Starting phenix.real_space_refine on Tue Aug 26 17:53:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w8u_21578/08_2025/6w8u_21578.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w8u_21578/08_2025/6w8u_21578.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/6w8u_21578/08_2025/6w8u_21578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w8u_21578/08_2025/6w8u_21578.map" model { file = "/net/cci-nas-00/data/ceres_data/6w8u_21578/08_2025/6w8u_21578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w8u_21578/08_2025/6w8u_21578.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 123 5.16 5 C 26404 2.51 5 N 6519 2.21 5 O 8036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41082 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "B" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "C" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "E" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "G" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "H" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "I" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "J" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "K" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "M" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "N" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "O" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "P" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "R" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "T" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "U" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "V" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "W" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "X" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "Y" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "Z" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "a" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "b" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "c" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "d" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "e" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "f" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "g" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "h" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "i" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "j" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "k" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "l" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "m" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "n" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "o" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1002 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Time building chain proxies: 8.72, per 1000 atoms: 0.21 Number of scatterers: 41082 At special positions: 0 Unit cell: (100.44, 100.44, 311.04, 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 123 16.00 O 8036 8.00 N 6519 7.00 C 26404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS F 80 " - pdb=" SG CYS F 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 139 " distance=2.03 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 139 " distance=2.03 Simple disulfide: pdb=" SG CYS J 80 " - pdb=" SG CYS J 139 " distance=2.03 Simple disulfide: pdb=" SG CYS K 80 " - pdb=" SG CYS K 139 " distance=2.03 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 139 " distance=2.03 Simple disulfide: pdb=" SG CYS M 80 " - pdb=" SG CYS M 139 " distance=2.03 Simple disulfide: pdb=" SG CYS N 80 " - pdb=" SG CYS N 139 " distance=2.03 Simple disulfide: pdb=" SG CYS O 80 " - pdb=" SG CYS O 139 " distance=2.03 Simple disulfide: pdb=" SG CYS P 80 " - pdb=" SG CYS P 139 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 80 " - pdb=" SG CYS Q 139 " distance=2.03 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 139 " distance=2.03 Simple disulfide: pdb=" SG CYS S 80 " - pdb=" SG CYS S 139 " distance=2.03 Simple disulfide: pdb=" SG CYS T 80 " - pdb=" SG CYS T 139 " distance=2.03 Simple disulfide: pdb=" SG CYS U 80 " - pdb=" SG CYS U 139 " distance=2.03 Simple disulfide: pdb=" SG CYS V 80 " - pdb=" SG CYS V 139 " distance=2.03 Simple disulfide: pdb=" SG CYS W 80 " - pdb=" SG CYS W 139 " distance=2.03 Simple disulfide: pdb=" SG CYS X 80 " - pdb=" SG CYS X 139 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 80 " - pdb=" SG CYS Y 139 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 80 " - pdb=" SG CYS Z 139 " distance=2.03 Simple disulfide: pdb=" SG CYS a 80 " - pdb=" SG CYS a 139 " distance=2.03 Simple disulfide: pdb=" SG CYS b 80 " - pdb=" SG CYS b 139 " distance=2.03 Simple disulfide: pdb=" SG CYS c 80 " - pdb=" SG CYS c 139 " distance=2.03 Simple disulfide: pdb=" SG CYS d 80 " - pdb=" SG CYS d 139 " distance=2.03 Simple disulfide: pdb=" SG CYS e 80 " - pdb=" SG CYS e 139 " distance=2.03 Simple disulfide: pdb=" SG CYS f 80 " - pdb=" SG CYS f 139 " distance=2.03 Simple disulfide: pdb=" SG CYS g 80 " - pdb=" SG CYS g 139 " distance=2.03 Simple disulfide: pdb=" SG CYS h 80 " - pdb=" SG CYS h 139 " distance=2.03 Simple disulfide: pdb=" SG CYS i 80 " - pdb=" SG CYS i 139 " distance=2.03 Simple disulfide: pdb=" SG CYS j 80 " - pdb=" SG CYS j 139 " distance=2.03 Simple disulfide: pdb=" SG CYS k 80 " - pdb=" SG CYS k 139 " distance=2.03 Simple disulfide: pdb=" SG CYS l 80 " - pdb=" SG CYS l 139 " distance=2.03 Simple disulfide: pdb=" SG CYS m 80 " - pdb=" SG CYS m 139 " distance=2.03 Simple disulfide: pdb=" SG CYS n 80 " - pdb=" SG CYS n 139 " distance=2.03 Simple disulfide: pdb=" SG CYS o 80 " - pdb=" SG CYS o 139 " distance=2.03 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: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10660 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 87 sheets defined 22.1% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 Processing helix chain 'B' and resid 2 through 32 Processing helix chain 'C' and resid 2 through 32 Processing helix chain 'D' and resid 2 through 32 Processing helix chain 'E' and resid 2 through 32 Processing helix chain 'F' and resid 2 through 32 Processing helix chain 'G' and resid 2 through 32 Processing helix chain 'H' and resid 2 through 32 Processing helix chain 'I' and resid 2 through 32 Processing helix chain 'J' and resid 2 through 32 Processing helix chain 'K' and resid 2 through 32 Processing helix chain 'L' and