Starting phenix.real_space_refine on Fri Oct 11 09:08:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/10_2024/8rmn_19365.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/10_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_19365/10_2024/8rmn_19365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/10_2024/8rmn_19365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/10_2024/8rmn_19365.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/10_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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 23.08, per 1000 atoms: 0.42 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: 10.86 Conformation dependent library (CDL) restraints added in 5.5 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: 4.53 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: 22.51 Time building geometry restraints manager: 12.86 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: 7.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.950 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 97.660 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.620 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.810 ------------------------------------------------------------------------------- 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 : 4.752 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: 0.5063 time to fit residues: 939.5722 Evaluate side-chains 822 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 784 time to evaluate : 4.722 ------------------------------------------------------------------------------- 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 : 4.741 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: 0.4795 time to fit residues: 813.1023 Evaluate side-chains 845 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 746 time to evaluate : 4.682 ------------------------------------------------------------------------------- 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: 0.9990 chunk 175 optimal weight: 0.5980 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: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 R 6 ASN S 238 GLN T 6 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 56600 Z= 0.175 Angle : 0.565 7.454 76620 Z= 0.294 Chirality : 0.037 0.214 8740 Planarity : 0.003 0.035 9540 Dihedral : 3.932 29.612 7624 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.74 % Allowed : 17.23 % Favored : 79.04 % 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: 2.47 (0.10), residues: 6820 helix: 2.51 (0.07), residues: 4000 sheet: 1.62 (0.14), residues: 980 loop : -0.36 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 36 HIS 0.003 0.001 HIS F 263 PHE 0.026 0.002 PHE F 105 TYR 0.019 0.001 TYR J 142 ARG 0.007 0.000 ARG Q 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 1056 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 831 time to evaluate : 4.767 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8000 (tt0) cc_final: 0.7793 (tt0) REVERT: B 231 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 244 MET cc_start: 0.8236 (tpt) cc_final: 0.7744 (tpp) REVERT: C 96 GLU cc_start: 0.5753 (mp0) cc_final: 0.5147 (mt-10) REVERT: C 244 MET cc_start: 0.7535 (tpt) cc_final: 0.7092 (tpp) REVERT: D 238 GLN cc_start: 0.7972 (tt0) cc_final: 0.7642 (tt0) REVERT: D 244 MET cc_start: 0.8270 (tpt) cc_final: 0.7713 (tpp) REVERT: E 187 MET cc_start: 0.7459 (mmm) cc_final: 0.6250 (ttp) REVERT: G 244 MET cc_start: 0.7851 (tpt) cc_final: 0.7238 (tpp) REVERT: H 238 GLN cc_start: 0.8074 (tt0) cc_final: 0.7843 (tt0) REVERT: H 244 MET cc_start: 0.8129 (tpt) cc_final: 0.7840 (tpp) REVERT: I 238 GLN cc_start: 0.8021 (tt0) cc_final: 0.7786 (tt0) REVERT: I 244 MET cc_start: 0.7934 (tpt) cc_final: 0.7452 (tpp) REVERT: J 105 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7794 (t80) REVERT: J 238 GLN cc_start: 0.8009 (tt0) cc_final: 0.7727 (tt0) REVERT: J 244 MET cc_start: 0.7832 (tpt) cc_final: 0.7287 (tpp) REVERT: K 238 GLN cc_start: 0.8051 (tt0) cc_final: 0.7766 (tt0) REVERT: L 274 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7898 (p0) REVERT: M 238 GLN cc_start: 0.7898 (tt0) cc_final: 0.7546 (tt0) REVERT: O 230 GLU cc_start: 0.8022 (tt0) cc_final: 0.7646 (tm-30) REVERT: P 7 ASN cc_start: 0.7097 (p0) cc_final: 0.6794 (p0) REVERT: P 238 GLN cc_start: 0.7991 (tt0) cc_final: 0.7752 (tt0) REVERT: Q 238 GLN cc_start: 0.7741 (tt0) cc_final: 0.7394 (tt0) REVERT: R 244 MET cc_start: 0.7225 (tpp) cc_final: 0.6492 (tpp) REVERT: S 187 MET cc_start: 0.7229 (mmm) cc_final: 0.6112 (ttp) REVERT: S 244 MET cc_start: 0.7363 (tpt) cc_final: 0.6644 (tpp) REVERT: T 244 MET cc_start: 0.7475 (tpt) cc_final: 0.7022 (tpp) REVERT: f 18 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4170 (mp) REVERT: f 22 CYS cc_start: 0.6343 (t) cc_final: 0.6087 (t) REVERT: g 82 GLN cc_start: 0.6344 (tm-30) cc_final: 0.6076 (tm-30) REVERT: k 34 MET cc_start: 0.2303 (mmm) cc_final: 0.1806 (mmm) REVERT: k 107 GLN cc_start: 0.5746 (tm-30) cc_final: 0.5112 (pm20) REVERT: m 58 THR cc_start: 0.5842 (t) cc_final: 0.5582 (p) outliers start: 225 outliers final: 143 residues processed: 961 average time/residue: 0.4835 time to fit residues: 803.1652 Evaluate side-chains 885 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 738 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL 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 175 ASP 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 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 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 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 47 LYS 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 L residue 274 ASP 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 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 192 LEU Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain O residue 57 VAL 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 192 LEU Chi-restraints excluded: chain P residue 206 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 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: 5.9990 chunk 478 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 639 optimal weight: 30.0000 chunk 676 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 605 optimal weight: 30.0000 chunk 182 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 6 ASN E 181 HIS E 238 GLN F 238 GLN H 181 HIS J 6 ASN J 181 HIS K 6 ASN K 181 HIS M 227 ASN N 6 ASN O 238 GLN P 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 HIS T 181 HIS Z 59 HIS c 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 56600 Z= 0.273 Angle : 0.627 9.073 76620 Z= 0.330 Chirality : 0.040 0.198 8740 Planarity : 0.004 0.038 9540 Dihedral : 4.161 17.853 7620 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.80 % Allowed : 18.24 % Favored : 76.96 % 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: 2.27 (0.10), residues: 6820 helix: 