Starting phenix.real_space_refine on Sat Jan 18 02:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bk0_12195/01_2025/7bk0_12195.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bk0_12195/01_2025/7bk0_12195.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/7bk0_12195/01_2025/7bk0_12195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bk0_12195/01_2025/7bk0_12195.map" model { file = "/net/cci-nas-00/data/ceres_data/7bk0_12195/01_2025/7bk0_12195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bk0_12195/01_2025/7bk0_12195.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 125 5.16 5 C 35287 2.51 5 N 10618 2.21 5 O 11506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 437 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 57536 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "B" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "C" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "E" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "F" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "G" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "H" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "I" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "J" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "K" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "L" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "M" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "O" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "P" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Q" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "R" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "T" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "U" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "V" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "W" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "X" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "Y" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "Z" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "a" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "b" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "c" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "d" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "e" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "f" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "g" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Chain: "h" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 3 Time building chain proxies: 26.27, per 1000 atoms: 0.46 Number of scatterers: 57536 At special positions: 0 Unit cell: (250.432, 251.264, 129.792, 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 125 16.00 O 11506 8.00 N 10618 7.00 C 35287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 11.01 Conformation dependent library (CDL) restraints added in 5.6 seconds 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14092 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 78 sheets defined 34.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 232 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'B' and resid 126 through 146 removed outlier: 3.661A pdb=" N VAL B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 232 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'C' and resid 126 through 145 removed outlier: 3.914A pdb=" N VAL C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 232 through 258 removed outlier: 3.576A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.504A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'D' and resid 232 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.657A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 146 removed outlier: 3.634A pdb=" N VAL E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 146 " --> pdb=" O ARG E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.610A pdb=" N VAL E 202 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 210 Processing helix chain 'E' and resid 232 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 420 removed outlier: 3.684A pdb=" N ILE E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'F' and resid 232 through 258 removed outlier: 3.583A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.612A pdb=" N ALA F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 420 Processing helix chain 'F' and resid 423 through 427 Processing helix chain 'G' and resid 126 through 145 removed outlier: 4.174A pdb=" N VAL G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 232 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 420 Processing helix chain 'H' and resid 126 through 145 removed outlier: 3.963A pdb=" N VAL H 130 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 232 through 258 removed outlier: 3.544A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 287 through 291 removed outlier: 3.524A pdb=" N ALA H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 420 Processing helix chain 'H' and resid 423 through 427 Processing helix chain 'I' and resid 126 through 146 removed outlier: 3.792A pdb=" N VAL I 130 " --> pdb=" O PHE I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 202 Processing helix chain 'I' and resid 232 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 420 Processing helix chain 'J' and resid 232 through 258 removed outlier: 3.767A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 287 through 291 Processing helix chain 'J' and resid 405 through 420 Processing helix chain 'K' and resid 126 through 145 removed outlier: 3.806A pdb=" N VAL K 130 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY K 138 " --> pdb=" O ARG K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 202 Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'K' and resid 232 through 258 removed outlier: 3.765A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 287 through 291 Processing helix chain 'K' and resid 405 through 420 Processing helix chain 'L' and resid 126 through 146 Processing helix chain 'L' and resid 187 through 202 Processing helix chain 'L' and resid 206 through 210 Processing helix chain 'L' and resid 232 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 420 Processing helix chain 'L' and resid 423 through 427 Processing helix chain 'M' and resid 232 through 258 removed outlier: 3.634A pdb=" N LYS M 236 " --> pdb=" O ASP M 232 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 287 through 291 Processing helix chain 'M' and resid 405 through 420 Processing helix chain 'M' and resid 423 through 427 Processing helix chain 'N' and resid 126 through 145 removed outlier: 4.023A pdb=" N VAL N 130 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY N 138 " --> pdb=" O ARG N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 202 Processing helix chain 'N' and resid 232 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 420 removed outlier: 3.553A pdb=" N ILE N 412 " --> pdb=" O GLN N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 427 Processing helix chain 'O' and resid 126 through 146 removed outlier: 3.801A pdb=" N VAL O 130 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY O 138 " --> pdb=" O ARG O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 202 removed outlier: 3.573A pdb=" N ILE O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'O' and resid 232 through 258 removed outlier: 3.558A pdb=" N LYS O 236 " --> pdb=" O ASP O 232 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 287 through 291 Processing helix chain 'O' and resid 405 through 420 Processing helix chain 'O' and resid 423 through 427 Processing helix chain 'P' and resid 232 through 258 removed outlier: 3.525A pdb=" N LYS P 236 " --> pdb=" O ASP P 232 " (cutoff:3.500A) Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 420 removed outlier: 3.689A pdb=" N ILE P 412 " --> pdb=" O GLN P 408 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 427 Processing helix chain 'Q' and resid 126 through 146 removed outlier: 3.873A pdb=" N VAL Q 130 " --> pdb=" O PHE Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 202 removed outlier: 3.536A pdb=" N ILE Q 191 " --> pdb=" O ASP Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 258 removed outlier: 3.762A pdb=" N LYS Q 236 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 420 removed outlier: 4.018A pdb=" N ILE Q 412 " --> pdb=" O GLN Q 408 " (cutoff:3.500A) Processing helix chain 'Q' and resid 423 through 427 Processing helix chain 'R' and resid 126 through 146 removed outlier: 3.991A pdb=" N VAL R 130 " --> pdb=" O PHE R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 202 Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'R' and resid 232 through 258 removed outlier: 3.609A pdb=" N LYS R 236 " --> pdb=" O ASP R 232 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 405 through 420 Processing helix chain 'S' and resid 232 through 258 removed outlier: 3.658A pdb=" N LYS S 236 " --> pdb=" O ASP S 232 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 287 through 291 Processing helix chain 'S' and resid 405 through 420 removed outlier: 3.888A pdb=" N ILE S 412 " --> pdb=" O GLN S 408 " (cutoff:3.500A) Processing helix chain 'S' and resid 423 through 427 Processing helix chain 'T' and resid 126 through 145 removed outlier: 3.905A pdb=" N GLU T 145 " --> pdb=" O ALA T 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 202 Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'T' and resid 232 through 258 removed outlier: 3.819A pdb=" N LYS T 236 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 Processing helix chain 'U' and resid 126 through 146 removed outlier: 3.929A pdb=" N GLY U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 202 Processing helix chain 'U' and resid 206 through 208 No H-bonds generated for 'chain 'U' and resid 206 through 208' Processing helix chain 'U' and resid 232 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.653A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 removed outlier: 3.579A pdb=" N LYS V 236 " --> pdb=" O ASP V 232 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 287 through 291 Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.586A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 423 through 427 Processing helix chain 'W' and resid 126 through 146 removed outlier: 3.966A pdb=" N VAL W 130 " --> pdb=" O PHE W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 187 through 202 Processing helix chain 'W' and resid 206 through 210 Processing helix chain 'W' and resid 232 through 258 removed outlier: 3.524A pdb=" N LYS W 236 " --> pdb=" O ASP W 232 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 287 through 291 removed outlier: 3.689A pdb=" N ALA W 291 " --> pdb=" O ALA W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.534A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 423 through 427 Processing helix chain 'X' and resid 126 through 146 removed outlier: 3.713A pdb=" N VAL X 130 " --> pdb=" O PHE X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 202 Processing helix chain 'X' and resid 206 through 208 No H-bonds generated for 'chain 'X' and resid 206 through 208' Processing helix chain 'X' and resid 232 through 258 removed outlier: 3.562A pdb=" N LYS X 236 " --> pdb=" O ASP X 232 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 420 Processing helix chain 'X' and resid 423 through 427 Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.993A pdb=" N VAL Y 130 " --> pdb=" O PHE Y 126 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY Y 138 " --> pdb=" O ARG Y 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR Y 146 " --> pdb=" O ARG Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 202 Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 232 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 420 removed outlier: 3.868A pdb=" N ILE Y 412 " --> pdb=" O GLN Y 408 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 258 removed outlier: 4.012A pdb=" N LYS Z 236 " --> pdb=" O ASP Z 232 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 287 through 291 Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.819A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 423 through 427 Processing helix chain 'a' and resid 126 through 146 removed outlier: 3.907A pdb=" N VAL a 130 " --> pdb=" O PHE a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 202 Processing helix chain 'a' and resid 206 through 208 No H-bonds generated for 'chain 'a' and resid 206 through 208' Processing helix chain 'a' and resid 232 through 258 removed