resid 2 through 32 Processing helix chain 'M' and resid 2 through 32 Processing helix chain 'N' and resid 2 through 32 Processing helix chain 'O' and resid 2 through 32 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'Q' and resid 2 through 32 Processing helix chain 'R' and resid 2 through 32 Processing helix chain 'S' and resid 2 through 32 Processing helix chain 'T' and resid 2 through 32 Processing helix chain 'U' and resid 2 through 32 Processing helix chain 'V' and resid 2 through 32 Processing helix chain 'W' and resid 2 through 32 Processing helix chain 'X' and resid 2 through 32 Processing helix chain 'Y' and resid 2 through 32 Processing helix chain 'Z' and resid 2 through 32 Processing helix chain 'a' and resid 2 through 32 Processing helix chain 'b' and resid 2 through 32 Processing helix chain 'c' and resid 2 through 32 Processing helix chain 'd' and resid 2 through 32 Processing helix chain 'e' and resid 2 through 32 Processing helix chain 'f' and resid 2 through 32 Processing helix chain 'g' and resid 2 through 32 Processing helix chain 'h' and resid 2 through 32 Processing helix chain 'i' and resid 2 through 32 Processing helix chain 'j' and resid 2 through 32 Processing helix chain 'k' and resid 2 through 32 Processing helix chain 'l' and resid 2 through 32 Processing helix chain 'm' and resid 2 through 32 removed outlier: 3.613A pdb=" N ILE m 6 " --> pdb=" O THR m 2 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 32 Processing helix chain 'o' and resid 2 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 96 removed outlier: 4.716A pdb=" N VAL A 52 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR A 53 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A 44 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN A 55 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA A 42 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR A 57 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N THR A 124 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA A 42 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL A 126 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 44 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 6.934A pdb=" N VAL A 112 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE A 71 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 110 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 96 removed outlier: 4.792A pdb=" N VAL B 52 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 53 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE B 44 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN B 55 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA B 42 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B 57 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N THR B 124 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA B 42 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL B 126 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 44 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.925A pdb=" N VAL B 112 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE B 71 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 110 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 96 removed outlier: 4.696A pdb=" N VAL C 52 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 53 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE C 44 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN C 55 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA C 42 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 57 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N THR C 124 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA C 42 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL C 126 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 44 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.900A pdb=" N VAL C 112 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE C 71 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG C 110 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 96 removed outlier: 4.737A pdb=" N VAL D 52 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR D 53 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE D 44 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN D 55 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA D 42 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR D 57 " --> pdb=" O THR D 40 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N THR D 124 " --> pdb=" O THR D 40 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA D 42 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL D 126 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 44 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 79 removed outlier: 6.891A pdb=" N VAL D 112 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE D 71 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG D 110 " --> pdb=" O ILE D 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 96 removed outlier: 4.654A pdb=" N VAL E 52 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR E 53 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE E 44 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN E 55 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA E 42 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR E 57 " --> pdb=" O THR E 40 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR E 124 " --> pdb=" O THR E 40 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA E 42 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL E 126 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE E 44 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.912A pdb=" N VAL E 112 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE E 71 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG E 110 " --> pdb=" O ILE E 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 90 through 96 removed outlier: 4.738A pdb=" N VAL F 52 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR F 53 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE F 44 " --> pdb=" O TYR F 53 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN F 55 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA F 42 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR F 57 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N THR F 124 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA F 42 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL F 126 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE F 44 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 76 through 79 removed outlier: 6.909A pdb=" N VAL F 112 " --> pdb=" O SER F 69 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE F 71 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG F 110 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 90 through 96 removed outlier: 4.691A pdb=" N VAL G 52 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR G 53 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE G 44 " --> pdb=" O TYR G 53 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN G 55 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA G 42 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR G 57 " --> pdb=" O THR G 40 " (cutoff:3.500A) removed outlier: 10.999A pdb=" N THR G 124 " --> pdb=" O THR G 40 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA G 42 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL G 126 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE G 44 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 76 through 79 removed outlier: 6.940A pdb=" N VAL G 112 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE G 71 " --> pdb=" O ARG G 110 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG G 110 " --> pdb=" O ILE G 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 90 through 96 removed outlier: 4.714A pdb=" N VAL H 52 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR H 53 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE H 44 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN H 55 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA H 42 " --> pdb=" O ASN H 55 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR H 57 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N THR H 124 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA H 42 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL H 126 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE H 44 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 76 through 79 removed outlier: 6.908A pdb=" N VAL H 112 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE H 71 " --> pdb=" O ARG H 110 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG H 110 " --> pdb=" O ILE H 71 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 90 through 96 removed outlier: 4.755A pdb=" N VAL I 52 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR I 53 " --> pdb=" O ILE I 44 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE I 44 " --> pdb=" O TYR I 53 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN I 55 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA I 42 " --> pdb=" O ASN I 55 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR I 57 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR I 124 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA I 42 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL I 126 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE I 44 " --> pdb=" O VAL I 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 76 through 79 removed outlier: 6.952A pdb=" N VAL I 112 " --> pdb=" O SER I 69 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE I 71 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG I 110 " --> pdb=" O ILE I 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 90 through 96 removed outlier: 4.708A pdb=" N VAL J 52 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR J 53 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE J 44 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN J 55 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA J 42 " --> pdb=" O ASN J 55 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR J 57 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N THR J 124 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA J 42 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL J 126 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE J 44 " --> pdb=" O VAL J 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 76 through 79 removed outlier: 4.187A pdb=" N VAL J 66 " --> pdb=" O VAL J 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 76 through 79 removed outlier: 6.940A pdb=" N VAL J 112 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE J 71 " --> pdb=" O ARG J 110 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG J 110 " --> pdb=" O ILE J 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 90 through 96 removed outlier: 4.783A pdb=" N VAL K 52 " --> pdb=" O LEU K 96 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR K 53 " --> pdb=" O ILE K 44 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE K 44 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASN K 55 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA K 42 " --> pdb=" O ASN K 55 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR K 57 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N THR K 124 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA K 42 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL K 126 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE K 44 " --> pdb=" O VAL K 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 76 through 79 removed outlier: 6.912A pdb=" N VAL K 112 " --> pdb=" O SER K 69 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE K 71 " --> pdb=" O ARG K 110 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG K 110 " --> pdb=" O ILE K 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 96 removed outlier: 4.787A pdb=" N VAL L 52 " --> pdb=" O LEU L 96 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR L 53 " --> pdb=" O ILE L 44 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE L 44 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN L 55 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA L 42 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR L 57 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N THR L 124 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA L 42 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL L 126 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE L 44 " --> pdb=" O VAL L 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 76 through 79 removed outlier: 6.975A pdb=" N VAL L 112 " --> pdb=" O SER L 69 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE L 71 " --> pdb=" O ARG L 110 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG L 110 " --> pdb=" O ILE L 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 90 through 96 removed outlier: 4.659A pdb=" N VAL M 52 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR M 53 " --> pdb=" O ILE M 44 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE M 44 " --> pdb=" O TYR M 53 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN M 55 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA M 42 " --> pdb=" O ASN M 55 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR M 57 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N THR M 124 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA M 42 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL M 126 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE M 44 " --> pdb=" O VAL M 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 76 through 79 removed outlier: 4.177A pdb=" N VAL M 66 " --> pdb=" O VAL M 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 76 through 79 removed outlier: 6.895A pdb=" N VAL M 112 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE M 71 " --> pdb=" O ARG M 110 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG M 110 " --> pdb=" O ILE M 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 90 through 96 removed outlier: 4.712A pdb=" N VAL N 52 " --> pdb=" O LEU N 96 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR N 53 " --> pdb=" O ILE N 44 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE N 44 " --> pdb=" O TYR N 53 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASN N 55 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA N 42 " --> pdb=" O ASN N 55 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR N 57 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N THR N 124 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA N 42 " --> pdb=" O THR N 124 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL N 126 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE N 44 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 76 through 79 removed outlier: 6.926A pdb=" N VAL N 112 " --> pdb=" O SER N 69 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE N 71 " --> pdb=" O ARG N 110 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG N 110 " --> pdb=" O ILE N 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 90 through 96 removed outlier: 4.714A pdb=" N VAL O 52 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR O 53 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE O 44 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN O 55 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA O 42 " --> pdb=" O ASN O 55 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N THR O 124 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA O 42 " --> pdb=" O THR O 124 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL O 126 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE O 44 " --> pdb=" O VAL O 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.953A pdb=" N VAL O 112 " --> pdb=" O SER O 69 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE O 71 " --> pdb=" O ARG O 110 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG O 110 " --> pdb=" O ILE O 71 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 90 through 96 removed outlier: 4.701A pdb=" N VAL P 52 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR P 53 " --> pdb=" O ILE P 44 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE P 44 " --> pdb=" O TYR P 53 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASN P 55 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA P 42 " --> pdb=" O ASN P 55 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR P 57 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N THR P 124 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA P 42 " --> pdb=" O THR P 124 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL P 126 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE P 44 " --> pdb=" O VAL P 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 76 through 79 removed outlier: 6.935A pdb=" N VAL P 112 " --> pdb=" O SER P 69 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE P 71 " --> pdb=" O ARG P 110 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG P 110 " --> pdb=" O ILE P 71 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 90 through 96 removed outlier: 4.675A pdb=" N VAL Q 52 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR Q 53 " --> pdb=" O ILE Q 44 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE Q 44 " --> pdb=" O TYR Q 53 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN Q 55 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA Q 42 " --> pdb=" O ASN Q 55 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR Q 57 " --> pdb=" O THR Q 40 " (cutoff:3.500A) removed outlier: 10.963A pdb=" N THR Q 124 " --> pdb=" O THR Q 40 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA Q 42 " --> pdb=" O THR Q 124 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL Q 126 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE Q 44 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 76 through 79 removed outlier: 6.963A pdb=" N VAL Q 112 " --> pdb=" O SER Q 69 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE Q 71 " --> pdb=" O ARG Q 110 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG Q 110 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 90 through 96 removed outlier: 4.703A pdb=" N VAL R 52 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR R 53 " --> pdb=" O ILE R 44 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE R 44 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN R 55 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA R 42 " --> pdb=" O ASN R 55 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR R 57 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N THR R 124 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA R 42 " --> pdb=" O THR R 124 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL R 126 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE R 44 " --> pdb=" O VAL R 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 76 through 79 removed outlier: 6.907A pdb=" N VAL R 112 " --> pdb=" O SER R 69 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE R 71 " --> pdb=" O ARG R 110 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG R 110 " --> pdb=" O ILE R 71 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 90 through 