Starting phenix.real_space_refine on Fri Jan 17 02:31:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmn_19365/01_2025/8rmn_19365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmn_19365/01_2025/8rmn_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/cci-nas-00/data/ceres_data/8rmn_19365/01_2025/8rmn_19365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmn_19365/01_2025/8rmn_19365.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmn_19365/01_2025/8rmn_19365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmn_19365/01_2025/8rmn_19365.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 460 5.16 5 C 35480 2.51 5 N 9480 2.21 5 O 10020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 55440 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "U" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "B" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "E" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "F" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "G" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "H" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "I" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "J" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "K" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "L" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "M" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "N" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "O" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "P" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "Q" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "R" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "S" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "T" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "V" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "W" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "X" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "Y" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "Z" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "a" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "b" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "c" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "d" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "e" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "f" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "g" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "h" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "i" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "j" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "k" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "l" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "m" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "n" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Time building chain proxies: 22.91, per 1000 atoms: 0.41 Number of scatterers: 55440 At special positions: 0 Unit cell: (138.012, 143.871, 254.541, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 460 16.00 O 10020 8.00 N 9480 7.00 C 35480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.02 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.02 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.02 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.02 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.02 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.02 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.02 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.02 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=2.02 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.02 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.02 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.02 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.02 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.74 Conformation dependent library (CDL) restraints added in 5.3 seconds 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13320 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 40 sheets defined 63.