outlier: 3.812A pdb=" N LYS a 236 " --> pdb=" O ASP a 232 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 287 through 291 removed outlier: 3.588A pdb=" N LYS a 290 " --> pdb=" O ASP a 287 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA a 291 " --> pdb=" O ALA a 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 287 through 291' Processing helix chain 'a' and resid 405 through 420 removed outlier: 3.572A pdb=" N ILE a 412 " --> pdb=" O GLN a 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 232 through 258 removed outlier: 3.677A pdb=" N LYS b 236 " --> pdb=" O ASP b 232 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.820A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 423 through 427 Processing helix chain 'c' and resid 126 through 146 removed outlier: 3.559A pdb=" N VAL c 130 " --> pdb=" O PHE c 126 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 202 Processing helix chain 'c' and resid 206 through 208 No H-bonds generated for 'chain 'c' and resid 206 through 208' Processing helix chain 'c' and resid 232 through 258 removed outlier: 3.684A pdb=" N LYS c 236 " --> pdb=" O ASP c 232 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 287 through 291 Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.814A pdb=" N ILE c 412 " --> pdb=" O GLN c 408 " (cutoff:3.500A) Processing helix chain 'c' and resid 423 through 427 Processing helix chain 'd' and resid 126 through 146 removed outlier: 3.641A pdb=" N VAL d 130 " --> pdb=" O PHE d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 206 through 208 No H-bonds generated for 'chain 'd' and resid 206 through 208' Processing helix chain 'd' and resid 232 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 287 through 291 Processing helix chain 'd' and resid 405 through 420 removed outlier: 3.743A pdb=" N ILE d 412 " --> pdb=" O GLN d 408 " (cutoff:3.500A) Processing helix chain 'd' and resid 423 through 427 Processing helix chain 'e' and resid 232 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 287 through 291 Processing helix chain 'e' and resid 405 through 420 Processing helix chain 'e' and resid 423 through 427 Processing helix chain 'f' and resid 126 through 146 removed outlier: 3.860A pdb=" N GLY f 138 " --> pdb=" O ARG f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 187 through 202 Processing helix chain 'f' and resid 232 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 287 through 291 Processing helix chain 'f' and resid 405 through 420 Processing helix chain 'g' and resid 126 through 146 removed outlier: 3.745A pdb=" N VAL g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 187 through 202 Processing helix chain 'g' and resid 232 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.665A pdb=" N ILE g 412 " --> pdb=" O GLN g 408 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 423 through 427 Processing helix chain 'h' and resid 126 through 145 Processing helix chain 'h' and resid 187 through 202 Processing helix chain 'h' and resid 232 through 258 removed outlier: 3.795A pdb=" N LYS h 236 " --> pdb=" O ASP h 232 " (cutoff:3.500A) Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 287 through 291 removed outlier: 3.540A pdb=" N ALA h 291 " --> pdb=" O ALA h 288 " (cutoff:3.500A) Processing helix chain 'h' and resid 405 through 421 removed outlier: 3.709A pdb=" N GLY h 421 " --> pdb=" O ARG h 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 3.640A pdb=" N ARG A 384 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP A 271 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 382 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR A 429 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 385 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASN A 431 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 387 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL A 433 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 389 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 303 removed outlier: 6.140A pdb=" N ARG h 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN h 365 " --> pdb=" O ARG h 294 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG h 296 " --> pdb=" O THR h 363 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR h 363 " --> pdb=" O ARG h 296 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU h 298 " --> pdb=" O ASN h 361 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN h 361 " --> pdb=" O LEU h 298 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE h 300 " --> pdb=" O GLN h 359 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN h 359 " --> pdb=" O ILE h 300 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU h 302 " --> pdb=" O SER h 357 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER h 357 " --> pdb=" O GLU h 302 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG g 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER g 357 " --> pdb=" O GLN g 303 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG f 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG e 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU e 293 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU e 367 " --> pdb=" O LEU e 293 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG d 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER d 357 " --> pdb=" O GLN d 303 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG c 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG b 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG a 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ARG Z 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER Z 301 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG Y 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU Y 293 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLU Y 367 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG X 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU W 302 " --> pdb=" O THR X 358 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG W 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG V 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG U 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG T 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG S 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG R 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG Q 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG P 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU P 293 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU P 367 " --> pdb=" O LEU P 293 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG O 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG N 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG M 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU M 293 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU M 367 " --> pdb=" O LEU M 293 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG L 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER L 357 " --> pdb=" O GLN L 303 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG K 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 357 " --> pdb=" O GLN K 303 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG J 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG I 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG H 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 364 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG G 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ARG F 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 357 " --> pdb=" O GLN F 303 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG E 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG D 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG C 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG B 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 153 through 158 Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.711A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 381 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR B 429 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 385 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ASN B 431 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 387 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL B 433 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 389 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 158 removed outlier: 3.551A pdb=" N SER C 152 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 262 through 271 removed outlier: 5.524A pdb=" N ASP C 271 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 382 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR C 429 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU C 385 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASN C 431 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL C 387 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL C 433 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 389 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 374 through 376 removed outlier: 3.519A pdb=" N ASN D 274 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 271 removed outlier: 3.622A pdb=" N ARG D 384 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP D 271 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE D 382 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 279 through 282 Processing sheet with id=AB1, first strand: chain 'E' and resid 150 through 158 removed outlier: 3.778A pdb=" N SER E 152 " --> pdb=" O THR E 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 262 through 271 removed outlier: 3.632A pdb=" N ARG E 384 " --> pdb=" O GLN E 269 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP E 271 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE E 382 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 277 through 279 Processing sheet with id=AB4, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.272A pdb=" N ASP F 271 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE F 382 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR F 429 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU F 385 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASN F 431 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL F 387 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL F 433 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL F 389 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER F 435 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL F 391 " --> pdb=" O SER F 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 280 through 282 Processing sheet with id=AB6, first strand: chain 'G' and resid 150 through 158 removed outlier: 3.750A pdb=" N SER G 152 " --> pdb=" O THR G 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 262 through 271 removed outlier: 3.547A pdb=" N ARG G 384 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP G 271 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE G 382 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR G 429 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU G 385 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN G 431 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL G 387 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL G 433 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 389 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 277 through 279 removed outlier: 3.603A pdb=" N THR G 375 " --> pdb=" O GLN G 277 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN H 274 " --> pdb=" O LYS G 376 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 152 through 158 removed outlier: 3.892A pdb=" N SER H 152 " --> pdb=" O THR H 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 262 through 271 removed outlier: 3.712A pdb=" N ARG H 384 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP H 271 " --> pdb=" O ILE H 382 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE H 382 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR H 429 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU H 385 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ASN H 431 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL H 387 " --> pdb=" O ASN H 431 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL H 433 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL H 389 " --> pdb=" O VAL H 433 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 371 through 373 Processing sheet with id=AC3, first strand: chain 'I' and resid 152 through 158 removed