVERT: D 238 GLN cc_start: 0.7965 (tt0) cc_final: 0.7679 (tt0) REVERT: D 244 MET cc_start: 0.8302 (tpt) cc_final: 0.7794 (tpp) REVERT: E 22 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8709 (tm) REVERT: E 244 MET cc_start: 0.7785 (tpp) cc_final: 0.7529 (tpp) REVERT: F 238 GLN cc_start: 0.8137 (tt0) cc_final: 0.7869 (tt0) REVERT: G 22 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8707 (tm) REVERT: G 244 MET cc_start: 0.7922 (tpt) cc_final: 0.7404 (tpp) REVERT: H 244 MET cc_start: 0.8079 (tpt) cc_final: 0.7657 (tpp) REVERT: I 238 GLN cc_start: 0.8013 (tt0) cc_final: 0.7802 (tt0) REVERT: I 244 MET cc_start: 0.8284 (tpt) cc_final: 0.8003 (tpp) REVERT: J 22 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8732 (tm) REVERT: J 238 GLN cc_start: 0.8014 (tt0) cc_final: 0.7738 (tt0) REVERT: J 244 MET cc_start: 0.7893 (tpt) cc_final: 0.7379 (tpp) REVERT: L 22 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8724 (tm) REVERT: L 244 MET cc_start: 0.8134 (tpt) cc_final: 0.7696 (tpp) REVERT: M 104 PHE cc_start: 0.6716 (t80) cc_final: 0.6454 (t80) REVERT: M 238 GLN cc_start: 0.7864 (tt0) cc_final: 0.7578 (tt0) REVERT: M 241 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7470 (tpt170) REVERT: M 264 ILE cc_start: 0.8577 (mm) cc_final: 0.8114 (pt) REVERT: N 244 MET cc_start: 0.7830 (tpp) cc_final: 0.7195 (tpp) REVERT: O 22 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8721 (tm) REVERT: O 230 GLU cc_start: 0.8121 (tt0) cc_final: 0.7696 (tm-30) REVERT: O 244 MET cc_start: 0.8223 (tpt) cc_final: 0.7970 (tpp) REVERT: P 7 ASN cc_start: 0.7286 (p0) cc_final: 0.7017 (p0) REVERT: Q 22 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8705 (tm) REVERT: Q 274 ASP cc_start: 0.7974 (p0) cc_final: 0.7755 (p0) REVERT: S 244 MET cc_start: 0.7652 (tpt) cc_final: 0.7196 (tpp) REVERT: T 22 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8724 (tm) REVERT: T 244 MET cc_start: 0.7795 (tpt) cc_final: 0.7315 (tpp) REVERT: X 83 MET cc_start: 0.6129 (ptm) cc_final: 0.5848 (ptm) REVERT: c 34 MET cc_start: 0.6110 (mmp) cc_final: 0.5726 (ttt) REVERT: h 34 MET cc_start: 0.7154 (mmp) cc_final: 0.6929 (mmp) REVERT: h 107 GLN cc_start: 0.5876 (tm-30) cc_final: 0.4765 (pm20) REVERT: i 107 GLN cc_start: 0.6133 (tm-30) cc_final: 0.5051 (pm20) REVERT: j 34 MET cc_start: 0.4026 (OUTLIER) cc_final: 0.3749 (mmm) REVERT: k 34 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.3702 (mmm) REVERT: k 107 GLN cc_start: 0.6023 (tm-30) cc_final: 0.5237 (pm20) outliers start: 171 outliers final: 151 residues processed: 834 average time/residue: 0.4653 time to fit residues: 682.4541 Evaluate side-chains 824 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 662 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 52 TYR Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain c residue 81 LEU Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain e residue 98 VAL Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 34 MET Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 58 THR Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 0.9980 chunk 591 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 512 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 556 optimal weight: 40.0000 chunk 232 optimal weight: 0.0980 chunk 571 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 181 HIS G 181 HIS K 181 HIS O 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS a 59 HIS b 59 HIS l 59 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.185360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.155826 restraints weight = 89252.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.152911 restraints weight = 195441.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.153989 restraints weight = 167825.760| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 56600 Z= 0.161 Angle : 0.600 9.641 76620 Z= 0.303 Chirality : 0.037 0.197 8740 Planarity : 0.003 0.049 9540 Dihedral : 4.106 18.091 7620 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.54 % Allowed : 22.52 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.10), residues: 6820 helix: 2.43 (0.08), residues: 4020 sheet: 1.43 (0.14), residues: 1100 loop : -0.64 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP m 36 HIS 0.006 0.000 HIS m 33 PHE 0.029 0.002 PHE F 105 TYR 0.023 0.001 TYR m 94 ARG 0.011 0.000 ARG Q 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12131.54 seconds wall clock time: 211 minutes 14.02 seconds (12674.02 seconds total)