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 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: 19.59 Time building geometry restraints manager: 12.71 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: 0.37 Found NCS groups: ncs_group { reference = chain 'U' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'n' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } 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: 5.720 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: 0.070 Extract box with map and model: 1.860 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 93.290 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.470 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.480 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 70 poor density : 1013 time to evaluate : 4.627 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: 0.4860 time to fit residues: 900.3466 Evaluate side-chains 822 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 784 time to evaluate : 4.595 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.182314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.137271 restraints weight = 86002.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139261 restraints weight = 63357.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139477 restraints weight = 51041.062| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 to be fit. rotamer outliers: 175 poor density : 883 time to evaluate : 4.692 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8036 (tt0) cc_final: 0.7782 (tt0) REVERT: B 231 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8409 (mm) REVERT: B 244 MET cc_start: 0.8282 (tpt) cc_final: 0.7653 (tpp) REVERT: C 96 GLU cc_start: 0.5874 (mp0) cc_final: 0.5224 (mt-10) REVERT: C 244 MET cc_start: 0.7511 (tpt) cc_final: 0.7184 (tpp) REVERT: C 273 LYS cc_start: 0.8466 (ptmt) cc_final: 0.8232 (mttt) REVERT: D 238 GLN cc_start: 0.7987 (tt0) cc_final: 0.7635 (tt0) REVERT: D 244 MET cc_start: 0.8193 (tpt) cc_final: 0.7927 (tpt) REVERT: E 187 MET cc_start: 0.7453 (mmm) cc_final: 0.6268 (ttp) REVERT: G 244 MET cc_start: 0.7887 (tpt) cc_final: 0.7381 (tpp) REVERT: H 244 MET cc_start: 0.8138 (tpt) cc_final: 0.7842 (tpp) REVERT: I 244 MET cc_start: 0.7890 (tpt) cc_final: 0.7422 (tpp) REVERT: J 238 GLN cc_start: 0.7972 (tt0) cc_final: 0.7604 (tt0) REVERT: J 244 MET cc_start: 0.7982 (tpt) cc_final: 0.7501 (tpp) REVERT: K 238 GLN cc_start: 0.8034 (tt0) cc_final: 0.7791 (tt0) REVERT: L 229 ARG cc_start: 0.8612 (tpp80) cc_final: 0.7442 (mtm110) REVERT: M 270 GLN cc_start: 0.6219 (tp-100) cc_final: 0.5945 (tp-100) REVERT: N 244 MET cc_start: 0.8303 (tpt) cc_final: 0.8068 (tpp) REVERT: O 230 GLU cc_start: 0.7862 (tt0) cc_final: 0.7617 (tm-30) REVERT: O 238 GLN cc_start: 0.7893 (tt0) cc_final: 0.7472 (tt0) REVERT: P 7 ASN cc_start: 0.6953 (p0) cc_final: 0.6651 (p0) REVERT: Q 238 GLN cc_start: 0.7729 (tt0) cc_final: 0.7305 (tt0) REVERT: R 244 MET cc_start: 0.7126 (tpp) cc_final: 0.6718 (tpp) REVERT: R 251 LEU cc_start: 0.8590 (tp) cc_final: 0.8375 (tp) REVERT: S 187 MET cc_start: 0.7189 (mmm) cc_final: 0.6101 (ttp) REVERT: S 244 MET cc_start: 0.7454 (tpt) cc_final: 0.6838 (tpp) REVERT: T 6 ASN cc_start: 0.4611 (t0) cc_final: 0.4268 (p0) REVERT: T 238 GLN cc_start: 0.7663 (tt0) cc_final: 0.7409 (tt0) REVERT: T 244 MET cc_start: 0.7512 (tpt) cc_final: 0.7065 (tpp) REVERT: a 19 ARG cc_start: 0.5547 (tpt90) cc_final: 0.5121 (mmm-85) REVERT: b 34 MET cc_start: 0.4717 (mmm) cc_final: 0.4507 (mmm) REVERT: g 34 MET cc_start: 0.4386 (mmm) cc_final: 0.4117 (mmm) REVERT: g 82 GLN cc_start: 0.6672 (tm-30) cc_final: 0.6353 (tm-30) REVERT: h 107 GLN cc_start: 0.5644 (tm-30) cc_final: 0.5170 (mm-40) REVERT: i 107 GLN cc_start: 0.6159 (tm-30) cc_final: 0.5409 (pm20) REVERT: l 58 THR cc_start: 0.5077 (t) cc_final: 0.4834 (p) REVERT: m 58 THR cc_start: 0.5539 (t) cc_final: 0.5307 (p) REVERT: n 68 PHE cc_start: 0.5334 (m-80) cc_final: 0.5072 (m-80) outliers start: 175 outliers final: 98 residues processed: 987 average time/residue: 0.4923 time to fit residues: 838.1853 Evaluate side-chains 844 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 745 time to evaluate : 4.735 ------------------------------------------------------------------------------- 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 340 optimal weight: 0.2980 chunk 623 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 638 optimal weight: 3.9990 chunk 558 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 532 optimal weight: 30.0000 chunk 268 optimal weight: 3.9990 chunk 616 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 181 HIS B 6 ASN B 181 HIS C 6 ASN D 6 ASN E 6 ASN E 181 HIS E 238 GLN F 6 ASN F 238 GLN G 6 ASN H 6 ASN H 181 HIS I 6 ASN J 6 ASN K 181 HIS L 6 ASN M 6 ASN M 227 ASN N 6 ASN O 6 ASN P 6 ASN P 181 HIS Q 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 ASN S 181 HIS S 238 GLN T 6 ASN T 181 HIS ** W 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 59 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.183836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.153883 restraints weight = 90063.