96 removed outlier: 4.744A pdb=" N VAL S 52 " --> pdb=" O LEU S 96 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR S 53 " --> pdb=" O ILE S 44 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE S 44 " --> pdb=" O TYR S 53 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN S 55 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA S 42 " --> pdb=" O ASN S 55 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR S 57 " --> pdb=" O THR S 40 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N THR S 124 " --> pdb=" O THR S 40 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA S 42 " --> pdb=" O THR S 124 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL S 126 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE S 44 " --> pdb=" O VAL S 126 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 76 through 79 removed outlier: 6.986A pdb=" N VAL S 112 " --> pdb=" O SER S 69 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE S 71 " --> pdb=" O ARG S 110 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG S 110 " --> pdb=" O ILE S 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 90 through 96 removed outlier: 3.512A pdb=" N LEU T 96 " --> pdb=" O VAL T 52 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL T 52 " --> pdb=" O LEU T 96 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR T 53 " --> pdb=" O ILE T 44 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE T 44 " --> pdb=" O TYR T 53 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASN T 55 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA T 42 " --> pdb=" O ASN T 55 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR T 57 " --> pdb=" O THR T 40 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N THR T 124 " --> pdb=" O THR T 40 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA T 42 " --> pdb=" O THR T 124 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL T 126 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE T 44 " --> pdb=" O VAL T 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 76 through 79 removed outlier: 6.913A pdb=" N VAL T 112 " --> pdb=" O SER T 69 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE T 71 " --> pdb=" O ARG T 110 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG T 110 " --> pdb=" O ILE T 71 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 90 through 96 removed outlier: 4.679A pdb=" N VAL U 52 " --> pdb=" O LEU U 96 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR U 53 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE U 44 " --> pdb=" O TYR U 53 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN U 55 " --> pdb=" O ALA U 42 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA U 42 " --> pdb=" O ASN U 55 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR U 57 " --> pdb=" O THR U 40 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N THR U 124 " --> pdb=" O THR U 40 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA U 42 " --> pdb=" O THR U 124 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL U 126 " --> pdb=" O ALA U 42 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE U 44 " --> pdb=" O VAL U 126 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 76 through 79 removed outlier: 6.955A pdb=" N VAL U 112 " --> pdb=" O SER U 69 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE U 71 " --> pdb=" O ARG U 110 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG U 110 " --> pdb=" O ILE U 71 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 90 through 96 removed outlier: 3.526A pdb=" N LEU V 96 " --> pdb=" O VAL V 52 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL V 52 " --> pdb=" O LEU V 96 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR V 53 " --> pdb=" O ILE V 44 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE V 44 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN V 55 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA V 42 " --> pdb=" O ASN V 55 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR V 57 " --> pdb=" O THR V 40 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR V 124 " --> pdb=" O THR V 40 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA V 42 " --> pdb=" O THR V 124 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL V 126 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE V 44 " --> pdb=" O VAL V 126 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 76 through 79 removed outlier: 6.959A pdb=" N VAL V 112 " --> pdb=" O SER V 69 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE V 71 " --> pdb=" O ARG V 110 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG V 110 " --> pdb=" O ILE V 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 90 through 96 removed outlier: 4.637A pdb=" N VAL W 52 " --> pdb=" O LEU W 96 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR W 53 " --> pdb=" O ILE W 44 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE W 44 " --> pdb=" O TYR W 53 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN W 55 " --> pdb=" O ALA W 42 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA W 42 " --> pdb=" O ASN W 55 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR W 57 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N THR W 124 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA W 42 " --> pdb=" O THR W 124 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL W 126 " --> pdb=" O ALA W 42 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE W 44 " --> pdb=" O VAL W 126 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 76 through 79 removed outlier: 6.970A pdb=" N VAL W 112 " --> pdb=" O SER W 69 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE W 71 " --> pdb=" O ARG W 110 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG W 110 " --> pdb=" O ILE W 71 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 90 through 96 removed outlier: 3.500A pdb=" N LEU X 96 " --> pdb=" O VAL X 52 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL X 52 " --> pdb=" O LEU X 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR X 53 " --> pdb=" O ILE X 44 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ILE X 44 " --> pdb=" O TYR X 53 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN X 55 " --> pdb=" O ALA X 42 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA X 42 " --> pdb=" O ASN X 55 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR X 57 " --> pdb=" O THR X 