outlier: 3.747A pdb=" N SER I 152 " --> pdb=" O THR I 179 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 262 through 271 removed outlier: 3.592A pdb=" N ARG I 384 " --> pdb=" O GLN I 269 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP I 271 " --> pdb=" O ILE I 382 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE I 382 " --> pdb=" O ASP I 271 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR I 429 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU I 385 " --> pdb=" O THR I 429 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASN I 431 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL I 387 " --> pdb=" O ASN I 431 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL I 433 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL I 389 " --> pdb=" O VAL I 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 371 through 373 Processing sheet with id=AC6, first strand: chain 'J' and resid 262 through 271 removed outlier: 3.622A pdb=" N ARG J 384 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP J 271 " --> pdb=" O ILE J 382 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE J 382 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR J 429 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU J 385 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN J 431 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL J 387 " --> pdb=" O ASN J 431 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL J 433 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL J 389 " --> pdb=" O VAL J 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 152 through 158 removed outlier: 3.883A pdb=" N SER K 152 " --> pdb=" O THR K 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.442A pdb=" N ASP K 271 " --> pdb=" O ILE K 382 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE K 382 " --> pdb=" O ASP K 271 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR K 429 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU K 385 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN K 431 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL K 387 " --> pdb=" O ASN K 431 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL K 433 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL K 389 " --> pdb=" O VAL K 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 371 through 373 Processing sheet with id=AD1, first strand: chain 'L' and resid 152 through 158 Processing sheet with id=AD2, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.002A pdb=" N ASP L 271 " --> pdb=" O ILE L 382 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE L 382 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 262 through 271 removed outlier: 3.525A pdb=" N ARG M 384 " --> pdb=" O GLN M 269 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP M 271 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE M 382 " --> pdb=" O ASP M 271 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 371 through 373 removed outlier: 4.443A pdb=" N LYS O 275 " --> pdb=" O MET O 377 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 152 through 158 removed outlier: 3.623A pdb=" N SER N 152 " --> pdb=" O THR N 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 262 through 271 removed outlier: 3.576A pdb=" N ARG N 384 " --> pdb=" O GLN N 269 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP N 271 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE N 382 " --> pdb=" O ASP N 271 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR N 429 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU N 385 " --> pdb=" O THR N 429 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ASN N 431 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL N 387 " --> pdb=" O ASN N 431 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL N 433 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL N 389 " --> pdb=" O VAL N 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 152 through 158 removed outlier: 3.873A pdb=" N SER O 152 " --> pdb=" O THR O 179 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 262 through 271 removed outlier: 3.554A pdb=" N ARG O 384 " --> pdb=" O GLN O 269 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP O 271 " --> pdb=" O ILE O 382 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE O 382 " --> pdb=" O ASP O 271 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR O 429 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU O 385 " --> pdb=" O THR O 429 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASN O 431 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL O 387 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL O 433 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL O 389 " --> pdb=" O VAL O 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 262 through 271 removed outlier: 3.730A pdb=" N ARG P 384 " --> pdb=" O GLN P 269 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP P 271 " --> pdb=" O ILE P 382 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE P 382 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N THR P 429 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU P 385 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASN P 431 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL P 387 " --> pdb=" O ASN P 431 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL P 433 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL P 389 " --> pdb=" O VAL P 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 275 through 276 removed outlier: 4.150A pdb=" N LYS P 275 " --> pdb=" O MET P 377 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 150 through 158 removed outlier: 6.643A pdb=" N THR Q 179 " --> pdb=" O LYS Q 151 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA Q 153 " --> pdb=" O THR Q 177 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR Q 177 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL Q 155 " --> pdb=" O SER Q 175 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER Q 175 " --> pdb=" O VAL Q 155 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU Q 157 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER Q 173 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.687A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR Q 429 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU Q 385 " --> pdb=" O THR Q 429 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN Q 431 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL Q 387 " --> pdb=" O ASN Q 431 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL Q 433 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL Q 389 " --> pdb=" O VAL Q 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 277 through 279 Processing sheet with id=AE5, first strand: chain 'R' and resid 150 through 158 removed outlier: 3.511A pdb=" N SER R 152 " --> pdb=" O THR R 179 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 262 through 271 removed outlier: 3.515A pdb=" N ARG R 384 " --> pdb=" O GLN R 269 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP R 271 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE R 382 " --> pdb=" O ASP R 271 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 371 through 373 Processing sheet with id=AE8, first strand: chain 'S' and resid 262 through 270 removed outlier: 6.734A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 152 through 158 removed outlier: 4.069A pdb=" N SER T 152 " --> pdb=" O THR T 179 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU T 212 " --> pdb=" O LEU T 219 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU T 219 " --> pdb=" O LEU T 212 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY T 217 " --> pdb=" O ASP T 214 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 262 through 271 removed outlier: 3.625A pdb=" N ARG T 384 " --> pdb=" O GLN T 269 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP T 271 " --> pdb=" O ILE T 382 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE T 382 " --> pdb=" O ASP T 271 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N THR T 429 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU T 385 " --> pdb=" O THR T 429 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ASN T 431 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL T 387 " --> pdb=" O ASN T 431 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL T 433 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL T 389 " --> pdb=" O VAL T 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 152 through 158 Processing sheet with id=AF3, first strand: chain 'U' and resid 262 through 271 removed outlier: 3.766A pdb=" N ARG U 384 " --> pdb=" O GLN U 269 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP U 271 " --> pdb=" O ILE U 382 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE U 382 " --> pdb=" O ASP U 271 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR U 429 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU U 385 " --> pdb=" O THR U 429 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASN U 431 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL U 387 " --> pdb=" O ASN U 431 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL U 433 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL U 389 " --> pdb=" O VAL U 433 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 262 through 271 removed outlier: 3.577A pdb=" N ARG V 384 " --> pdb=" O GLN V 269 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ASP V 271 " --> pdb=" O ILE V 382 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE V 382 " --> pdb=" O ASP V 271 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 275 through 276 removed outlier: 4.315A pdb=" N LYS V 275 " --> pdb=" O MET V 377 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN W 274 " --> pdb=" O LYS V 376 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 150 through 158 removed outlier: 3.824A pdb=" N SER W 152 " --> pdb=" O THR W 179 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.024A pdb=" N ASP W 271 " --> pdb=" O ILE W 382 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE W 382 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 152 through 158 Processing sheet with id=AF9, first strand: chain 'X' and resid 262 through 271 removed outlier: 3.669A pdb=" N ARG X 384 " --> pdb=" O GLN X 269 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP X 271 " --> pdb=" O ILE X 382 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE X 382 " --> pdb=" O ASP X 271 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR X 429 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU X 385 " --> pdb=" O THR X 429 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN X 431 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL X 387 " --> pdb=" O ASN X 431 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL X 433 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL X 389 " --> pdb=" O VAL X 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 152 through 158 removed outlier: 3.800A pdb=" N SER Y 152 " --> pdb=" O THR Y 179 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.378A pdb=" N ASP Y 271 " --> pdb=" O ILE Y 382 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE Y 382 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR Y 429 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU Y 385 " --> pdb=" O THR Y 429 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ASN Y 431 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL Y 387 " --> pdb=" O ASN Y 431 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL Y 433 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL Y 389 " --> pdb=" O VAL Y 433 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 262 through 270 removed outlier: 3.822A pdb=" N ARG Z 384 " --> pdb=" O GLN Z 269 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR Z 429 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU Z 385 " --> pdb=" O THR Z 429 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN Z 431 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL Z 387 " --> pdb=" O ASN Z 431 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL Z 433 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL Z 389 " --> pdb=" O VAL Z 433 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 279 through 282 Processing sheet with id=AG5, first strand: chain 'a' and resid 152 through 158 removed outlier: 3.716A pdb=" N SER a 152 " --> pdb=" O THR a 179 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.021A pdb=" N ASP a 271 " --> pdb=" O ILE a 382 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE a 382 " --> pdb=" O ASP a 271 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.801A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 152 through 158 removed outlier: 3.696A pdb=" N SER c 152 " --> pdb=" O THR c 179 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c' and resid 262 through 271 removed outlier: 3.569A pdb=" N ARG c 384 " --> pdb=" O GLN c 269 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP c 271 " --> pdb=" O ILE c 382 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE c 382 " --> pdb=" O ASP c 271 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR c 429 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU c 385 " --> pdb=" O THR c 429 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ASN c 431 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL c 387 " --> pdb=" O ASN c 431 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL c 433 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL c 389 " --> pdb=" O VAL c 433 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'c' and resid 277 through 279 Processing sheet with id=AH2, first strand: chain 'd' and resid 152 through 158 removed outlier: 6.950A pdb=" N ALA d 174 " --> pdb=" O THR d 211 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL d 213 " --> pdb=" O ALA d 174 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL d 176 " --> pdb=" O VAL d 213 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 262 through 271 removed outlier: 3.702A pdb=" N ARG d 384 " --> pdb=" O GLN d 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP d 271 " --> pdb=" O ILE d 382 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE d 382 " --> pdb=" O ASP d 271 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR d 429 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU d 385 " --> pdb=" O THR d 429 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN d 431 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL d 387 " --> pdb=" O ASN d 431 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL d 433 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL d 389 " --> pdb=" O VAL d 433 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 371 through 373 Processing sheet with id=AH5, first strand: chain 'e' and resid 262 through 271 removed outlier: 3.636A pdb=" N ARG e 384 " --> pdb=" O GLN e 269 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP e 271 " --> pdb=" O ILE e 382 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE e 382 " --> pdb=" O ASP e 271 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR e 429 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU e 385 " --> pdb=" O THR e 429 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN e 431 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL e 387 " --> pdb=" O ASN e 431 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL e 433 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL e 389 " --> pdb=" O VAL e 433 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 371 through 373 Processing sheet with id=AH7, first strand: chain 'f' and resid 150 through 158 removed outlier: 3.881A pdb=" N SER f 152 " --> pdb=" O THR f 179 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA f 174 " --> pdb=" O THR f 211 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL f 213 " --> pdb=" O ALA f 174 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL f 176 " --> pdb=" O VAL f 213 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'f' and resid 262 through 271 removed outlier: 3.761A pdb=" N ARG f 384 " --> pdb=" O GLN f 269 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASP f 271 " --> pdb=" O ILE f 382 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE f 382 " --> pdb=" O ASP f 271 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 150 through 158 removed outlier: 6.605A pdb=" N THR g 179 " --> pdb=" O LYS g 151 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA g 153 " --> pdb=" O THR g 177 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR g 177 " --> pdb=" O ALA g 153 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL g 155 " --> pdb=" O SER g 175 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER g 175 " --> pdb=" O VAL g 155 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU g 157 " --> pdb=" O SER g 173 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER g 173 " --> pdb=" O LEU g 157 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA g 174 " --> pdb=" O THR g 211 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL g 213 " --> pdb=" O ALA g 174 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL g 176 " --> pdb=" O VAL g 213 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.106A pdb=" N ASP g 271 " --> pdb=" O ILE g 382 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE g 382 " --> pdb=" O ASP g 271 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR g 429 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU g 385 " --> pdb=" O THR g 429 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASN g 431 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL g 387 " --> pdb=" O ASN g 431 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL g 433 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL g 389 " --> pdb=" O VAL g 433 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 277 through 279 Processing sheet with id=AI3, first strand: chain 'h' and resid 152 through 158 removed outlier: 3.651A pdb=" N SER h 152 " --> pdb=" O THR h 179 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA h 174 " --> pdb=" O THR h 211 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL h 213 " --> pdb=" O ALA h 174 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL h 176 " --> pdb=" O VAL h 213 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU h 212 " --> pdb=" O LEU h 219 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU h 219 " --> pdb=" O LEU h 212 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'h' and resid 262 through 266 removed outlier: 6.309A pdb=" N VAL h 387 " --> pdb=" O ASN h 431 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL h 433 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL h 389 " --> pdb=" O VAL h 433 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'h' and resid 269 through 270 removed outlier: 6.483A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'h' and resid 279 through 282 2997 hydrogen bonds defined for protein. 8478 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: 24.52 Time building geometry restraints manager: 13.15 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: 20339 1.34 - 1.46: 9138 1.46 - 1.58: 28493 1.58 - 1.70: 0 1.70 - 1.82: 250 Bond restraints: 58220 Sorted by residual: bond pdb=" CB ARG H 154 " pdb=" CG ARG H 154 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" CG GLU V 280 " pdb=" CD GLU V 280 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.50e+00 bond pdb=" CG GLU C 137 " pdb=" CD GLU C 137 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CB GLU c 137 " pdb=" CG GLU c 137 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB MET D 377 " pdb=" CG MET D 377 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.42e+00 ... (remaining 58215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 78183 3.43 - 6.86: 442 6.86 - 10.29: 53 10.29 - 13.72: 15 13.72 - 17.14: 6 Bond angle restraints: 78699 Sorted by residual: angle pdb=" C TYR K 282 " pdb=" N SER K 283 " pdb=" CA SER K 283 " ideal model delta sigma weight residual 121.61 111.24 10.37 1.39e+00 5.18e-01 5.57e+01 angle pdb=" N VAL L 166 " pdb=" CA VAL L 166 " pdb=" C VAL L 166 " ideal model delta sigma weight residual 111.91 106.03 5.88 8.90e-01 1.26e+00 4.36e+01 angle pdb=" C TYR U 282 " pdb=" N SER U 283 " pdb=" CA SER U 283 " ideal model delta sigma weight residual 121.48 109.28 12.20 2.04e+00 2.40e-01 3.57e+01 angle pdb=" N VAL N 166 " pdb=" CA VAL N 166 " pdb=" C VAL N 166 " ideal model delta sigma weight residual 109.34 97.74 11.60 2.08e+00 2.31e-01 3.11e+01 angle pdb=" C LEU H 164 " pdb=" N PHE H 165 " pdb=" CA PHE H 165 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 ... (remaining 78694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 32760 17.98 - 35.96: 2900 35.96 - 53.94: 406 53.94 - 71.91: 96 71.91 - 89.89: 89 Dihedral angle restraints: 36251 sinusoidal: 14748 harmonic: 21503 Sorted by residual: dihedral pdb=" CA PHE H 165 " pdb=" C PHE H 165 " pdb=" N VAL H 166 " pdb=" CA VAL H 166 " ideal model delta harmonic sigma weight residual 180.00 138.98 41.02 0 5.00e+00 4.00e-02 6.73e+01 dihedral pdb=" CA PHE G 165 " pdb=" C PHE G 165 " pdb=" N VAL G 166 " pdb=" CA VAL G 166 " ideal model delta harmonic sigma weight residual 180.00 -140.93 -39.07 0 5.00e+00 4.00e-02 6.11e+01 dihedral pdb=" CA SER B 163 " pdb=" C SER B 163 " pdb=" N LEU B 164 " pdb=" CA LEU B 164 " ideal model delta harmonic sigma weight residual -180.00 -143.08 -36.92 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 36248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 7805 0.067 - 0.135: 1302 0.135 - 0.202: 56 0.202 - 0.270: 10 0.270 - 0.337: 3 Chirality restraints: 9176 Sorted by residual: chirality pdb=" CB ILE V 372 " pdb=" CA ILE V 372 " pdb=" CG1 ILE V 372 " pdb=" CG2 ILE V 372 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE C 372 " pdb=" CA ILE C 372 " pdb=" CG1 ILE C 372 " pdb=" CG2 ILE C 372 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB THR g 143 " pdb=" CA THR g 143 " pdb=" OG1 THR g 143 " pdb=" CG2 THR g 143 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 9173 not shown) Planarity restraints: 10494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS a 161 " -0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO a 162 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO a 162 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO a 162 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 161 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO G 162 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 162 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 162 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 161 " 0.049 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO I 162 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 162 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 162 " 0.041 5.00e-02 4.00e+02 ... (remaining 10491 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1191 2.63 - 3.20: 56449 3.20 - 3.77: 92198 3.77 - 4.33: 124122 4.33 - 4.90: 202408 Nonbonded interactions: 476368 Sorted by model distance: nonbonded pdb=" OG1 THR Y 405 " pdb=" OD1 ASP Y 407 " model vdw 2.066 3.040 nonbonded pdb=" O LEU N 140 " pdb=" OG1 THR N 143 " model vdw 2.080 3.040 nonbonded pdb=" OG SER X 199 " pdb=" O LEU X 205 " model vdw 2.083 3.040 nonbonded pdb=" O GLU V 250 " pdb=" OG SER V 254 " model vdw 2.087 3.040 nonbonded pdb=" OE2 GLU X 362 " pdb=" OG SER X 364 " model vdw 2.097 3.040 ... (remaining 476363 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' } 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: 36.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.810 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 111.790 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.550 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: 0.020 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.007 0.071 58220 Z= 0.449 Angle : 0.862 17.145 78699 Z= 0.477 Chirality : 0.048 0.337 9176 Planarity : 0.004 0.085 10494 Dihedral : 14.409 89.893 22159 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.07 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.10), residues: 7161 helix: 0.55 (0.11), residues: 2147 sheet: -0.29 (0.10), residues: 2909 loop : -2.32 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS c 218 PHE 0.024 0.002 PHE f 165 TYR 0.021 0.002 TYR Y 393 ARG 0.022 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 5.