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.151296 restraints weight = 195148.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.151709 restraints weight = 168554.107| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 56600 Z= 0.241 Angle : 0.616 6.943 76620 Z= 0.324 Chirality : 0.039 0.220 8740 Planarity : 0.004 0.056 9540 Dihedral : 4.146 28.059 7624 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.88 % Allowed : 17.52 % Favored : 77.59 % 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: 2.22 (0.10), residues: 6820 helix: 2.33 (0.08), residues: 3980 sheet: 1.54 (0.15), residues: 880 loop : -0.38 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 36 HIS 0.005 0.001 HIS C 141 PHE 0.030 0.002 PHE F 105 TYR 0.021 0.002 TYR J 142 ARG 0.008 0.001 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 294 poor density : 821 time to evaluate : 4.694 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.7766 (mmm) cc_final: 0.7560 (mmm) REVERT: A 238 GLN cc_start: 0.8120 (tt0) cc_final: 0.7914 (tt0) REVERT: U 52 TYR cc_start: 0.3104 (OUTLIER) cc_final: 0.2222 (m-80) REVERT: B 244 MET cc_start: 0.8213 (tpt) cc_final: 0.7735 (tpp) REVERT: C 104 PHE cc_start: 0.6852 (t80) cc_final: 0.6624 (t80) REVERT: C 244 MET cc_start: 0.7569 (tpt) cc_final: 0.7089 (tpp) REVERT: D 187 MET cc_start: 0.7918 (mmm) cc_final: 0.7599 (mmm) REVERT: D 238 GLN cc_start: 0.8083 (tt0) cc_final: 0.7818 (tt0) REVERT: D 244 MET cc_start: 0.8258 (tpt) cc_final: 0.7683 (tpp) REVERT: F 187 MET cc_start: 0.7730 (mmm) cc_final: 0.7499 (mmm) REVERT: G 244 MET cc_start: 0.7903 (tpt) cc_final: 0.7305 (tpp) REVERT: I 244 MET cc_start: 0.8029 (tpt) cc_final: 0.7528 (tpp) REVERT: J 238 GLN cc_start: 0.8133 (tt0) cc_final: 0.7882 (tt0) REVERT: J 244 MET cc_start: 0.7832 (tpt) cc_final: 0.7319 (tpp) REVERT: K 187 MET cc_start: 0.7733 (mmm) cc_final: 0.7462 (mmm) REVERT: K 238 GLN cc_start: 0.8163 (tt0) cc_final: 0.7894 (tt0) REVERT: L 104 PHE cc_start: 0.6752 (t80) cc_final: 0.6447 (t80) REVERT: L 105 PHE cc_start: 0.8124 (t80) cc_final: 0.7874 (t80) REVERT: L 244 MET cc_start: 0.7947 (tpt) cc_final: 0.7700 (tpp) REVERT: M 238 GLN cc_start: 0.8175 (tt0) cc_final: 0.7914 (tt0) REVERT: O 230 GLU cc_start: 0.7922 (tt0) cc_final: 0.7688 (tm-30) REVERT: P 7 ASN cc_start: 0.6926 (p0) cc_final: 0.6607 (p0) REVERT: P 187 MET cc_start: 0.7869 (mmm) cc_final: 0.7587 (mmm) REVERT: Q 238 GLN cc_start: 0.7965 (tt0) cc_final: 0.7705 (tt0) REVERT: R 96 GLU cc_start: 0.6131 (mp0) cc_final: 0.5730 (mt-10) REVERT: R 244 MET cc_start: 0.7371 (tpp) cc_final: 0.6733 (tpp) REVERT: R 251 LEU cc_start: 0.8549 (tp) cc_final: 0.8320 (tp) REVERT: S 10 SER cc_start: 0.7071 (OUTLIER) cc_final: 0.6860 (t) REVERT: S 244 MET cc_start: 0.7525 (tpt) cc_final: 0.7184 (tpp) REVERT: T 244 MET cc_start: 0.7631 (tpt) cc_final: 0.7150 (tpp) REVERT: V 34 MET cc_start: 0.3049 (mmm) cc_final: 0.2748 (mmm) REVERT: X 35 ARG cc_start: 0.5973 (mtt90) cc_final: 0.5741 (mtt-85) REVERT: d 35 ARG cc_start: 0.5834 (mtt90) cc_final: 0.5634 (mtt-85) REVERT: f 18 LEU cc_start: 0.5239 (OUTLIER) cc_final: 0.4760 (mp) REVERT: h 35 ARG cc_start: 0.6304 (mtt90) cc_final: 0.6006 (mtt-85) REVERT: j 35 ARG cc_start: 0.5693 (mtt90) cc_final: 0.5488 (mtt-85) REVERT: k 34 MET cc_start: 0.2545 (mmm) cc_final: 0.2122 (mmm) REVERT: k 107 GLN cc_start: 0.5374 (tm-30) cc_final: 0.5157 (pm20) REVERT: l 58 THR cc_start: 0.5524 (t) cc_final: 0.5140 (p) REVERT: l 79 VAL cc_start: 0.5691 (t) cc_final: 0.4779 (t) REVERT: m 58 THR cc_start: 0.5819 (t) cc_final: 0.5413 (p) outliers start: 294 outliers final: 171 residues processed: 1004 average time/residue: 0.4728 time to fit residues: 826.8958 Evaluate side-chains 867 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 693 time to evaluate : 4.