2.41 (0.08), residues: 3900 sheet: 1.44 (0.14), residues: 980 loop : -0.36 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Z 47 HIS 0.004 0.001 HIS P 181 PHE 0.031 0.003 PHE F 105 TYR 0.014 0.002 TYR J 142 ARG 0.008 0.001 ARG B 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 1062 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 773 time to evaluate : 4.750 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8095 (tt0) cc_final: 0.7855 (tt0) REVERT: U 52 TYR cc_start: 0.3795 (OUTLIER) cc_final: 0.3233 (m-80) REVERT: B 244 MET cc_start: 0.8319 (tpt) cc_final: 0.7813 (tpp) REVERT: C 244 MET cc_start: 0.7722 (tpt) cc_final: 0.7197 (tpp) REVERT: C 273 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8280 (mttt) REVERT: D 238 GLN cc_start: 0.8075 (tt0) cc_final: 0.7763 (tt0) REVERT: D 244 MET cc_start: 0.8293 (tpt) cc_final: 0.7727 (tpp) REVERT: E 244 MET cc_start: 0.7805 (tpp) cc_final: 0.7463 (tpp) REVERT: F 238 GLN cc_start: 0.8055 (tt0) cc_final: 0.7683 (tt0) REVERT: G 244 MET cc_start: 0.7900 (tpt) cc_final: 0.7324 (tpp) REVERT: H 244 MET cc_start: 0.8166 (tpt) cc_final: 0.7871 (tpp) REVERT: I 238 GLN cc_start: 0.8124 (tt0) cc_final: 0.7867 (tt0) REVERT: I 244 MET cc_start: 0.8136 (tpt) cc_final: 0.7645 (tpp) REVERT: J 104 PHE cc_start: 0.6713 (t80) cc_final: 0.6483 (t80) REVERT: J 105 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7887 (t80) REVERT: J 238 GLN cc_start: 0.8099 (tt0) cc_final: 0.7859 (tt0) REVERT: J 244 MET cc_start: 0.7885 (tpt) cc_final: 0.7297 (tpp) REVERT: K 238 GLN cc_start: 0.8134 (tt0) cc_final: 0.7834 (tt0) REVERT: L 104 PHE cc_start: 0.6800 (t80) cc_final: 0.6498 (t80) REVERT: L 105 PHE cc_start: 0.8184 (t80) cc_final: 0.7905 (t80) REVERT: M 238 GLN cc_start: 0.8091 (tt0) cc_final: 0.7777 (tt0) REVERT: O 230 GLU cc_start: 0.8095 (tt0) cc_final: 0.7741 (tm-30) REVERT: P 7 ASN cc_start: 0.7150 (p0) cc_final: 0.6899 (p0) REVERT: P 238 GLN cc_start: 0.8137 (tt0) cc_final: 0.7919 (tt0) REVERT: Q 238 GLN cc_start: 0.7944 (tt0) cc_final: 0.7649 (tt0) REVERT: R 6 ASN cc_start: 0.4510 (t160) cc_final: 0.4009 (p0) REVERT: R 96 GLU cc_start: 0.6021 (mp0) cc_final: 0.5662 (mt-10) REVERT: R 135 GLU cc_start: 0.7707 (tt0) cc_final: 0.7167 (tt0) REVERT: R 244 MET cc_start: 0.7534 (tpp) cc_final: 0.6871 (tpp) REVERT: S 104 PHE cc_start: 0.6709 (t80) cc_final: 0.6492 (t80) REVERT: S 244 MET cc_start: 0.7527 (tpt) cc_final: 0.7136 (tpp) REVERT: T 244 MET cc_start: 0.7662 (tpt) cc_final: 0.7138 (tpp) REVERT: V 34 MET cc_start: 0.3375 (OUTLIER) cc_final: 0.2949 (mmm) REVERT: X 52 TYR cc_start: 0.4190 (OUTLIER) cc_final: 0.3107 (m-10) REVERT: h 35 ARG cc_start: 0.5714 (mtt90) cc_final: 0.5303 (mtt-85) REVERT: h 107 GLN cc_start: 0.5663 (tm-30) cc_final: 0.4993 (pm20) REVERT: i 107 GLN cc_start: 0.5809 (tm-30) cc_final: 0.4981 (pm20) REVERT: k 34 MET cc_start: 0.3002 (mmm) cc_final: 0.2594 (mmm) REVERT: k 107 GLN cc_start: 0.5802 (tm-30) cc_final: 0.5077 (pm20) REVERT: m 58 THR cc_start: 0.5863 (t) cc_final: 0.5628 (p) REVERT: n 34 MET cc_start: 0.3341 (OUTLIER) cc_final: 0.2946 (mmm) REVERT: n 58 THR cc_start: 0.5237 (t) cc_final: 0.4981 (p) outliers start: 289 outliers final: 203 residues processed: 968 average time/residue: 0.4569 time to fit residues: 777.5376 Evaluate side-chains 865 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 657 time to evaluate : 4.775 ------------------------------------------------------------------------------- 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 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 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 B residue 231 LEU 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 57 VAL Chi-restraints excluded: chain D residue 108 THR 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 57 VAL Chi-restraints excluded: chain E residue 108 THR 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 213 LEU 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 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 F residue 245 MET Chi-restraints excluded: chain G residue 9 VAL 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 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 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 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 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 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 57 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 116 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 116 LEU Chi-restraints excluded: chain M residue 192 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 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 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 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 108 THR Chi-restraints excluded: chain P residue 116 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 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 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU 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 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 108 THR 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 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 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain X residue 52 TYR 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 Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 34 MET 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 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 h residue 58 THR 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 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 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET 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: 4.9990 chunk 9 optimal weight: 0.8980 chunk 503 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 577 optimal weight: 20.0000 chunk 467 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 345 optimal weight: 9.9990 chunk 607 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** C 147 ASN D 147 ASN E 147 ASN F 147 ASN G 6 ASN G 147 ASN H 147 ASN H 238 GLN I 6 ASN I 147 ASN J 147 ASN K 147 ASN M 6 ASN M 147 ASN M 227 ASN N 147 ASN O 147 ASN P 6 ASN P 147 ASN Q 147 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 ASN T 6 ASN b 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56600 Z= 0.186 Angle : 0.569 8.619 76620 Z= 0.297 Chirality : 0.037 0.177 8740 Planarity : 0.003 0.041 9540 Dihedral : 4.104 17.425 7620 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.14 % Allowed : 19.70 % Favored : 76.16 % 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: 2.20 (0.10), residues: 6820 helix: 2.33 (0.08), residues: 4000 sheet: 1.42 (0.14), residues: 980 loop : -0.50 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 47 HIS 0.006 0.001 HIS b 33 PHE 0.027 0.002 PHE F 105 TYR 0.012 0.001 TYR P 81 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 999 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 750 time to evaluate : 4.