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8117 (tmtt) REVERT: D 271 ASP cc_start: 0.8119 (t0) cc_final: 0.7733 (p0) REVERT: I 167 ARG cc_start: 0.4054 (mtt180) cc_final: 0.2121 (mmt180) REVERT: I 280 GLU cc_start: 0.7960 (tt0) cc_final: 0.7693 (mt-10) REVERT: J 372 ILE cc_start: 0.9243 (mt) cc_final: 0.8876 (mt) REVERT: K 161 LYS cc_start: 0.6858 (tmmt) cc_final: 0.6323 (ptmt) REVERT: L 377 MET cc_start: 0.7230 (mpp) cc_final: 0.6833 (mpp) REVERT: N 159 MET cc_start: 0.7870 (mpp) cc_final: 0.7054 (mmm) REVERT: O 409 MET cc_start: 0.8300 (tpt) cc_final: 0.7708 (tpp) REVERT: P 271 ASP cc_start: 0.8074 (m-30) cc_final: 0.7699 (p0) REVERT: P 363 THR cc_start: 0.8538 (m) cc_final: 0.8075 (p) REVERT: R 218 HIS cc_start: 0.7879 (m90) cc_final: 0.7464 (m90) REVERT: S 267 THR cc_start: 0.8094 (p) cc_final: 0.7873 (p) REVERT: S 412 ILE cc_start: 0.9398 (mt) cc_final: 0.9029 (tp) REVERT: X 136 LEU cc_start: 0.8960 (tp) cc_final: 0.8750 (tt) REVERT: X 159 MET cc_start: 0.7719 (ptp) cc_final: 0.7385 (mmp) REVERT: Y 420 MET cc_start: 0.8706 (pmm) cc_final: 0.8489 (pmm) REVERT: Y 425 LYS cc_start: 0.9104 (pttm) cc_final: 0.8899 (pttt) REVERT: Z 393 TYR cc_start: 0.8234 (m-10) cc_final: 0.7835 (m-10) REVERT: a 159 MET cc_start: 0.7296 (tpp) cc_final: 0.6742 (mmp) REVERT: a 275 LYS cc_start: 0.8938 (mmpt) cc_final: 0.8535 (mmmt) REVERT: c 377 MET cc_start: 0.8174 (mpp) cc_final: 0.7864 (mpp) REVERT: f 167 ARG cc_start: 0.3084 (mtt180) cc_final: -0.0317 (mmt180) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.5704 time to fit residues: 626.4507 Evaluate side-chains 476 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 5.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 624 optimal weight: 6.9990 chunk 560 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 191 optimal weight: 0.0980 chunk 378 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 580 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 352 optimal weight: 0.9990 chunk 431 optimal weight: 5.9990 chunk 672 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 378 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 GLN G 431 ASN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN K 261 ASN L 196 HIS M 359 GLN ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS O 361 ASN P 261 ASN ** P 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 ASN R 196 HIS ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 HIS S 411 GLN ** S 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 GLN ** T 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 218 HIS ** W 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 261 ASN Z 374 HIS ** Z 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 133 GLN c 281 HIS c 378 ASN ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 GLN d 239 ASN ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 434 ASN f 281 HIS f 434 ASN ** g 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.056582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.046694 restraints weight = 324487.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.047876 restraints weight = 156971.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048609 restraints weight = 92237.262| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 58220 Z= 0.282 Angle : 0.678 13.830 78699 Z= 0.350 Chirality : 0.045 0.226 9176 Planarity : 0.005 0.070 10494 Dihedral : 5.665 38.763 7934 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 0.73 % Allowed : 6.93 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 7161 helix: 0.96 (0.11), residues: 2175 sheet: -0.15 (0.10), residues: 2904 loop : -2.09 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS R 281 PHE 0.030 0.002 PHE f 126 TYR 0.018 0.002 TYR Q 132 ARG 0.007 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 599 time to evaluate : 5.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ARG cc_start: 0.1599 (mtt180) cc_final: -0.0317 (mmt180) REVERT: D 415 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9163 (mp) REVERT: I 167 ARG cc_start: 0.4152 (mtt180) cc_final: 0.2332 (mmt180) REVERT: I 280 GLU cc_start: 0.7921 (tt0) cc_final: 0.7689 (mt-10) REVERT: K 161 LYS cc_start: 0.6973 (tmmt) cc_final: 0.6487 (tttm) REVERT: L 196 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8287 (m90) REVERT: M 267 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.7923 (p) REVERT: N 159 MET cc_start: 0.7792 (mpp) cc_final: 0.6970 (mmm) REVERT: O 409 MET cc_start: 0.8435 (tpt) cc_final: 0.7988 (tpp) REVERT: P 297 GLN cc_start: 0.8178 (tp40) cc_final: 0.7931 (tp40) REVERT: R 196 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8044 (t70) REVERT: R 218 HIS cc_start: 0.7829 (m90) cc_final: 0.7450 (m90) REVERT: S 267 THR cc_start: 0.8009 (p) cc_final: 0.7784 (p) REVERT: S 412 ILE cc_start: 0.9369 (mt) cc_final: 0.9074 (tp) REVERT: T 425 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8479 (pttm) REVERT: U 409 MET cc_start: 0.8768 (tmm) cc_final: 0.8482 (tmm) REVERT: V 415 LEU cc_start: 0.8928 (mm) cc_final: 0.8610 (tp) REVERT: W 410 LYS cc_start: 0.9378 (tmmt) cc_final: 0.9164 (tmmt) REVERT: X 159 MET cc_start: 0.7739 (ptp) cc_final: 0.7441 (mmp) REVERT: X 409 MET cc_start: 0.8365 (tpt) cc_final: 0.7718 (tpt) REVERT: Y 236 LYS cc_start: 0.9202 (pttp) cc_final: 0.8997 (pptt) REVERT: Y 420 MET cc_start: 0.8720 (pmm) cc_final: 0.8458 (pmm) REVERT: Y 425 LYS cc_start: 0.9092 (pttm) cc_final: 0.8883 (ptpt) REVERT: Z 410 LYS cc_start: 0.9245 (pptt) cc_final: 0.9022 (pptt) REVERT: a 159 MET cc_start: 0.7428 (tpp) cc_final: 0.6857 (mmm) REVERT: a 420 MET cc_start: 0.8627 (ptp) cc_final: 0.8373 (ptp) REVERT: b 413 GLU cc_start: 0.8650 (pp20) cc_final: 0.8374 (pp20) REVERT: c 376 LYS cc_start: 0.8901 (tptt) cc_final: 0.8668 (tptp) REVERT: d 151 LYS cc_start: 0.8875 (pttt) cc_final: 0.8490 (pttp) REVERT: d 420 MET cc_start: 0.9234 (ppp) cc_final: 0.9003 (ppp) REVERT: f 167 ARG cc_start: 0.2943 (mtt180) cc_final: -0.0397 (mmt180) REVERT: h 159 MET cc_start: 0.8001 (mmm) cc_final: 0.7644 (mmt) outliers start: 47 outliers final: 20 residues processed: 620 average time/residue: 0.5729 time to fit residues: 589.0831 Evaluate side-chains 501 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 476 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain L residue 196 HIS Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain R residue 196 HIS Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain Z residue 374 HIS Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 285 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 511 optimal weight: 10.0000 chunk 539 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 597 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 396 optimal weight: 9.9990 chunk 311 optimal weight: 4.9990 chunk 471 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 434 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 ASN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 GLN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 434 ASN ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 HIS S 411 GLN ** S 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 196 HIS V 281 HIS ** W 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 269 GLN Z 411 GLN ** Z 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 281 HIS ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 281 HIS ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 GLN ** g 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.056298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.046367 restraints weight = 324096.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047528 restraints weight = 155576.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048237 restraints weight = 90719.018| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 58220 Z= 0.296 Angle : 0.641 13.269 78699 Z= 0.332 Chirality : 0.043 0.236 9176 Planarity : 0.004 0.073 10494 Dihedral : 5.479 37.790 7934 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 0.97 % Allowed : 10.66 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 7161 helix: 1.09 (0.11), residues: 2177 sheet: -0.17 (0.10), residues: 2894 loop : -2.01 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.001 HIS L 196 PHE 0.024 0.002 PHE f 126 TYR 0.013 0.002 TYR Z 393 ARG 0.005 0.001 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 544 time to evaluate : 5.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 LYS cc_start: 0.9207 (tmmt) cc_final: 0.8965 (tptp) REVERT: C 167 ARG cc_start: 0.1625 (mtt180) cc_final: -0.0307 (mmt180) REVERT: D 415 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9157 (mp) REVERT: F 409 MET cc_start: 0.8746 (tpt) cc_final: 0.8509 (tpp) REVERT: I 167 ARG cc_start: 0.4015 (mtt180) cc_final: 0.2312 (mmt180) REVERT: I 280 GLU cc_start: 0.7962 (tt0) cc_final: 0.7714 (mt-10) REVERT: J 420 MET cc_start: 0.8373 (ttt) cc_final: 0.8143 (ttt) REVERT: K 161 LYS cc_start: 0.7048 (tmmt) cc_final: 0.6664 (tttm) REVERT: L 151 LYS cc_start: 0.8220 (pttt) cc_final: 0.7999 (pmtt) REVERT: L 157 LEU cc_start: 0.8482 (pp) cc_final: 0.7809 (tp) REVERT: M 267 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.7972 (p) REVERT: N 159 MET cc_start: 0.7800 (mpp) cc_final: 0.6990 (mmm) REVERT: O 409 MET cc_start: 0.8451 (tpt) cc_final: 0.8047 (tpp) REVERT: P 416 THR cc_start: 0.9597 (t) cc_final: 0.9388 (p) REVERT: R 196 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8229 (t70) REVERT: S 275 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7656 (mmmt) REVERT: S 362 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7464 (tm-30) REVERT: S 412 ILE cc_start: 0.9377 (mt) cc_final: 0.9075 (tp) REVERT: U 409 MET cc_start: 0.8737 (tmm) cc_final: 0.8474 (tmm) REVERT: V 414 ASP cc_start: 0.8984 (m-30) cc_final: 0.8709 (m-30) REVERT: V 415 LEU cc_start: 0.8893 (mm) cc_final: 0.8581 (tp) REVERT: W 361 ASN cc_start: 0.8221 (t0) cc_final: 0.7952 (m-40) REVERT: W 410 LYS cc_start: 0.9410 (tmmt) cc_final: 0.9172 (tmmt) REVERT: X 159 MET cc_start: 0.7832 (ptp) cc_final: 0.7460 (mmp) REVERT: Y 236 LYS cc_start: 0.9211 (pttp) cc_final: 0.9005 (pptt) REVERT: Y 420 MET cc_start: 0.8761 (pmm) cc_final: 0.8236 (ppp) REVERT: Y 425 LYS cc_start: 0.9063 (pttm) cc_final: 0.8822 (ptpt) REVERT: a 159 MET cc_start: 0.7324 (tpp) cc_final: 0.6538 (tmm) REVERT: b 252 ILE cc_start: 0.8977 (tp) cc_final: 0.8685 (tp) REVERT: b 409 MET cc_start: 0.8921 (tpp) cc_final: 0.8700 (tpp) REVERT: b 424 ASP cc_start: 0.8700 (p0) cc_final: 0.8478 (p0) REVERT: c 139 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5615 (mt-10) REVERT: c 259 ASN cc_start: 0.7698 (p0) cc_final: 0.7377 (p0) REVERT: c 376 LYS cc_start: 0.8867 (tptt) cc_final: 0.8640 (tptp) REVERT: f 167 ARG cc_start: 0.3205 (mtt180) cc_final: -0.0077 (mmt180) REVERT: g 252 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8820 (tt) REVERT: g 409 MET cc_start: 0.8758 (tpp) cc_final: 0.8510 (tpp) REVERT: h 147 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8550 (mm) REVERT: h 409 MET cc_start: 0.8651 (tpp) cc_final: 0.8432 (tpp) outliers start: 63 outliers final: 33 residues processed: 583 average time/residue: 0.5656 time to fit residues: 551.1816 Evaluate side-chains 508 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 469 time to evaluate : 5.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain R residue 196 HIS Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain f residue 143 THR Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain h residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 136 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 548 optimal weight: 1.9990 chunk 617 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 522 optimal weight: 0.5980 chunk 280 optimal weight: 10.0000 chunk 725 optimal weight: 5.9990 chunk 525 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 721 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 HIS ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 GLN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 HIS ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 HIS S 411 GLN ** S 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 HIS ** W 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 359 GLN ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 374 HIS ** Z 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 434 ASN ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 431 ASN f 281 HIS g 156 HIS ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.056140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.046186 restraints weight = 323541.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.047346 restraints weight = 155868.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.048059 restraints weight = 91119.750| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 58220 Z= 0.302 Angle : 0.628 13.091 78699 Z= 0.325 Chirality : 0.043 0.235 9176 Planarity : 0.004 0.076 10494 Dihedral : 5.369 36.781 7934 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.49 % Rotamer: Outliers : 1.55 % Allowed : 12.42 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 7161 helix: 1.18 (0.11), residues: 2179 sheet: -0.19 (0.10), residues: 2903 loop : -1.97 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS G 281 PHE 0.020 0.002 PHE f 126 TYR 0.019 0.002 TYR Z 393 ARG 0.005 0.001 ARG U 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 524 time to evaluate : 5.