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR 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 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 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 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 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 9 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 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 108 THR 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 188 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 206 VAL 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 108 THR Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 188 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 180 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 141 HIS 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 9 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL 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 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 64 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 188 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 THR 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 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 9 VAL Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 108 THR 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 T residue 9 VAL 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 58 THR Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 90 ASP Chi-restraints excluded: chain d residue 12 VAL Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 81 LEU 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 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 5 VAL 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 90 ASP Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 218 optimal weight: 2.9990 chunk 629 optimal weight: 50.0000 chunk 133 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 662 optimal weight: 7.9990 chunk 481 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 562 optimal weight: 6.9990 chunk 685 optimal weight: 20.0000 chunk 381 optimal weight: 3.9990 chunk 500 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN B 147 ASN C 6 ASN C 181 HIS D 6 ASN D 181 HIS E 147 ASN F 6 ASN F 181 HIS G 6 ASN G 181 HIS H 6 ASN H 238 GLN I 6 ASN I 181 HIS J 6 ASN J 181 HIS K 147 ASN L 147 ASN L 181 HIS M 6 ASN M 181 HIS M 270 GLN N 6 ASN N 147 ASN O 6 ASN O 147 ASN O 181 HIS P 6 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS S 238 GLN T 6 ASN T 238 GLN c 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.176534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.148258 restraints weight = 94737.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146230 restraints weight = 198396.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.145996 restraints weight = 189097.818| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 56600 Z= 0.441 Angle : 0.750 7.798 76620 Z= 0.399 Chirality : 0.045 0.285 8740 Planarity : 0.005 0.050 9540 Dihedral : 4.809 20.958 7620 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.76 % Allowed : 18.46 % Favored : 75.78 % 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: 1.35 (0.10), residues: 6820 helix: 1.74 (0.08), residues: 3900 sheet: 1.14 (0.14), residues: 1080 loop : -1.09 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP l 47 HIS 0.006 0.001 HIS F 239 PHE 0.033 0.003 PHE C 160 TYR 0.023 0.003 TYR F 220 ARG 0.009 0.001 ARG Q 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 1041 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 347 poor density : 694 time to evaluate : 4.657 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8193 (tt0) cc_final: 0.7904 (tt0) REVERT: B 22 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8555 (tm) REVERT: B 244 MET cc_start: 0.8292 (tpt) cc_final: 0.7734 (tpp) REVERT: C 244 MET cc_start: 0.7916 (tpt) cc_final: 0.7336 (tpp) REVERT: D 22 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8819 (tm) REVERT: D 104 PHE cc_start: 0.7019 (t80) cc_final: 0.6764 (t80) REVERT: D 238 GLN cc_start: 0.8208 (tt0) cc_final: 0.7957 (tt0) REVERT: D 244 MET cc_start: 0.8326 (tpt) cc_final: 0.7785 (tpp) REVERT: E 22 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8637 (tm) REVERT: E 104 PHE cc_start: 0.7004 (t80) cc_final: 0.6777 (t80) REVERT: E 105 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7960 (t80) REVERT: E 244 MET cc_start: 0.7930 (tpp) cc_final: 0.7654 (tpp) REVERT: G 22 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8580 (tm) REVERT: G 99 LEU cc_start: 0.7891 (mt) cc_final: 0.7584 (mp) REVERT: G 244 MET cc_start: 0.8061 (tpt) cc_final: 0.7444 (tpp) REVERT: I 104 PHE cc_start: 0.6998 (t80) cc_final: 0.6786 (t80) REVERT: I 244 MET cc_start: 0.8192 (tpt) cc_final: 0.7680 (tpp) REVERT: J 22 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8686 (tm) REVERT: J 238 GLN cc_start: 0.8218 (tt0) cc_final: 0.7987 (tt0) REVERT: J 244 MET cc_start: 0.8081 (tpt) cc_final: 0.7423 (tpp) REVERT: K 104 PHE cc_start: 0.6950 (t80) cc_final: 0.6713 (t80) REVERT: K 238 GLN cc_start: 0.8243 (tt0) cc_final: 0.7950 (tt0) REVERT: L 22 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8568 (tm) REVERT: L 104 PHE cc_start: 0.7085 (t80) cc_final: 0.6793 (t80) REVERT: L 244 MET cc_start: 0.8280 (tpt) cc_final: 0.7619 (tpp) REVERT: M 104 PHE cc_start: 0.6963 (t80) cc_final: 0.6732 (t80) REVERT: N 244 MET cc_start: 0.7975 (tpp) cc_final: 0.7648 (tpp) REVERT: O 22 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8704 (tm) REVERT: P 7 ASN cc_start: 0.6940 (p0) cc_final: 0.6658 (p0) REVERT: P 104 PHE cc_start: 0.6930 (t80) cc_final: 0.6690 (t80) REVERT: Q 22 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8587 (tm) REVERT: Q 104 PHE cc_start: 0.7005 (t80) cc_final: 0.6781 (t80) REVERT: Q 238 GLN cc_start: 0.8092 (tt0) cc_final: 0.7891 (tt0) REVERT: R 6 ASN cc_start: 0.4823 (t160) cc_final: 0.4333 (p0) REVERT: R 105 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7977 (t80) REVERT: R 244 MET cc_start: 0.7620 (tpp) cc_final: 0.7088 (tpp) REVERT: S 10 SER cc_start: 0.7083 (OUTLIER) cc_final: 0.6875 (t) REVERT: S 104 PHE cc_start: 0.7038 (t80) cc_final: 0.6826 (t80) REVERT: S 244 MET cc_start: 0.7826 (tpt) cc_final: 0.7343 (tpp) REVERT: T 22 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8697 (tm) REVERT: T 244 MET cc_start: 0.7956 (tpt) cc_final: 0.7405 (tpp) REVERT: X 52 TYR cc_start: 0.4223 (OUTLIER) cc_final: 0.3310 (m-80) REVERT: i 107 GLN cc_start: 0.5828 (tm-30) cc_final: 0.4990 (pm20) REVERT: k 34 MET cc_start: 0.3289 (OUTLIER) cc_final: 0.3044 (mmm) REVERT: l 19 ARG cc_start: 0.5625 (tpt170) cc_final: 0.5389 (tpp80) REVERT: l 58 THR cc_start: 0.5476 (t) cc_final: 0.5260 (p) REVERT: m 58 THR cc_start: 0.5628 (t) cc_final: 0.5411 (p) outliers start: 347 outliers final: 228 residues processed: 939 average time/residue: 0.4530 time to fit residues: 749.3324 Evaluate side-chains 814 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 572 time to evaluate : 4.689 ------------------------------------------------------------------------------- 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 112 VAL 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 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 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 9 VAL Chi-restraints excluded: chain C residue 47 LYS 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 231 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 22 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 231 LEU 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 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 175 ASP 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 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 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 10 SER 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 192 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 10 SER 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 K residue 264 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 188 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 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 141 HIS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU 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 195 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 108 THR Chi-restraints excluded: chain P residue 112 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 P residue 231 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 147 ASN 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 245 MET 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 10 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 233 GLU Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 116 LEU 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 7 SER 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 52 TYR Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 34 MET Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 7 SER Chi-restraints