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 GLN cc_start: 0.7981 (tt0) cc_final: 0.7721 (tt0) REVERT: B 22 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8695 (tm) REVERT: B 244 MET cc_start: 0.8269 (tpt) cc_final: 0.7785 (tpp) REVERT: C 6 ASN cc_start: 0.4928 (t160) cc_final: 0.4211 (p0) REVERT: C 244 MET cc_start: 0.7655 (tpt) cc_final: 0.7170 (tpp) REVERT: C 273 LYS cc_start: 0.8505 (ptmt) cc_final: 0.8251 (mttm) REVERT: D 238 GLN cc_start: 0.7946 (tt0) cc_final: 0.7621 (tt0) REVERT: D 244 MET cc_start: 0.8271 (tpt) cc_final: 0.7710 (tpp) REVERT: E 22 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8662 (tm) REVERT: E 244 MET cc_start: 0.7801 (tpp) cc_final: 0.7470 (tpp) REVERT: G 22 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8708 (tm) REVERT: G 244 MET cc_start: 0.7789 (tpt) cc_final: 0.7237 (tpp) REVERT: H 244 MET cc_start: 0.8159 (tpt) cc_final: 0.7897 (tpp) REVERT: I 238 GLN cc_start: 0.8035 (tt0) cc_final: 0.7794 (tt0) REVERT: I 244 MET cc_start: 0.8134 (tpt) cc_final: 0.7670 (tpp) REVERT: J 22 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8733 (tm) REVERT: J 104 PHE cc_start: 0.6623 (t80) cc_final: 0.6362 (t80) REVERT: J 105 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7839 (t80) REVERT: J 238 GLN cc_start: 0.8035 (tt0) cc_final: 0.7801 (tt0) REVERT: J 244 MET cc_start: 0.7800 (tpt) cc_final: 0.7286 (tpp) REVERT: K 238 GLN cc_start: 0.8060 (tt0) cc_final: 0.7758 (tt0) REVERT: K 244 MET cc_start: 0.8208 (tpt) cc_final: 0.7632 (tpp) REVERT: L 22 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8725 (tm) REVERT: L 104 PHE cc_start: 0.6652 (t80) cc_final: 0.6351 (t80) REVERT: L 244 MET cc_start: 0.8015 (tpt) cc_final: 0.7450 (tpp) REVERT: M 238 GLN cc_start: 0.7952 (tt0) cc_final: 0.7646 (tt0) REVERT: O 22 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8727 (tm) REVERT: P 7 ASN cc_start: 0.7193 (p0) cc_final: 0.6946 (p0) REVERT: P 238 GLN cc_start: 0.8029 (tt0) cc_final: 0.7804 (tt0) REVERT: Q 22 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8697 (tm) REVERT: Q 238 GLN cc_start: 0.7867 (tt0) cc_final: 0.7570 (tt0) REVERT: R 6 ASN cc_start: 0.4488 (t160) cc_final: 0.4123 (p0) REVERT: R 244 MET cc_start: 0.7523 (tpp) cc_final: 0.7288 (tpp) REVERT: S 104 PHE cc_start: 0.6563 (t80) cc_final: 0.6342 (t80) REVERT: S 105 PHE cc_start: 0.8269 (t80) cc_final: 0.8014 (t80) REVERT: S 244 MET cc_start: 0.7422 (tpt) cc_final: 0.7144 (tpp) REVERT: T 22 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8740 (tm) REVERT: T 244 MET cc_start: 0.7603 (tpt) cc_final: 0.7175 (tpp) REVERT: V 34 MET cc_start: 0.3659 (OUTLIER) cc_final: 0.3232 (mmm) REVERT: W 34 MET cc_start: 0.4263 (OUTLIER) cc_final: 0.4038 (tpp) REVERT: W 35 ARG cc_start: 0.4897 (mtt90) cc_final: 0.4211 (mtt-85) REVERT: h 107 GLN cc_start: 0.5728 (tm-30) cc_final: 0.4982 (pm20) REVERT: i 107 GLN cc_start: 0.5684 (tm-30) cc_final: 0.4828 (pm20) REVERT: j 34 MET cc_start: 0.3377 (OUTLIER) cc_final: 0.2995 (mmm) REVERT: k 34 MET cc_start: 0.3244 (mmm) cc_final: 0.2853 (mmm) REVERT: k 107 GLN cc_start: 0.5744 (tm-30) cc_final: 0.5067 (pm20) REVERT: m 58 THR cc_start: 0.5913 (t) cc_final: 0.5665 (p) outliers start: 249 outliers final: 155 residues processed: 936 average time/residue: 0.4513 time to fit residues: 741.5447 Evaluate side-chains 831 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 664 time to evaluate : 4.704 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 206 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 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 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 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 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 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 213 LEU 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 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 206 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 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 99 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 57 VAL 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 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 57 VAL 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 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN 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 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 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 O residue 264 ILE Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR 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 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 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 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 180 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 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 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 34 MET 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 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 98 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain d residue 12 VAL 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 58 THR 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 34 MET Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP 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: 0.0980 chunk 609 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 397 optimal weight: 0.0470 chunk 167 optimal weight: 3.9990 chunk 677 optimal weight: 1.9990 chunk 562 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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 181 HIS F 6 ASN H 6 ASN H 238 GLN M 227 ASN O 6 ASN O 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 56600 Z= 0.153 Angle : 0.564 9.118 76620 Z= 0.288 Chirality : 0.037 0.171 8740 Planarity : 0.003 0.044 9540 Dihedral : 3.991 16.778 7620 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.39 % Allowed : 20.32 % Favored : 76.30 % 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: 2.46 (0.08), residues: 4020 sheet: 1.48 (0.13), residues: 1100 loop : -0.65 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 47 HIS 0.003 0.000 HIS a 33 PHE 0.025 0.002 PHE G 105 TYR 0.013 0.001 TYR l 52 ARG 0.009 0.000 ARG B 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 966 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 762 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 GLN cc_start: 0.7971 (tt0) cc_final: 0.7701 (tt0) REVERT: B 22 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8682 (tm) REVERT: B 244 MET cc_start: 0.8247 (tpt) cc_final: 0.7782 (tpp) REVERT: C 6 ASN cc_start: 0.4913 (t160) cc_final: 0.4134 (p0) REVERT: C 244 MET cc_start: 0.7597 (tpt) cc_final: 0.7157 (tpp) REVERT: C 273 LYS cc_start: 0.8424 (ptmt) cc_final: 0.8170 (mttt) REVERT: C 274 ASP cc_start: 0.8254 (p0) cc_final: 0.7814 (p0) REVERT: D 238 GLN cc_start: 0.7919 (tt0) cc_final: 0.7650 (tt0) REVERT: D 244 MET cc_start: 0.8255 (tpt) cc_final: 0.7393 (tpp) REVERT: E 22 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8649 (tm) REVERT: E 244 MET cc_start: 0.7747 (tpp) cc_final: 0.7467 (tpp) REVERT: G 22 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8722 (tm) REVERT: G 74 MET cc_start: 0.8236 (tpp) cc_final: 0.7972 (tpt) REVERT: G 244 MET cc_start: 0.7685 (tpt) cc_final: 0.7222 (tpp) REVERT: H 244 MET cc_start: 0.8145 (tpt) cc_final: 0.7871 (tpp) REVERT: I 238 GLN cc_start: 0.7969 (tt0) cc_final: 0.7724 (tt0) REVERT: I 244 MET cc_start: 0.8129 (tpt) cc_final: 0.7666 (tpp) REVERT: J 22 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8654 (tm) REVERT: J 237 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7729 (tm-30) REVERT: J 238 GLN cc_start: 0.7989 (tt0) cc_final: 0.7656 (tt0) REVERT: J 244 MET cc_start: 0.7712 (tpt) cc_final: 0.7261 (tpp) REVERT: K 238 GLN cc_start: 0.8031 (tt0) cc_final: 0.7667 (tt0) REVERT: K 244 MET cc_start: 0.8178 (tpt) cc_final: 0.7617 (tpp) REVERT: L 22 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8702 (tm) REVERT: L 244 MET cc_start: 0.8032 (tpt) cc_final: 0.7508 (tpp) REVERT: M 68 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8764 (m-80) REVERT: M 238 GLN cc_start: 0.7853 (tt0) cc_final: 0.7573 (tt0) REVERT: O 22 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (tm) REVERT: P 7 ASN cc_start: 0.7237 (p0) cc_final: 0.6979 (p0) REVERT: P 238 GLN cc_start: 0.7976 (tt0) cc_final: 0.7771 (tt0) REVERT: Q 22 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8690 (tm) REVERT: Q 238 GLN cc_start: 0.7779 (tt0) cc_final: 0.7489 (tt0) REVERT: Q 274 ASP cc_start: 0.8081 (p0) cc_final: 0.7859 (p0) REVERT: R 244 MET cc_start: 0.7503 (tpp) cc_final: 0.7269 (tpp) REVERT: S 105 PHE cc_start: 0.8213 (t80) cc_final: 0.8004 (t80) REVERT: S 244 MET cc_start: 0.7365 (tpt) cc_final: 0.7007 (tpp) REVERT: T 22 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8698 (tm) REVERT: T 244 MET cc_start: 0.7554 (tpt) cc_final: 0.7116 (tpp) REVERT: V 34 MET cc_start: 0.3653 (mmm) cc_final: 0.3299 (mmm) REVERT: W 35 ARG cc_start: 0.5013 (mtt90) cc_final: 0.4291 (mtt-85) REVERT: h 107 GLN cc_start: 0.5758 (tm-30) cc_final: 0.4985 (pm20) REVERT: i 107 GLN cc_start: 0.5744 (tm-30) cc_final: 0.4994 (pm20) REVERT: j 34 MET cc_start: 0.3446 (OUTLIER) cc_final: 0.3062 (mmm) REVERT: k 107 GLN cc_start: 0.5851 (tm-30) cc_final: 0.5214 (pm20) REVERT: m 58 THR cc_start: 0.5894 (t) cc_final: 0.5674 (p) outliers start: 204 outliers final: 140 residues processed: 924 average time/residue: 0.5216 time to fit residues: 851.9931 Evaluate side-chains 825 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 675 time to evaluate : 4.724 ------------------------------------------------------------------------------- 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 192 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 188 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 216 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 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 116 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 245 MET 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 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 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 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 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 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 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 116 LEU Chi-restraints excluded: chain L residue 180 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 68 PHE Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain M residue 251 LEU 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 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 147 ASN Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain P residue 57 VAL 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 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 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 264 ILE Chi-restraints excluded: chain R residue 274 ASP 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 233 GLU Chi-restraints excluded: chain S residue 264 ILE 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 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 Y residue 90 ASP Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 51 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 90 ASP 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 i residue 12 VAL Chi-restraints excluded: chain i residue 58 THR 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 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 34 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 385 optimal weight: 9.9990 chunk 494 optimal weight: 0.9980 chunk 383 optimal weight: 2.9990 chunk 570 optimal weight: 6.9990 chunk 378 optimal weight: 2.9990 chunk 674 optimal weight: 9.9990 chunk 422 optimal weight: 3.9990 chunk 411 optimal weight: 10.0000 chunk 311 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** H 238 GLN L 6 ASN M 227 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 238 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 56600 Z= 0.203 Angle : 0.592 10.491 76620 Z= 0.304 Chirality : 0.038 0.177 8740 Planarity : 0.003 0.045 9540 Dihedral : 4.065 17.468 7620 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.77 % Allowed : 20.65 % Favored : 75.58 % 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: 2.29 (0.10), residues: 6820 helix: 2.40 (0.08), residues: 4020 sheet: 1.47 (0.14), residues: 1100 loop : -0.68 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 221 HIS 0.005 0.001 HIS b 33 PHE 0.025 0.002 PHE G 105 TYR 0.014 0.001 TYR I 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 975 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 748 time to evaluate : 4.