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ARG cc_start: 0.1764 (mtt180) cc_final: -0.0304 (mmt180) REVERT: D 250 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8072 (mm-30) REVERT: F 409 MET cc_start: 0.8766 (tpt) cc_final: 0.8523 (tpp) REVERT: G 281 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7508 (m90) REVERT: I 167 ARG cc_start: 0.4211 (mtt180) cc_final: 0.2470 (mmt180) REVERT: I 280 GLU cc_start: 0.7979 (tt0) cc_final: 0.7728 (mt-10) REVERT: J 367 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7980 (tm-30) REVERT: L 145 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: L 151 LYS cc_start: 0.8298 (pttt) cc_final: 0.8053 (pttt) REVERT: L 166 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.8010 (t) REVERT: M 267 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.7927 (p) REVERT: M 290 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8487 (tmtt) REVERT: N 159 MET cc_start: 0.7744 (mpp) cc_final: 0.7392 (mmm) REVERT: O 409 MET cc_start: 0.8481 (tpt) cc_final: 0.8090 (tpp) REVERT: P 276 GLU cc_start: 0.7935 (pm20) cc_final: 0.7720 (pm20) REVERT: P 416 THR cc_start: 0.9591 (t) cc_final: 0.9378 (p) REVERT: Q 429 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8503 (p) REVERT: R 196 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8188 (t70) REVERT: R 218 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: U 409 MET cc_start: 0.8755 (tmm) cc_final: 0.8474 (tmm) REVERT: V 414 ASP cc_start: 0.8984 (m-30) cc_final: 0.8732 (m-30) REVERT: W 361 ASN cc_start: 0.8175 (t0) cc_final: 0.7873 (m-40) REVERT: X 159 MET cc_start: 0.7890 (ptp) cc_final: 0.7338 (mmp) REVERT: X 409 MET cc_start: 0.8340 (tpt) cc_final: 0.7789 (tpt) REVERT: Y 236 LYS cc_start: 0.9234 (pttp) cc_final: 0.9021 (pptt) REVERT: Y 420 MET cc_start: 0.8753 (pmm) cc_final: 0.8333 (ppp) REVERT: Y 425 LYS cc_start: 0.9027 (pttm) cc_final: 0.8811 (ptpt) REVERT: a 159 MET cc_start: 0.7281 (tpp) cc_final: 0.6468 (tmm) REVERT: a 409 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7983 (tmm) REVERT: b 252 ILE cc_start: 0.8964 (tp) cc_final: 0.8683 (tp) REVERT: b 424 ASP cc_start: 0.8678 (p0) cc_final: 0.8455 (p0) REVERT: c 139 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5545 (mt-10) REVERT: c 259 ASN cc_start: 0.7781 (p0) cc_final: 0.7461 (p0) REVERT: c 376 LYS cc_start: 0.8874 (tptt) cc_final: 0.8670 (tptp) REVERT: d 164 LEU cc_start: 0.6823 (tp) cc_final: 0.6583 (tt) REVERT: d 420 MET cc_start: 0.9229 (ppp) cc_final: 0.9018 (ppp) REVERT: f 167 ARG cc_start: 0.3173 (mtt180) cc_final: -0.0152 (mmt180) REVERT: g 252 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8839 (tt) REVERT: h 147 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8551 (mm) outliers start: 100 outliers final: 48 residues processed: 590 average time/residue: 0.5624 time to fit residues: 556.3082 Evaluate side-chains 519 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 460 time to evaluate : 5.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain R residue 196 HIS Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 281 HIS Chi-restraints excluded: chain S residue 259 ASN Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Z residue 250 GLU Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain d residue 382 ILE Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 143 THR Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain h residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 665 optimal weight: 8.9990 chunk 359 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 590 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 608 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 ASN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 GLN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 169 GLN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 HIS ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 HIS S 411 GLN ** S 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 281 HIS ** W 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 269 GLN ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 156 HIS ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.046429 restraints weight = 322065.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.047591 restraints weight = 155060.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.048304 restraints weight = 90571.314| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 58220 Z= 0.245 Angle : 0.600 11.650 78699 Z= 0.309 Chirality : 0.042 0.227 9176 Planarity : 0.004 0.079 10494 Dihedral : 5.214 35.590 7934 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 1.56 % Allowed : 13.98 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.10), residues: 7161 helix: 1.33 (0.11), residues: 2179 sheet: -0.13 (0.10), residues: 2908 loop : -1.88 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS G 281 PHE 0.017 0.001 PHE f 126 TYR 0.012 0.001 TYR E 132 ARG 0.004 0.000 ARG U 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 509 time to evaluate : 5.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.9489 (tp) cc_final: 0.9231 (tt) REVERT: C 167 ARG cc_start: 0.1812 (mtt180) cc_final: -0.0107 (mmt180) REVERT: G 281 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7581 (m170) REVERT: I 167 ARG cc_start: 0.4005 (mtt180) cc_final: 0.2368 (mmt180) REVERT: I 280 GLU cc_start: 0.7985 (tt0) cc_final: 0.7698 (mt-10) REVERT: K 168 GLU cc_start: 0.7037 (pp20) cc_final: 0.6439 (pp20) REVERT: L 166 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8086 (t) REVERT: M 267 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.7950 (p) REVERT: N 159 MET cc_start: 0.7771 (mpp) cc_final: 0.7383 (mmm) REVERT: O 409 MET cc_start: 0.8487 (tpt) cc_final: 0.8151 (tpp) REVERT: P 276 GLU cc_start: 0.7816 (pm20) cc_final: 0.7588 (pm20) REVERT: P 416 THR cc_start: 0.9591 (t) cc_final: 0.9370 (p) REVERT: R 144 ILE cc_start: 0.8787 (mm) cc_final: 0.8393 (pt) REVERT: R 196 HIS cc_start: 0.8614 (m90) cc_final: 0.8311 (t70) REVERT: R 218 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7698 (t-90) REVERT: U 409 MET cc_start: 0.8752 (tmm) cc_final: 0.8484 (tmm) REVERT: W 361 ASN cc_start: 0.8181 (t0) cc_final: 0.7889 (m-40) REVERT: X 159 MET cc_start: 0.7952 (ptp) cc_final: 0.7326 (mmp) REVERT: X 409 MET cc_start: 0.8336 (tpt) cc_final: 0.7833 (tpt) REVERT: Y 420 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8370 (ppp) REVERT: Y 426 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7615 (mtm180) REVERT: a 159 MET cc_start: 0.7338 (tpp) cc_final: 0.6459 (tmm) REVERT: a 409 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8001 (tmm) REVERT: b 252 ILE cc_start: 0.8939 (tp) cc_final: 0.8662 (tp) REVERT: b 424 ASP cc_start: 0.8660 (p0) cc_final: 0.8438 (p0) REVERT: c 139 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5536 (mt-10) REVERT: c 259 ASN cc_start: 0.7836 (p0) cc_final: 0.7502 (p0) REVERT: d 164 LEU cc_start: 0.6781 (tp) cc_final: 0.6553 (tt) REVERT: d 420 MET cc_start: 0.9174 (ppp) cc_final: 0.8943 (ppp) REVERT: f 167 ARG cc_start: 0.2996 (mtt180) cc_final: -0.0276 (mmt180) REVERT: g 252 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8796 (tt) outliers start: 101 outliers final: 54 residues processed: 584 average time/residue: 0.5505 time to fit residues: 540.8047 Evaluate side-chains 523 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 460 time to evaluate : 5.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 194 VAL Chi-restraints excluded: chain K residue 280 GLU Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 281 HIS Chi-restraints excluded: chain S residue 259 ASN Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 372 ILE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain Y residue 420 MET Chi-restraints excluded: chain Y residue 426 ARG Chi-restraints excluded: chain Z residue 250 GLU Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain a residue 212 LEU Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 143 THR Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 24 optimal weight: 0.0370 chunk 558 optimal weight: 10.0000 chunk 604 optimal weight: 8.9990 chunk 587 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 chunk 369 optimal weight: 0.0040 chunk 622 optimal weight: 7.9990 chunk 735 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 669 optimal weight: 7.9990 chunk 712 optimal weight: 0.0570 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 HIS ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 359 GLN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 411 GLN S 431 ASN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 156 HIS ** W 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 411 GLN ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 222 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.056779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046821 restraints weight = 320279.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047987 restraints weight = 153727.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.048707 restraints weight = 89554.055| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58220 Z= 0.204 Angle : 0.578 10.534 78699 Z= 0.298 Chirality : 0.042 0.209 9176 Planarity : 0.004 0.081 10494 Dihedral : 5.038 34.347 7934 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 1.50 % Allowed : 14.88 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 7161 helix: 1.48 (0.11), residues: 2178 sheet: -0.05 (0.10), residues: 2919 loop : -1.80 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS R 281 PHE 0.016 0.001 PHE f 126 TYR 0.012 0.001 TYR H 132 ARG 0.004 0.000 ARG B 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 533 time to evaluate : 5.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ARG cc_start: 0.1797 (mtt180) cc_final: -0.0190 (mmt180) REVERT: G 281 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7394 (m170) REVERT: I 167 ARG cc_start: 0.4197 (mtt180) cc_final: 0.2596 (mmt180) REVERT: I 280 GLU cc_start: 0.7946 (tt0) cc_final: 0.7662 (mt-10) REVERT: I 410 LYS cc_start: 0.8930 (mmtm) cc_final: 0.8715 (mmtm) REVERT: J 271 ASP cc_start: 0.7007 (p0) cc_final: 0.6707 (p0) REVERT: J 383 GLU cc_start: 0.7420 (pm20) cc_final: 0.7201 (pm20) REVERT: K 168 GLU cc_start: 0.7063 (pp20) cc_final: 0.6680 (pp20) REVERT: L 151 LYS cc_start: 0.8117 (pttt) cc_final: 0.7822 (mmtt) REVERT: M 267 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.7991 (p) REVERT: N 159 MET cc_start: 0.7785 (mpp) cc_final: 0.7389 (mmm) REVERT: P 276 GLU cc_start: 0.7799 (pm20) cc_final: 0.7410 (pm20) REVERT: P 416 THR cc_start: 0.9584 (t) cc_final: 0.9343 (p) REVERT: Q 252 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8734 (mm) REVERT: R 144 ILE cc_start: 0.8786 (mm) cc_final: 0.8386 (pt) REVERT: R 196 HIS cc_start: 0.8607 (m90) cc_final: 0.8307 (t70) REVERT: R 218 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: S 429 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8683 (p) REVERT: U 409 MET cc_start: 0.8715 (tmm) cc_final: 0.8449 (tmm) REVERT: W 361 ASN cc_start: 0.8213 (t0) cc_final: 0.7930 (m-40) REVERT: X 159 MET cc_start: 0.7935 (ptp) cc_final: 0.7330 (mmp) REVERT: X 409 MET cc_start: 0.8342 (tpt) cc_final: 0.7863 (tpt) REVERT: Z 298 LEU cc_start: 0.9223 (tp) cc_final: 0.8981 (tt) REVERT: a 409 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8002 (tmm) REVERT: b 252 ILE cc_start: 0.8916 (tp) cc_final: 0.8622 (tp) REVERT: b 424 ASP cc_start: 0.8650 (p0) cc_final: 0.8411 (p0) REVERT: c 139 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5506 (mt-10) REVERT: c 259 ASN cc_start: 0.7786 (p0) cc_final: 0.7466 (p0) REVERT: e 236 LYS cc_start: 0.9092 (mptt) cc_final: 0.8841 (mmmt) REVERT: f 167 ARG cc_start: 0.2966 (mtt180) cc_final: -0.0312 (mmt180) outliers start: 97 outliers final: 56 residues processed: 603 average time/residue: 0.5599 time to fit residues: 563.6852 Evaluate side-chains 530 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 467 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 280 GLU Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain O residue 262 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain S residue 259 ASN Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 372 ILE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Z residue 420 MET Chi-restraints excluded: chain a residue 212 LEU Chi-restraints excluded: chain a residue 357 SER Chi-restraints excluded: chain a residue 409 MET Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 420 MET Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 159 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 406 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 chunk 465 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 394 optimal weight: 10.0000 chunk 295 optimal weight: 3.9990 chunk 526 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 281 HIS S 411 GLN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 281 HIS W 365 ASN ** W 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 190 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.056749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.046770 restraints weight = 320697.