excluded: chain b residue 52 TYR Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 52 TYR Chi-restraints excluded: chain d residue 5 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 7 SER Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 68 PHE 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 34 MET Chi-restraints excluded: chain i residue 52 TYR 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 34 MET Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 7 SER Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 58 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 69 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 387 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 626 optimal weight: 0.0170 chunk 441 optimal weight: 3.9990 chunk 671 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 690 optimal weight: 0.8980 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 238 GLN L 6 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 ASN a 59 HIS b 59 HIS g 82 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.181246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.152205 restraints weight = 89869.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.150198 restraints weight = 185892.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.150533 restraints weight = 183172.257| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3501 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= 0.192 Angle : 0.601 9.862 76620 Z= 0.312 Chirality : 0.038 0.195 8740 Planarity : 0.003 0.038 9540 Dihedral : 4.392 19.003 7620 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.50 % Allowed : 21.06 % Favored : 75.43 % 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: 1.88 (0.10), residues: 6820 helix: 2.19 (0.08), residues: 3900 sheet: 1.03 (0.13), residues: 1100 loop : -0.70 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 47 HIS 0.003 0.001 HIS b 33 PHE 0.030 0.002 PHE P 105 TYR 0.017 0.001 TYR I 220 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 897 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 686 time to evaluate : 4.884 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8032 (tt0) cc_final: 0.7756 (tt0) REVERT: B 244 MET cc_start: 0.8237 (tpt) cc_final: 0.7700 (tpp) REVERT: B 251 LEU cc_start: 0.8300 (tp) cc_final: 0.8087 (tp) REVERT: C 6 ASN cc_start: 0.5124 (t0) cc_final: 0.4549 (p0) REVERT: C 244 MET cc_start: 0.7700 (tpt) cc_final: 0.7265 (tpp) REVERT: D 238 GLN cc_start: 0.8033 (tt0) cc_final: 0.7641 (tt0) REVERT: D 244 MET cc_start: 0.8269 (tpt) cc_final: 0.7749 (tpp) REVERT: E 104 PHE cc_start: 0.6731 (t80) cc_final: 0.6424 (t80) REVERT: E 244 MET cc_start: 0.7812 (tpp) cc_final: 0.7594 (tpp) REVERT: F 238 GLN cc_start: 0.8253 (tt0) cc_final: 0.7931 (tt0) REVERT: G 104 PHE cc_start: 0.6831 (t80) cc_final: 0.6572 (t80) REVERT: G 244 MET cc_start: 0.7858 (tpt) cc_final: 0.7390 (tpp) REVERT: H 104 PHE cc_start: 0.6707 (t80) cc_final: 0.6402 (t80) REVERT: I 104 PHE cc_start: 0.6671 (t80) cc_final: 0.6445 (t80) REVERT: I 244 MET cc_start: 0.8189 (tpt) cc_final: 0.7661 (tpp) REVERT: J 238 GLN cc_start: 0.8038 (tt0) cc_final: 0.7782 (tt0) REVERT: J 244 MET cc_start: 0.7846 (tpt) cc_final: 0.7389 (tpp) REVERT: K 104 PHE cc_start: 0.6738 (t80) cc_final: 0.6515 (t80) REVERT: K 105 PHE cc_start: 0.8171 (t80) cc_final: 0.7971 (t80) REVERT: K 238 GLN cc_start: 0.8065 (tt0) cc_final: 0.7740 (tt0) REVERT: L 104 PHE cc_start: 0.6821 (t80) cc_final: 0.6555 (t80) REVERT: L 244 MET cc_start: 0.8201 (tpt) cc_final: 0.7934 (tpp) REVERT: L 251 LEU cc_start: 0.8305 (tp) cc_final: 0.8086 (tp) REVERT: M 104 PHE cc_start: 0.6613 (t80) cc_final: 0.6375 (t80) REVERT: M 238 GLN cc_start: 0.8032 (tt0) cc_final: 0.7740 (tt0) REVERT: M 244 MET cc_start: 0.8066 (tpt) cc_final: 0.7848 (tpp) REVERT: N 244 MET cc_start: 0.7983 (tpp) cc_final: 0.7657 (tpp) REVERT: O 251 LEU cc_start: 0.8296 (tp) cc_final: 0.8048 (tp) REVERT: P 7 ASN cc_start: 0.6930 (p0) cc_final: 0.6642 (p0) REVERT: Q 104 PHE cc_start: 0.6708 (t80) cc_final: 0.6460 (t80) REVERT: Q 238 GLN cc_start: 0.7924 (tt0) cc_final: 0.7694 (tt0) REVERT: Q 251 LEU cc_start: 0.8575 (tp) cc_final: 0.8371 (tp) REVERT: R 6 ASN cc_start: 0.4772 (t0) cc_final: 0.4542 (p0) REVERT: R 244 MET cc_start: 0.7448 (tpp) cc_final: 0.6926 (tpp) REVERT: S 104 PHE cc_start: 0.6790 (t80) cc_final: 0.6572 (t80) REVERT: S 244 MET cc_start: 0.7547 (tpt) cc_final: 0.7240 (tpp) REVERT: T 244 MET cc_start: 0.7675 (tpt) cc_final: 0.7319 (tpp) REVERT: T 251 LEU cc_start: 0.8553 (tp) cc_final: 0.8305 (tp) REVERT: g 90 ASP cc_start: 0.5510 (OUTLIER) cc_final: 0.5230 (t0) REVERT: h 107 GLN cc_start: 0.5842 (tm-30) cc_final: 0.4930 (pm20) REVERT: i 107 GLN cc_start: 0.5821 (tm-30) cc_final: 0.4949 (pm20) REVERT: j 34 MET cc_start: 0.3446 (OUTLIER) cc_final: 0.3232 (mmm) REVERT: m 58 THR cc_start: 0.5874 (t) cc_final: 0.5627 (p) outliers start: 211 outliers final: 169 residues processed: 853 average time/residue: 0.4946 time to fit residues: 745.5330 Evaluate side-chains 767 residues out of total 6020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 596 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 57 VAL 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 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 98 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 216 LEU 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 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL 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 116 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 264 ILE 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 112 VAL 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 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE 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 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 47 LYS 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 57 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 141 HIS Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain P residue 47 LYS 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 47 LYS Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL 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 116 LEU 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 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 116 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 52 TYR Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 ASP 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 b residue 81 LEU Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 70 ILE 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 52 TYR Chi-restraints excluded: chain g residue 90 ASP 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 j residue 81 LEU Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 90 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6518 > 50: distance: 29 - 47: 6.746 distance: 35 - 53: 9.481 distance: 40 - 60: 12.284 distance: 43 - 47: 9.520 distance: 44 - 65: 21.780 distance: 47 - 48: 8.097 distance: 48 - 49: 8.988 distance: 48 - 51: 7.328 distance: 49 - 50: 9.477 distance: 49 - 53: 7.789 distance: 50 - 74: 18.349 distance: 51 - 52: 32.409 distance: 53 - 54: 12.824 distance: 54 - 55: 7.625 distance: 54 - 57: 6.051 distance: 55 - 56: 16.149 distance: 55 - 60: 10.269 distance: 56 - 80: 10.403 distance: 57 - 58: 14.085 distance: 57 - 59: 19.870 distance: 60 - 61: 15.387 distance: 61 - 64: 12.625 distance: 62 - 65: 3.478 distance: 63 - 86: 18.795 distance: 65 - 66: 14.697 distance: 66 - 67: 13.360 distance: 66 - 69: 13.805 distance: 67 - 68: 15.727 distance: 67 - 74: 19.034 distance: 69 - 70: 3.888 distance: 70 - 71: 5.777 distance: 71 - 72: 19.312 distance: 72 - 73: 23.747 distance: 74 - 75: 15.499 distance: 75 - 76: 13.914 distance: 75 - 78: 9.323 distance: 76 - 77: 14.460 distance: 76 - 80: 19.127 distance: 78 - 79: 26.629 distance: 80 - 81: 11.227 distance: 81 - 82: 9.318 distance: 81 - 84: 11.292 distance: 82 - 83: 20.226 distance: 82 - 86: 9.348 distance: 84 - 85: 20.330 distance: 86 - 87: 22.375 distance: 87 - 88: 18.574 distance: 87 - 90: 8.669 distance: 88 - 89: 6.178 distance: 88 - 92: 29.877 distance: 90 - 91: 8.263 distance: 92 - 93: 21.343 distance: 92 - 98: 16.539 distance: 93 - 94: 14.460 distance: 93 - 96: 32.335 distance: 94 - 95: 7.564 distance: 94 - 99: 9.741 distance: 96 - 97: 28.162 distance: 97 - 98: 32.339 distance: 99 - 100: 9.870 distance: 100 - 101: 10.221 distance: 100 - 103: 5.269 distance: 101 - 102: 14.598 distance: 101 - 107: 25.005 distance: 103 - 104: 4.380 distance: 104 - 105: 19.094 distance: 104 - 106: 13.379 distance: 107 - 108: 4.277 distance: 108 - 109: 10.671 distance: 108 - 111: 7.933 distance: 109 - 110: 8.650 distance: 109 - 114: 6.213 distance: 110 - 136: 13.896 distance: 111 - 112: 9.979 distance: 111 - 113: 7.917