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7867 (mmm) cc_final: 0.7578 (mmm) REVERT: A 238 GLN cc_start: 0.7989 (tt0) cc_final: 0.7719 (tt0) REVERT: U 34 MET cc_start: 0.5492 (mmm) cc_final: 0.5218 (mmm) REVERT: B 22 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8704 (tm) REVERT: B 244 MET cc_start: 0.8283 (tpt) cc_final: 0.7840 (tpp) REVERT: C 6 ASN cc_start: 0.4950 (t160) cc_final: 0.4106 (p0) REVERT: C 244 MET cc_start: 0.7701 (tpt) cc_final: 0.7169 (tpp) REVERT: C 273 LYS cc_start: 0.8431 (ptmt) cc_final: 0.8226 (mttt) REVERT: D 238 GLN cc_start: 0.7953 (tt0) cc_final: 0.7676 (tt0) REVERT: D 244 MET cc_start: 0.8116 (tpt) cc_final: 0.7791 (tpp) REVERT: E 22 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8658 (tm) REVERT: E 244 MET cc_start: 0.7780 (tpp) cc_final: 0.7472 (tpp) REVERT: F 99 LEU cc_start: 0.7652 (mt) cc_final: 0.7427 (mp) REVERT: G 22 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8712 (tm) REVERT: G 104 PHE cc_start: 0.6548 (t80) cc_final: 0.6287 (t80) REVERT: G 244 MET cc_start: 0.7803 (tpt) cc_final: 0.7275 (tpp) REVERT: H 241 ARG cc_start: 0.7994 (ttt90) cc_final: 0.7638 (ttp80) REVERT: H 244 MET cc_start: 0.8163 (tpt) cc_final: 0.7923 (tpp) REVERT: I 238 GLN cc_start: 0.7999 (tt0) cc_final: 0.7766 (tt0) REVERT: I 244 MET cc_start: 0.8164 (tpt) cc_final: 0.7717 (tpp) REVERT: I 274 ASP cc_start: 0.8334 (p0) cc_final: 0.8045 (p0) REVERT: J 22 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8677 (tm) REVERT: J 238 GLN cc_start: 0.8023 (tt0) cc_final: 0.7786 (tt0) REVERT: J 244 MET cc_start: 0.7810 (tpt) cc_final: 0.7247 (tpp) REVERT: K 244 MET cc_start: 0.8206 (tpt) cc_final: 0.7667 (tpp) REVERT: L 22 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8711 (tm) REVERT: L 244 MET cc_start: 0.8084 (tpt) cc_final: 0.7600 (tpp) REVERT: M 238 GLN cc_start: 0.7899 (tt0) cc_final: 0.7657 (tt0) REVERT: O 22 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8709 (tm) REVERT: O 230 GLU cc_start: 0.8136 (tt0) cc_final: 0.7674 (tm-30) REVERT: P 7 ASN cc_start: 0.7250 (p0) cc_final: 0.6987 (p0) REVERT: Q 22 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8720 (tm) REVERT: Q 238 GLN cc_start: 0.7799 (tt0) cc_final: 0.7550 (tt0) REVERT: Q 274 ASP cc_start: 0.8076 (p0) cc_final: 0.7824 (p0) REVERT: R 237 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8054 (tm-30) REVERT: R 244 MET cc_start: 0.7587 (tpp) cc_final: 0.7366 (tpp) REVERT: S 74 MET cc_start: 0.8146 (tpp) cc_final: 0.7860 (tpt) REVERT: S 105 PHE cc_start: 0.8289 (t80) cc_final: 0.8023 (t80) REVERT: S 230 GLU cc_start: 0.7994 (tt0) cc_final: 0.7727 (tm-30) REVERT: S 244 MET cc_start: 0.7506 (tpt) cc_final: 0.7075 (tpp) REVERT: T 22 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8679 (tm) REVERT: T 230 GLU cc_start: 0.7952 (tt0) cc_final: 0.7734 (tm-30) REVERT: T 237 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7890 (tm-30) REVERT: T 244 MET cc_start: 0.7663 (tpt) cc_final: 0.7191 (tpp) REVERT: V 34 MET cc_start: 0.3843 (OUTLIER) cc_final: 0.3477 (mmm) REVERT: W 35 ARG cc_start: 0.4941 (mtt90) cc_final: 0.4080 (mtt-85) REVERT: a 11 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5136 (pt) REVERT: c 34 MET cc_start: 0.7328 (mmt) cc_final: 0.6362 (tmm) REVERT: f 34 MET cc_start: 0.4848 (mtt) cc_final: 0.4456 (ttt) REVERT: h 107 GLN cc_start: 0.5823 (tm-30) cc_final: 0.5041 (pm20) REVERT: i 107 GLN cc_start: 0.5876 (tm-30) cc_final: 0.5008 (pm20) REVERT: j 34 MET cc_start: 0.3650 (OUTLIER) cc_final: 0.3288 (mmm) REVERT: k 107 GLN cc_start: 0.5867 (tm-30) cc_final: 0.5183 (pm20) outliers start: 227 outliers final: 183 residues processed: 935 average time/residue: 0.4554 time to fit residues: 746.4693 Evaluate side-chains 882 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 688 time to evaluate : 4.804 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 ILE 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 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 216 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 112 VAL 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 116 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 213 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 264 ILE 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 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 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 206 VAL Chi-restraints excluded: chain G residue 274 ASP 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 95 LEU 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 206 VAL 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 108 THR Chi-restraints excluded: chain I residue 112 VAL 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 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 J residue 206 VAL Chi-restraints excluded: chain J residue 264 ILE 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 K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE 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 L residue 206 VAL Chi-restraints excluded: chain M residue 36 SER 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 M residue 227 ASN 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 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 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 264 ILE 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 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 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 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 116 LEU 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 213 LEU 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 34 MET 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 Y residue 90 ASP Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain e residue 7 SER 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 h 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 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 34 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 402 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 428 optimal weight: 2.9990 chunk 459 optimal weight: 0.8980 chunk 333 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 530 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 ASN E 238 GLN M 227 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 56600 Z= 0.200 Angle : 0.593 10.335 76620 Z= 0.304 Chirality : 0.038 0.185 8740 Planarity : 0.003 0.044 9540 Dihedral : 4.090 17.450 7620 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.74 % Allowed : 21.10 % Favored : 75.17 % 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: 2.26 (0.10), residues: 6820 helix: 2.38 (0.08), residues: 4020 sheet: 1.45 (0.14), residues: 1100 loop : -0.68 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 221 HIS 0.003 0.001 HIS b 33 PHE 0.033 0.002 PHE F 105 TYR 0.011 0.001 TYR T 220 ARG 0.009 0.000 ARG Q 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 954 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 729 time to evaluate : 4.