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047942 restraints weight = 154751.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.048662 restraints weight = 90211.813| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58220 Z= 0.210 Angle : 0.580 11.124 78699 Z= 0.298 Chirality : 0.042 0.201 9176 Planarity : 0.004 0.083 10494 Dihedral : 4.967 33.640 7934 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.92 % Rotamer: Outliers : 1.59 % Allowed : 15.33 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 7161 helix: 1.57 (0.11), residues: 2178 sheet: 0.00 (0.10), residues: 2933 loop : -1.74 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.001 HIS G 281 PHE 0.015 0.001 PHE f 126 TYR 0.015 0.001 TYR K 366 ARG 0.007 0.000 ARG S 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 509 time to evaluate : 5.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ARG cc_start: 0.1918 (mtt180) cc_final: -0.0187 (mmt180) REVERT: C 281 HIS cc_start: 0.7712 (t70) cc_final: 0.7390 (t-90) REVERT: C 282 TYR cc_start: 0.8162 (m-80) cc_final: 0.7848 (m-80) REVERT: I 167 ARG cc_start: 0.4201 (mtt180) cc_final: 0.2621 (mmt180) REVERT: I 280 GLU cc_start: 0.7938 (tt0) cc_final: 0.7619 (mt-10) REVERT: I 410 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8732 (mmtm) REVERT: J 271 ASP cc_start: 0.7047 (p0) cc_final: 0.6791 (p0) REVERT: J 383 GLU cc_start: 0.7424 (pm20) cc_final: 0.7187 (pm20) REVERT: K 168 GLU cc_start: 0.7150 (pp20) cc_final: 0.6888 (pp20) REVERT: K 420 MET cc_start: 0.8647 (ptm) cc_final: 0.8333 (tmm) REVERT: L 151 LYS cc_start: 0.8157 (pttt) cc_final: 0.7918 (pttt) REVERT: L 371 THR cc_start: 0.9033 (m) cc_final: 0.8621 (p) REVERT: M 267 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8005 (p) REVERT: N 159 MET cc_start: 0.7787 (mpp) cc_final: 0.7389 (mmm) REVERT: P 276 GLU cc_start: 0.7826 (pm20) cc_final: 0.7544 (pm20) REVERT: P 416 THR cc_start: 0.9588 (t) cc_final: 0.9342 (p) REVERT: Q 252 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8735 (mm) REVERT: R 144 ILE cc_start: 0.8775 (mm) cc_final: 0.8368 (pt) REVERT: R 196 HIS cc_start: 0.8605 (m90) cc_final: 0.8307 (t70) REVERT: R 218 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.7784 (t-90) REVERT: S 429 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8664 (p) REVERT: U 159 MET cc_start: 0.7826 (mmm) cc_final: 0.7454 (tpt) REVERT: U 409 MET cc_start: 0.8717 (tmm) cc_final: 0.8445 (tmm) REVERT: W 361 ASN cc_start: 0.8211 (t0) cc_final: 0.7938 (m-40) REVERT: X 159 MET cc_start: 0.7930 (ptp) cc_final: 0.7325 (mmp) REVERT: Y 426 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7578 (ttp-170) REVERT: Z 298 LEU cc_start: 0.9202 (tp) cc_final: 0.8983 (tt) REVERT: Z 409 MET cc_start: 0.8935 (tpp) cc_final: 0.8237 (mpp) REVERT: a 159 MET cc_start: 0.7293 (tpp) cc_final: 0.6733 (mmm) REVERT: b 252 ILE cc_start: 0.8916 (tp) cc_final: 0.8633 (tp) REVERT: c 139 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5563 (mt-10) REVERT: c 259 ASN cc_start: 0.7785 (p0) cc_final: 0.7465 (p0) REVERT: d 220 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7936 (mp) REVERT: e 236 LYS cc_start: 0.9098 (mptt) cc_final: 0.8849 (mmmt) REVERT: f 167 ARG cc_start: 0.2978 (mtt180) cc_final: -0.0291 (mmt180) REVERT: f 178 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8429 (m) REVERT: f 219 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7295 (tt) REVERT: g 252 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8987 (tp) outliers start: 103 outliers final: 66 residues processed: 586 average time/residue: 0.5624 time to fit residues: 554.4234 Evaluate side-chains 540 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 464 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 280 GLU Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain L residue 130 VAL Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain O residue 262 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 281 HIS Chi-restraints excluded: chain R residue 410 LYS Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 372 ILE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 426 ARG Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 212 LEU Chi-restraints excluded: chain a residue 357 SER Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 220 LEU Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 143 THR Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 178 VAL Chi-restraints excluded: chain f residue 219 LEU Chi-restraints excluded: chain f residue 420 MET Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 567 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 86 optimal weight: 0.0270 chunk 194 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 607 optimal weight: 4.9990 chunk 19 optimal weight: 0.0020 chunk 4 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 410 optimal weight: 8.9990 chunk 178 optimal weight: 0.3980 overall best weight: 1.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 HIS ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 411 GLN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 218 HIS ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 431 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.057192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.047197 restraints weight = 319592.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048380 restraints weight = 152784.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.049106 restraints weight = 88789.510| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 58220 Z= 0.172 Angle : 0.574 12.429 78699 Z= 0.294 Chirality : 0.042 0.192 9176 Planarity : 0.004 0.085 10494 Dihedral : 4.854 32.846 7934 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 1.45 % Allowed : 15.99 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 7161 helix: 1.67 (0.11), residues: 2178 sheet: 0.07 (0.10), residues: 2934 loop : -1.65 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS G 281 PHE 0.013 0.001 PHE f 126 TYR 0.015 0.001 TYR K 132 ARG 0.006 0.000 ARG S 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 534 time to evaluate : 5.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.9483 (tp) cc_final: 0.9261 (tt) REVERT: B 131 ASN cc_start: 0.8878 (m110) cc_final: 0.8672 (m-40) REVERT: C 167 ARG cc_start: 0.1792 (mtt180) cc_final: 0.0031 (mmt180) REVERT: C 281 HIS cc_start: 0.7805 (t70) cc_final: 0.7480 (t-90) REVERT: C 282 TYR cc_start: 0.8117 (m-80) cc_final: 0.7794 (m-80) REVERT: D 303 GLN cc_start: 0.8313 (mp10) cc_final: 0.8017 (mp10) REVERT: I 167 ARG cc_start: 0.4062 (mtt180) cc_final: 0.2541 (mmt180) REVERT: I 280 GLU cc_start: 0.7999 (tt0) cc_final: 0.7638 (mt-10) REVERT: J 271 ASP cc_start: 0.7071 (p0) cc_final: 0.6817 (p0) REVERT: J 383 GLU cc_start: 0.7422 (pm20) cc_final: 0.7190 (pm20) REVERT: K 161 LYS cc_start: 0.7008 (tmmt) cc_final: 0.6652 (tttm) REVERT: K 168 GLU cc_start: 0.7141 (pp20) cc_final: 0.6909 (pp20) REVERT: K 420 MET cc_start: 0.8693 (ptm) cc_final: 0.8390 (tmm) REVERT: L 151 LYS cc_start: 0.8153 (pttt) cc_final: 0.7835 (mmmt) REVERT: L 371 THR cc_start: 0.9018 (m) cc_final: 0.8604 (p) REVERT: M 267 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8018 (p) REVERT: N 159 MET cc_start: 0.7805 (mpp) cc_final: 0.7364 (mmm) REVERT: P 276 GLU cc_start: 0.7765 (pm20) cc_final: 0.7450 (pm20) REVERT: P 416 THR cc_start: 0.9593 (t) cc_final: 0.9327 (p) REVERT: Q 252 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8697 (mm) REVERT: R 196 HIS cc_start: 0.8622 (m90) cc_final: 0.8324 (t70) REVERT: R 218 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7801 (t-90) REVERT: U 409 MET cc_start: 0.8768 (tmm) cc_final: 0.8485 (tmm) REVERT: V 409 MET cc_start: 0.9110 (tpp) cc_final: 0.8835 (tpp) REVERT: W 361 ASN cc_start: 0.8330 (t0) cc_final: 0.8090 (m-40) REVERT: X 159 MET cc_start: 0.7903 (ptp) cc_final: 0.7286 (mmp) REVERT: Z 298 LEU cc_start: 0.9188 (tp) cc_final: 0.8988 (tt) REVERT: Z 409 MET cc_start: 0.8976 (tpp) cc_final: 0.8284 (mpp) REVERT: a 159 MET cc_start: 0.7367 (tpp) cc_final: 0.6785 (mmm) REVERT: a 170 LYS cc_start: 0.6713 (mmtm) cc_final: 0.6511 (mmtm) REVERT: b 252 ILE cc_start: 0.8905 (tp) cc_final: 0.8641 (tp) REVERT: b 409 MET cc_start: 0.8844 (tpp) cc_final: 0.8486 (tpp) REVERT: c 139 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5545 (mt-10) REVERT: c 259 ASN cc_start: 0.7829 (p0) cc_final: 0.7509 (p0) REVERT: d 220 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7992 (mt) REVERT: e 236 LYS cc_start: 0.9127 (mptt) cc_final: 0.8858 (mmmt) REVERT: f 167 ARG cc_start: 0.2950 (mtt180) cc_final: -0.0325 (mmt180) REVERT: g 252 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8987 (tp) REVERT: h 159 MET cc_start: 0.8251 (mmm) cc_final: 0.7962 (mmt) REVERT: h 410 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8873 (ptmm) outliers start: 94 outliers final: 63 residues processed: 608 average time/residue: 0.5480 time to fit residues: 559.7788 Evaluate side-chains 553 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 483 time to evaluate : 5.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 280 GLU Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain L residue 281 HIS Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain O residue 262 VAL Chi-restraints excluded: chain P residue 415 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain S residue 259 ASN Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 154 ARG Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 372 ILE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 408 GLN Chi-restraints excluded: chain a residue 357 SER Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 220 LEU Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 143 THR Chi-restraints excluded: chain f residue 420 MET Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain h residue 410 LYS Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 74 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 chunk 631 optimal weight: 6.9990 chunk 550 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 569 optimal weight: 0.8980 chunk 547 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 694 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 378 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 434 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 HIS ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 281 HIS ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 196 HIS ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.056360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046459 restraints weight = 321862.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.047576 restraints weight = 155142.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.048289 restraints weight = 90891.840| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 58220 Z= 0.257 Angle : 0.607 12.010 78699 Z= 0.311 Chirality : 0.042 0.239 9176 Planarity : 0.004 0.089 10494 Dihedral : 4.932 33.456 7934 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 1.50 % Allowed : 16.18 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 7161 helix: 1.64 (0.11), residues: 2176 sheet: 0.03 (0.10), residues: 2926 loop : -1.68 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS R 281 PHE 0.044 0.001 PHE O 165 TYR 0.011 0.001 TYR K 366 ARG 0.007 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 485 time to evaluate : 5.