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7852 (mmm) cc_final: 0.7573 (mmm) REVERT: A 238 GLN cc_start: 0.7982 (tt0) cc_final: 0.7724 (tt0) REVERT: U 34 MET cc_start: 0.5555 (mmm) cc_final: 0.5251 (mmm) REVERT: B 22 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8698 (tm) REVERT: B 244 MET cc_start: 0.8259 (tpt) cc_final: 0.7819 (tpp) REVERT: C 6 ASN cc_start: 0.4900 (t160) cc_final: 0.4122 (p0) REVERT: C 244 MET cc_start: 0.7704 (tpt) cc_final: 0.7166 (tpp) REVERT: C 273 LYS cc_start: 0.8409 (ptmt) cc_final: 0.8193 (mttt) REVERT: D 238 GLN cc_start: 0.7958 (tt0) cc_final: 0.7647 (tt0) REVERT: D 244 MET cc_start: 0.8018 (tpt) cc_final: 0.7657 (tpp) REVERT: E 22 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8648 (tm) REVERT: E 244 MET cc_start: 0.7731 (tpp) cc_final: 0.7463 (tpp) REVERT: F 99 LEU cc_start: 0.7658 (mt) cc_final: 0.7047 (mp) REVERT: F 238 GLN cc_start: 0.8096 (tt0) cc_final: 0.7804 (tt0) REVERT: G 22 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8713 (tm) REVERT: G 244 MET cc_start: 0.7822 (tpt) cc_final: 0.7305 (tpp) REVERT: H 244 MET cc_start: 0.8169 (tpt) cc_final: 0.7949 (tpp) REVERT: I 238 GLN cc_start: 0.7981 (tt0) cc_final: 0.7740 (tt0) REVERT: I 244 MET cc_start: 0.8164 (tpt) cc_final: 0.7747 (tpp) REVERT: J 22 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8690 (tm) REVERT: J 238 GLN cc_start: 0.7991 (tt0) cc_final: 0.7769 (tt0) REVERT: J 244 MET cc_start: 0.7820 (tpt) cc_final: 0.7272 (tpp) REVERT: K 244 MET cc_start: 0.8211 (tpt) cc_final: 0.7685 (tpp) REVERT: L 22 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8718 (tm) REVERT: L 244 MET cc_start: 0.8091 (tpt) cc_final: 0.7644 (tpp) REVERT: M 238 GLN cc_start: 0.7917 (tt0) cc_final: 0.7646 (tt0) REVERT: O 22 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8724 (tm) REVERT: P 7 ASN cc_start: 0.7238 (p0) cc_final: 0.7000 (p0) REVERT: Q 22 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8709 (tm) REVERT: Q 238 GLN cc_start: 0.7801 (tt0) cc_final: 0.7564 (tt0) REVERT: Q 274 ASP cc_start: 0.8074 (p0) cc_final: 0.7817 (p0) REVERT: R 237 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7836 (tm-30) REVERT: R 244 MET cc_start: 0.7575 (tpp) cc_final: 0.7370 (tpp) REVERT: S 105 PHE cc_start: 0.8232 (t80) cc_final: 0.7990 (t80) REVERT: S 244 MET cc_start: 0.7553 (tpt) cc_final: 0.7115 (tpp) REVERT: T 22 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8693 (tm) REVERT: T 104 PHE cc_start: 0.6612 (t80) cc_final: 0.6350 (t80) REVERT: T 230 GLU cc_start: 0.7997 (tt0) cc_final: 0.7709 (tm-30) REVERT: T 244 MET cc_start: 0.7698 (tpt) cc_final: 0.7242 (tpp) REVERT: W 35 ARG cc_start: 0.4732 (mtt90) cc_final: 0.4362 (mtt-85) REVERT: a 11 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5206 (pt) REVERT: c 34 MET cc_start: 0.7232 (mmt) cc_final: 0.6316 (tmm) REVERT: h 107 GLN cc_start: 0.5977 (tm-30) cc_final: 0.5134 (pm20) REVERT: i 107 GLN cc_start: 0.6004 (tm-30) cc_final: 0.5088 (pm20) REVERT: j 34 MET cc_start: 0.3816 (OUTLIER) cc_final: 0.3460 (mmm) REVERT: k 107 GLN cc_start: 0.5912 (tm-30) cc_final: 0.5202 (pm20) outliers start: 225 outliers final: 194 residues processed: 909 average time/residue: 0.4656 time to fit residues: 739.8017 Evaluate side-chains 878 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 674 time to evaluate : 4.728 ------------------------------------------------------------------------------- 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 206 VAL Chi-restraints excluded: chain A residue 264 ILE 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 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 216 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 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 116 LEU Chi-restraints excluded: chain E residue 175 ASP 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 213 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 264 ILE 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 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 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 206 VAL Chi-restraints excluded: chain G residue 274 ASP 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 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 H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 10 SER 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 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 J residue 264 ILE 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 K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE 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 L residue 206 VAL 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 108 THR 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 10 SER 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 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 147 ASN Chi-restraints excluded: chain O residue 175 ASP 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 264 ILE 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 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 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 213 LEU 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 255 ILE 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 108 THR Chi-restraints excluded: chain S residue 116 LEU 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 213 LEU 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 45 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 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 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 83 MET Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain c residue 98 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 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 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 81 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 34 MET 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: 2.9990 chunk 589 optimal weight: 5.9990 chunk 628 optimal weight: 40.0000 chunk 378 optimal weight: 0.0170 chunk 273 optimal weight: 0.8980 chunk 493 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 568 optimal weight: 30.0000 chunk 594 optimal weight: 20.0000 chunk 626 optimal weight: 5.9990 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 227 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56600 Z= 0.201 Angle : 0.600 8.627 76620 Z= 0.308 Chirality : 0.038 0.180 8740 Planarity : 0.003 0.045 9540 Dihedral : 4.119 19.792 7620 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.69 % Allowed : 21.28 % Favored : 75.03 % 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: 2.24 (0.10), residues: 6820 helix: 2.36 (0.08), residues: 4020 sheet: 1.45 (0.14), residues: 1100 loop : -0.70 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 221 HIS 0.004 0.001 HIS h 33 PHE 0.030 0.002 PHE F 105 TYR 0.016 0.001 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 930 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 708 time to evaluate : 4.835 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7858 (mmm) cc_final: 0.7584 (mmm) REVERT: A 238 GLN cc_start: 0.7995 (tt0) cc_final: 0.7734 (tt0) REVERT: U 34 MET cc_start: 0.5618 (mmm) cc_final: 0.5296 (mmm) REVERT: B 22 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8697 (tm) REVERT: C 6 ASN cc_start: 0.4980 (t160) cc_final: 0.4182 (p0) REVERT: C 244 MET cc_start: 0.7744 (tpt) cc_final: 0.7197 (tpp) REVERT: C 273 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8185 (mttt) REVERT: D 238 GLN cc_start: 0.7945 (tt0) cc_final: 0.7648 (tt0) REVERT: D 244 MET cc_start: 0.7983 (tpt) cc_final: 0.7630 (tpp) REVERT: E 22 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8637 (tm) REVERT: E 244 MET cc_start: 0.7738 (tpp) cc_final: 0.7460 (tpp) REVERT: G 22 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8718 (tm) REVERT: G 104 PHE cc_start: 0.6560 (t80) cc_final: 0.6265 (t80) REVERT: G 244 MET cc_start: 0.7848 (tpt) cc_final: 0.7332 (tpp) REVERT: H 244 MET cc_start: 0.8183 (tpt) cc_final: 0.7952 (tpp) REVERT: I 220 TYR cc_start: 0.8845 (t80) cc_final: 0.8640 (t80) REVERT: I 238 GLN cc_start: 0.7992 (tt0) cc_final: 0.7757 (tt0) REVERT: I 244 MET cc_start: 0.8171 (tpt) cc_final: 0.7776 (tpp) REVERT: I 274 ASP cc_start: 0.8348 (p0) cc_final: 0.8083 (p0) REVERT: J 22 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8688 (tm) REVERT: J 238 GLN cc_start: 0.7976 (tt0) cc_final: 0.7756 (tt0) REVERT: J 244 MET cc_start: 0.7823 (tpt) cc_final: 0.7279 (tpp) REVERT: K 244 MET cc_start: 0.8218 (tpt) cc_final: 0.7698 (tpp) REVERT: L 22 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8717 (tm) REVERT: L 244 MET cc_start: 0.8161 (tpt) cc_final: 0.7710 (tpp) REVERT: M 238 GLN cc_start: 0.7913 (tt0) cc_final: 0.7656 (tt0) REVERT: O 22 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8722 (tm) REVERT: P 7 ASN cc_start: 0.7270 (p0) cc_final: 0.7012 (p0) REVERT: Q 22 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8710 (tm) REVERT: Q 238 GLN cc_start: 0.7839 (tt0) cc_final: 0.7621 (tt0) REVERT: Q 274 ASP cc_start: 0.8074 (p0) cc_final: 0.7793 (p0) REVERT: R 244 MET cc_start: 0.7640 (tpp) cc_final: 0.7422 (tpp) REVERT: S 244 MET cc_start: 0.7636 (tpt) cc_final: 0.7173 (tpp) REVERT: T 22 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8696 (tm) REVERT: T 104 PHE cc_start: 0.6580 (t80) cc_final: 0.6352 (t80) REVERT: T 152 LYS cc_start: 0.7543 (tptp) cc_final: 0.7294 (tptp) REVERT: T 230 GLU cc_start: 0.7972 (tt0) cc_final: 0.7697 (tm-30) REVERT: T 237 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7830 (tm-30) REVERT: T 244 MET cc_start: 0.7738 (tpt) cc_final: 0.7283 (tpp) REVERT: a 11 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5211 (pt) REVERT: c 34 MET cc_start: 0.7206 (mmt) cc_final: 0.6322 (ttt) REVERT: f 109 THR cc_start: 0.3362 (p) cc_final: 0.3103 (p) REVERT: g 34 MET cc_start: 0.6031 (mmm) cc_final: 0.5738 (mmm) REVERT: h 107 GLN cc_start: 0.6077 (tm-30) cc_final: 0.5168 (pm20) REVERT: i 107 GLN cc_start: 0.6097 (tm-30) cc_final: 0.5107 (pm20) REVERT: j 34 MET cc_start: 0.3886 (OUTLIER) cc_final: 0.3550 (mmm) REVERT: k 34 MET cc_start: 0.3944 (OUTLIER) cc_final: 0.3650 (mmm) REVERT: k 107 GLN cc_start: 0.5896 (tm-30) cc_final: 0.5180 (pm20) outliers start: 222 outliers final: 196 residues processed: 890 average time/residue: 0.4541 time to fit residues: 709.8063 Evaluate side-chains 873 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 666 time to evaluate : 4.724 ------------------------------------------------------------------------------- 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 206 VAL Chi-restraints excluded: chain A residue 264 ILE 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 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 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL 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 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 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 116 LEU Chi-restraints excluded: chain E residue 175 ASP 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 213 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 264 ILE 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 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 116 LEU Chi-restraints excluded: chain G residue 188 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 10 SER 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 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 10 SER 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 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 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 J residue 264 ILE 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 K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE 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 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 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 M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN 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 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 116 LEU Chi-restraints excluded: chain O residue 147 ASN Chi-restraints excluded: chain O residue 175 ASP 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 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 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 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 108 THR Chi-restraints excluded: chain S residue 116 LEU 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 213 LEU 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 45 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 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 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 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 98 VAL Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain c residue 98 VAL 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 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 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 81 LEU Chi-restraints excluded: chain k residue 34 MET Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 34 MET 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: 1.9990 chunk 664 optimal weight: 9.9990 chunk 405 optimal weight: 0.0040 chunk 315 optimal weight: 1.9990 chunk 462 optimal weight: 3.9990 chunk 697 optimal weight: 5.9990 chunk 641 optimal weight: 40.0000 chunk 555 optimal weight: 20.0000 chunk 57 optimal weight: 0.7980 chunk 428 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 GLN ** K 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 56600 Z= 0.231 Angle : 0.671 59.200 76620 Z= 0.355 Chirality : 0.038 0.322 8740 Planarity : 0.003 0.053 9540 Dihedral : 4.128 19.852 7620 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.69 % Allowed : 21.28 % Favored : 75.03 % 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: 2.25 (0.10), residues: 6820 helix: 2.37 (0.08), residues: 4020 sheet: 1.47 (0.14), residues: 1100 loop : -0.71 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP V 36 HIS 0.004 0.001 HIS h 33 PHE 0.029 0.002 PHE F 105 TYR 0.041 0.001 TYR j 52 ARG 0.011 0.000 ARG P 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 890 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 668 time to evaluate : 4.919 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7848 (mmm) cc_final: 0.7572 (mmm) REVERT: A 238 GLN cc_start: 0.7984 (tt0) cc_final: 0.7719 (tt0) REVERT: U 34 MET cc_start: 0.5615 (mmm) cc_final: 0.5296 (mmm) REVERT: B 22 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8692 (tm) REVERT: C 6 ASN cc_start: 0.4986 (t160) cc_final: 0.4181 (p0) REVERT: C 244 MET cc_start: 0.7739 (tpt) cc_final: 