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.9485 (tp) cc_final: 0.9249 (tt) REVERT: C 167 ARG cc_start: 0.1904 (mtt180) cc_final: -0.0089 (mmt180) REVERT: C 281 HIS cc_start: 0.7714 (t70) cc_final: 0.7413 (t-90) REVERT: I 167 ARG cc_start: 0.4227 (mtt180) cc_final: 0.2660 (mmt180) REVERT: J 271 ASP cc_start: 0.7068 (p0) cc_final: 0.6814 (p0) REVERT: J 383 GLU cc_start: 0.7414 (pm20) cc_final: 0.7166 (pm20) REVERT: J 420 MET cc_start: 0.8298 (mmm) cc_final: 0.7998 (mmm) REVERT: K 420 MET cc_start: 0.8672 (ptm) cc_final: 0.8333 (tmm) REVERT: L 151 LYS cc_start: 0.8120 (pttt) cc_final: 0.7849 (pttt) REVERT: M 267 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8061 (p) REVERT: M 290 LYS cc_start: 0.8733 (ptmm) cc_final: 0.8422 (tmmt) REVERT: N 159 MET cc_start: 0.7806 (mpp) cc_final: 0.7372 (mmm) REVERT: P 416 THR cc_start: 0.9590 (t) cc_final: 0.9339 (p) REVERT: R 196 HIS cc_start: 0.8623 (m90) cc_final: 0.8345 (t70) REVERT: S 429 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8646 (p) REVERT: U 159 MET cc_start: 0.7361 (mmm) cc_final: 0.6815 (mmm) REVERT: U 362 GLU cc_start: 0.7592 (tm-30) cc_final: 0.6941 (tm-30) REVERT: U 409 MET cc_start: 0.8728 (tmm) cc_final: 0.8455 (tmm) REVERT: W 361 ASN cc_start: 0.8135 (t0) cc_final: 0.7810 (m-40) REVERT: X 159 MET cc_start: 0.7910 (ptp) cc_final: 0.7296 (mmp) REVERT: Z 298 LEU cc_start: 0.9197 (tp) cc_final: 0.8982 (tt) REVERT: a 159 MET cc_start: 0.7236 (tpp) cc_final: 0.6664 (mmm) REVERT: b 290 LYS cc_start: 0.8358 (pttp) cc_final: 0.7963 (ptpt) REVERT: b 409 MET cc_start: 0.8863 (tpp) cc_final: 0.8551 (tpp) REVERT: b 424 ASP cc_start: 0.8684 (p0) cc_final: 0.8395 (p0) REVERT: c 139 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5511 (mt-10) REVERT: c 259 ASN cc_start: 0.7783 (p0) cc_final: 0.7472 (p0) REVERT: d 151 LYS cc_start: 0.8831 (pttt) cc_final: 0.8304 (pttp) REVERT: d 220 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8000 (mt) REVERT: e 236 LYS cc_start: 0.9096 (mptt) cc_final: 0.8850 (mmmt) REVERT: f 159 MET cc_start: 0.7091 (tmm) cc_final: 0.6880 (ttt) REVERT: f 167 ARG cc_start: 0.2926 (mtt180) cc_final: -0.0354 (mmt180) REVERT: h 188 GLU cc_start: 0.8207 (pm20) cc_final: 0.7953 (mp0) REVERT: h 410 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8877 (ptmm) outliers start: 97 outliers final: 77 residues processed: 560 average time/residue: 0.5457 time to fit residues: 513.8781 Evaluate side-chains 545 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 463 time to evaluate : 5.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 362 GLU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 280 GLU Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain O residue 262 VAL Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain P residue 376 LYS Chi-restraints excluded: chain P residue 415 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain R residue 281 HIS Chi-restraints excluded: chain S residue 259 ASN Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 252 ILE Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 154 ARG Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 372 ILE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain X residue 420 MET Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 408 GLN Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 212 LEU Chi-restraints excluded: chain a residue 357 SER Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 220 LEU Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 143 THR Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 420 MET Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain h residue 405 THR Chi-restraints excluded: chain h residue 410 LYS Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 740 random chunks: chunk 502 optimal weight: 0.9990 chunk 603 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 356 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 485 optimal weight: 3.9990 chunk 481 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 680 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 HIS E 431 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 131 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 HIS ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 281 HIS ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 434 ASN ** Y 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 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 = 0.3458 r_free = 0.3458 target = 0.057244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047164 restraints weight = 319010.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.048360 restraints weight = 152815.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049093 restraints weight = 88799.506| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 58220 Z= 0.171 Angle : 0.587 12.954 78699 Z= 0.300 Chirality : 0.042 0.182 9176 Planarity : 0.004 0.089 10494 Dihedral : 4.781 31.572 7934 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.58 % Rotamer: Outliers : 1.39 % Allowed : 16.46 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.11), residues: 7161 helix: 1.70 (0.11), residues: 2177 sheet: 0.10 (0.10), residues: 2931 loop : -1.57 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS E 218 PHE 0.025 0.001 PHE O 165 TYR 0.040 0.001 TYR R 282 ARG 0.006 0.000 ARG S 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14322 Ramachandran restraints generated. 7161 Oldfield, 0 Emsley, 7161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 530 time to evaluate : 5.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.9495 (tp) cc_final: 0.9272 (tt) REVERT: B 131 ASN cc_start: 0.8872 (m110) cc_final: 0.8646 (m-40) REVERT: C 167 ARG cc_start: 0.1813 (mtt180) cc_final: -0.0042 (mpt180) REVERT: C 281 HIS cc_start: 0.7783 (t70) cc_final: 0.7471 (t-90) REVERT: C 282 TYR cc_start: 0.8108 (m-80) cc_final: 0.7769 (m-80) REVERT: D 303 GLN cc_start: 0.8293 (mp10) cc_final: 0.7987 (mp10) REVERT: I 167 ARG cc_start: 0.4054 (mtt180) cc_final: 0.2563 (mmt180) REVERT: I 280 GLU cc_start: 0.7951 (tp30) cc_final: 0.7583 (tp30) REVERT: J 271 ASP cc_start: 0.7076 (p0) cc_final: 0.6807 (p0) REVERT: J 363 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8645 (p) REVERT: J 383 GLU cc_start: 0.7470 (pm20) cc_final: 0.7221 (pm20) REVERT: J 409 MET cc_start: 0.8798 (tpt) cc_final: 0.8509 (tpp) REVERT: J 420 MET cc_start: 0.8360 (mmm) cc_final: 0.8035 (mmm) REVERT: K 161 LYS cc_start: 0.7004 (tmmt) cc_final: 0.6662 (tttm) REVERT: K 420 MET cc_start: 0.8688 (ptm) cc_final: 0.8416 (tmm) REVERT: L 151 LYS cc_start: 0.8079 (pttt) cc_final: 0.7765 (pttt) REVERT: L 371 THR cc_start: 0.8992 (m) cc_final: 0.8494 (p) REVERT: M 267 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8047 (p) REVERT: M 290 LYS cc_start: 0.8766 (ptmm) cc_final: 0.8428 (tmmt) REVERT: N 159 MET cc_start: 0.7775 (mpp) cc_final: 0.7316 (mmm) REVERT: P 416 THR cc_start: 0.9577 (t) cc_final: 0.9304 (p) REVERT: R 196 HIS cc_start: 0.8670 (m90) cc_final: 0.8379 (t70) REVERT: R 218 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7784 (t-90) REVERT: S 429 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8687 (p) REVERT: U 159 MET cc_start: 0.7335 (mmm) cc_final: 0.6802 (mmm) REVERT: U 362 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6895 (tm-30) REVERT: U 409 MET cc_start: 0.8763 (tmm) cc_final: 0.8495 (tmm) REVERT: U 415 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9181 (mt) REVERT: W 290 LYS cc_start: 0.8542 (pttp) cc_final: 0.8273 (pttp) REVERT: W 361 ASN cc_start: 0.8356 (t0) cc_final: 0.8133 (m-40) REVERT: X 159 MET cc_start: 0.7881 (ptp) cc_final: 0.7262 (mmp) REVERT: Z 298 LEU cc_start: 0.9194 (tp) cc_final: 0.8966 (tt) REVERT: Z 409 MET cc_start: 0.9023 (tpp) cc_final: 0.8378 (mpp) REVERT: a 159 MET cc_start: 0.7234 (tpp) cc_final: 0.6703 (mmm) REVERT: b 290 LYS cc_start: 0.8362 (pttp) cc_final: 0.7942 (ptpt) REVERT: b 409 MET cc_start: 0.8841 (tpp) cc_final: 0.8517 (tpp) REVERT: c 139 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5450 (mt-10) REVERT: c 259 ASN cc_start: 0.7828 (p0) cc_final: 0.7518 (p0) REVERT: d 151 LYS cc_start: 0.8756 (pttt) cc_final: 0.8231 (pttp) REVERT: d 155 VAL cc_start: 0.7156 (p) cc_final: 0.6826 (p) REVERT: d 220 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8041 (mt) REVERT: e 236 LYS cc_start: 0.9130 (mptt) cc_final: 0.8854 (mmmt) REVERT: f 167 ARG cc_start: 0.2984 (mtt180) cc_final: -0.0314 (mmt180) REVERT: f 410 LYS cc_start: 0.9129 (ptpp) cc_final: 0.8803 (ptpp) REVERT: h 159 MET cc_start: 0.8258 (mmm) cc_final: 0.7989 (mmt) outliers start: 90 outliers final: 69 residues processed: 596 average time/residue: 0.5587 time to fit residues: 557.8572 Evaluate side-chains 563 residues out of total 6465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 487 time to evaluate : 5.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 281 HIS Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 280 GLU Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 372 ILE Chi-restraints excluded: chain O residue 262 VAL Chi-restraints excluded: chain P residue 415 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 418 GLU Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 281 HIS Chi-restraints excluded: chain S residue 259 ASN Chi-restraints excluded: chain S residue 372 ILE Chi-restraints excluded: chain S residue 420 MET Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 372 ILE Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 154 ARG Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 272 PHE Chi-restraints excluded: chain X residue 372 ILE Chi-restraints excluded: chain X residue 415 LEU Chi-restraints excluded: chain X residue 420 MET Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Z residue 408 GLN Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 212 LEU Chi-restraints excluded: chain a residue 357 SER Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain d residue 220 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain f residue 143 THR Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 420 MET Chi-restraints excluded: chain g residue 143 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain h residue 405 THR Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 69.4689 > 50: distance: 40 - 139: 34.645 distance: 43 - 136: 32.890 distance: 54 - 122: 26.374 distance: 57 - 119: 20.541 distance: 89 - 95: 16.026 distance: 95 - 96: 23.424 distance: 96 - 97: 24.355 distance: 96 - 99: 5.428 distance: 97 - 98: 25.774 distance: 97 - 103: 18.631 distance: 99 - 100: 35.392 distance: 100 - 102: 12.642 distance: 103 - 104: 15.711 distance: 104 - 105: 24.043 distance: 104 - 107: 44.447 distance: 105 - 106: 13.327 distance: 105 - 114: 34.663 distance: 107 - 108: 23.737 distance: 108 - 109: 34.460 distance: 108 - 110: 36.328 distance: 109 - 111: 25.871 distance: 110 - 112: 5.089 distance: 111 - 113: 36.483 distance: 112 - 113: 46.131 distance: 114 - 115: 5.393 distance: 115 - 116: 40.494 distance: 115 - 118: 56.085 distance: 116 - 119: 46.842 distance: 119 - 120: 19.330 distance: 120 - 121: 52.380 distance: 120 - 123: 49.724 distance: 121 - 127: 12.833 distance: 123 - 124: 7.907 distance: 124 - 125: 15.036 distance: 124 - 126: 56.196 distance: 127 - 128: 32.588 distance: 128 - 129: 22.655 distance: 128 - 131: 8.336 distance: 129 - 130: 14.904 distance: 129 - 136: 21.879 distance: 131 - 132: 8.548 distance: 132 - 133: 30.596 distance: 133 - 134: 20.871 distance: 134 - 135: 17.747 distance: 136 - 137: 32.921 distance: 137 - 138: 56.174 distance: 137 - 140: 6.735 distance: 138 - 139: 30.427 distance: 138 - 145: 26.473 distance: 140 - 141: 40.662 distance: 141 - 142: 11.176 distance: 142 - 143: 30.233 distance: 142 - 144: 11.953 distance: 145 - 146: 10.374 distance: 146 - 147: 6.884 distance: 146 - 149: 44.141 distance: 147 - 148: 69.469 distance: 147 - 154: 52.416 distance: 149 - 150: 21.469 distance: 150 - 151: 31.105 distance: 151 - 152: 14.187 distance: 151 - 153: 34.995 distance: 154 - 155: 37.652 distance: 155 - 156: 13.895 distance: 155 - 158: 47.557 distance: 156 - 157: 33.034 distance: 156 - 161: 31.339 distance: 158 - 159: 7.954 distance: 158 - 160: 15.738 distance: 161 - 162: 20.093 distance: 161 - 211: 22.769 distance: 162 - 163: 41.132 distance: 162 - 165: 41.066 distance: 163 - 164: 23.404 distance: 163 - 170: 17.074 distance: 164 - 208: 31.766 distance: 165 - 166: 46.040 distance: 166 - 167: 54.877 distance: 167 - 168: 14.160 distance: 167 - 169: 42.617 distance: 171 - 172: 22.013 distance: 171 - 174: 5.951 distance: 172 - 173: 14.328 distance: 172 - 179: 20.746 distance: 174 - 175: 34.700 distance: 175 - 176: 14.784 distance: 176 - 177: 33.315 distance: 176 - 178: 43.045