0.7200 (tpp) REVERT: C 273 LYS cc_start: 0.8435 (ptmt) cc_final: 0.8180 (mttt) REVERT: D 238 GLN cc_start: 0.7938 (tt0) cc_final: 0.7645 (tt0) REVERT: D 244 MET cc_start: 0.7982 (tpt) cc_final: 0.7621 (tpp) REVERT: E 22 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8660 (tm) REVERT: E 244 MET cc_start: 0.7748 (tpp) cc_final: 0.7491 (tpp) REVERT: G 22 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8715 (tm) REVERT: G 104 PHE cc_start: 0.6523 (t80) cc_final: 0.6251 (t80) REVERT: G 244 MET cc_start: 0.7845 (tpt) cc_final: 0.7333 (tpp) REVERT: H 244 MET cc_start: 0.8179 (tpt) cc_final: 0.7955 (tpp) REVERT: I 220 TYR cc_start: 0.8836 (t80) cc_final: 0.8634 (t80) REVERT: I 238 GLN cc_start: 0.7965 (tt0) cc_final: 0.7743 (tt0) REVERT: I 244 MET cc_start: 0.8186 (tpt) cc_final: 0.7772 (tpp) REVERT: I 274 ASP cc_start: 0.8335 (p0) cc_final: 0.8073 (p0) REVERT: J 22 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8690 (tm) REVERT: J 238 GLN cc_start: 0.7967 (tt0) cc_final: 0.7751 (tt0) REVERT: J 244 MET cc_start: 0.7823 (tpt) cc_final: 0.7290 (tpp) REVERT: K 244 MET cc_start: 0.8206 (tpt) cc_final: 0.7694 (tpp) REVERT: L 22 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8717 (tm) REVERT: L 244 MET cc_start: 0.8123 (tpt) cc_final: 0.7698 (tpp) REVERT: M 238 GLN cc_start: 0.7925 (tt0) cc_final: 0.7684 (tt0) REVERT: O 22 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8721 (tm) REVERT: P 7 ASN cc_start: 0.7272 (p0) cc_final: 0.7012 (p0) REVERT: Q 22 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8705 (tm) REVERT: Q 238 GLN cc_start: 0.7832 (tt0) cc_final: 0.7616 (tt0) REVERT: Q 274 ASP cc_start: 0.8050 (p0) cc_final: 0.7796 (p0) REVERT: R 244 MET cc_start: 0.7638 (tpp) cc_final: 0.7427 (tpp) REVERT: S 244 MET cc_start: 0.7629 (tpt) cc_final: 0.7172 (tpp) REVERT: T 22 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8691 (tm) REVERT: T 104 PHE cc_start: 0.6578 (t80) cc_final: 0.6322 (t80) REVERT: T 230 GLU cc_start: 0.7972 (tt0) cc_final: 0.7697 (tm-30) REVERT: T 244 MET cc_start: 0.7740 (tpt) cc_final: 0.7284 (tpp) REVERT: a 11 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5212 (pt) REVERT: c 34 MET cc_start: 0.7199 (mmt) cc_final: 0.6324 (ttt) REVERT: f 109 THR cc_start: 0.3410 (p) cc_final: 0.3161 (p) REVERT: g 34 MET cc_start: 0.6013 (mmm) cc_final: 0.5726 (mmm) REVERT: h 107 GLN cc_start: 0.6077 (tm-30) cc_final: 0.5165 (pm20) REVERT: i 107 GLN cc_start: 0.6107 (tm-30) cc_final: 0.5108 (pm20) REVERT: j 34 MET cc_start: 0.3874 (OUTLIER) cc_final: 0.3539 (mmm) REVERT: k 34 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.3636 (mmm) REVERT: k 107 GLN cc_start: 0.5904 (tm-30) cc_final: 0.5178 (pm20) outliers start: 222 outliers final: 204 residues processed: 845 average time/residue: 0.4575 time to fit residues: 680.6670 Evaluate side-chains 872 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 657 time to evaluate : 4.833 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 ILE 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 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 216 LEU 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 77 ILE 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 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 116 LEU Chi-restraints excluded: chain E residue 175 ASP 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 213 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 112 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 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 116 LEU Chi-restraints excluded: chain G residue 188 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 10 SER 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 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 10 SER Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 112 VAL 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 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 57 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 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 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 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 M residue 206 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 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 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 147 ASN Chi-restraints excluded: chain O residue 154 GLU Chi-restraints excluded: chain O residue 175 ASP 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 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 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 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 255 ILE 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 108 THR Chi-restraints excluded: chain S residue 116 LEU 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 213 LEU 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 45 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 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 52 TYR Chi-restraints excluded: chain X residue 70 ILE 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 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 98 VAL Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain c residue 98 VAL 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 f residue 34 MET 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 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 70 ILE Chi-restraints excluded: chain j residue 81 LEU 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 34 MET Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 52 TYR 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: 1.9990 chunk 591 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 512 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 556 optimal weight: 40.0000 chunk 232 optimal weight: 3.9990 chunk 571 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.183324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.154966 restraints weight = 89891.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.152691 restraints weight = 190215.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.153295 restraints weight = 177122.438| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 56600 Z= 0.231 Angle : 0.671 59.200 76620 Z= 0.355 Chirality : 0.038 0.322 8740 Planarity : 0.003 0.053 9540 Dihedral : 4.128 19.852 7620 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.59 % Allowed : 21.35 % Favored : 75.07 % 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: 2.25 (0.10), residues: 6820 helix: 2.37 (0.08), residues: 4020 sheet: 1.47 (0.14), residues: 1100 loop : -0.71 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP V 36 HIS 0.004 0.001 HIS h 33 PHE 0.029 0.002 PHE F 105 TYR 0.041 0.001 TYR j 52 ARG 0.011 0.000 ARG P 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11870.28 seconds wall clock time: 209 minutes 18.65 seconds (12558.65 seconds total)