40 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR X 124 " --> pdb=" O THR X 40 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA X 42 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL X 126 " --> pdb=" O ALA X 42 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE X 44 " --> pdb=" O VAL X 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 76 through 79 removed outlier: 6.978A pdb=" N VAL X 112 " --> pdb=" O SER X 69 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE X 71 " --> pdb=" O ARG X 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG X 110 " --> pdb=" O ILE X 71 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 90 through 96 removed outlier: 4.700A pdb=" N VAL Y 52 " --> pdb=" O LEU Y 96 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR Y 53 " --> pdb=" O ILE Y 44 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE Y 44 " --> pdb=" O TYR Y 53 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASN Y 55 " --> pdb=" O ALA Y 42 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA Y 42 " --> pdb=" O ASN Y 55 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR Y 57 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N THR Y 124 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA Y 42 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL Y 126 " --> pdb=" O ALA Y 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE Y 44 " --> pdb=" O VAL Y 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 76 through 79 removed outlier: 6.976A pdb=" N VAL Y 112 " --> pdb=" O SER Y 69 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE Y 71 " --> pdb=" O ARG Y 110 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG Y 110 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 90 through 96 removed outlier: 4.678A pdb=" N VAL Z 52 " --> pdb=" O LEU Z 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR Z 53 " --> pdb=" O ILE Z 44 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE Z 44 " --> pdb=" O TYR Z 53 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASN Z 55 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA Z 42 " --> pdb=" O ASN Z 55 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR Z 57 " --> pdb=" O THR Z 40 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N THR Z 124 " --> pdb=" O THR Z 40 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA Z 42 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL Z 126 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE Z 44 " --> pdb=" O VAL Z 126 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 76 through 79 removed outlier: 6.932A pdb=" N VAL Z 112 " --> pdb=" O SER Z 69 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE Z 71 " --> pdb=" O ARG Z 110 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG Z 110 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 90 through 96 removed outlier: 3.520A pdb=" N LEU a 96 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL a 52 " --> pdb=" O LEU a 96 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR a 53 " --> pdb=" O ILE a 44 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE a 44 " --> pdb=" O TYR a 53 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN a 55 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA a 42 " --> pdb=" O ASN a 55 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR a 57 " --> pdb=" O THR a 40 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N THR a 124 " --> pdb=" O THR a 40 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA a 42 " --> pdb=" O THR a 124 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL a 126 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE a 44 " --> pdb=" O VAL a 126 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 76 through 79 removed outlier: 6.965A pdb=" N VAL a 112 " --> pdb=" O SER a 69 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE a 71 " --> pdb=" O ARG a 110 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG a 110 " --> pdb=" O ILE a 71 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 90 through 96 removed outlier: 4.639A pdb=" N VAL b 52 " --> pdb=" O LEU b 96 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR b 53 " --> pdb=" O ILE b 44 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE b 44 " --> pdb=" O TYR b 53 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN b 55 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA b 42 " --> pdb=" O ASN b 55 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR b 57 " --> pdb=" O THR b 40 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N THR b 124 " --> pdb=" O THR b 40 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA b 42 " --> pdb=" O THR b 124 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL b 126 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE b 44 " --> pdb=" O VAL b 126 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 76 through 79 removed outlier: 4.132A pdb=" N VAL b 66 " --> pdb=" O VAL b 86 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 76 through 79 removed outlier: 6.904A pdb=" N VAL b 112 " --> pdb=" O SER b 69 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE b 71 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG b 110 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 90 through 96 removed outlier: 3.554A pdb=" N LEU c 96 " --> pdb=" O VAL c 52 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL c 52 " --> pdb=" O LEU c 96 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR c 53 " --> pdb=" O ILE c 44 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE c 44 " --> pdb=" O TYR c 53 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN c 55 " --> pdb=" O ALA c 42 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA c 42 " --> pdb=" O ASN c 55 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR c 57 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N THR c 124 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA c 42 " --> pdb=" O THR c 124 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL c 126 " --> pdb=" O ALA c 42 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE c 44 " --> pdb=" O VAL c 126 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 76 through 79 removed outlier: 6.951A pdb=" N VAL c 112 " --> pdb=" O SER c 69 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE c 71 " --> pdb=" O ARG c 110 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG c 110 " --> pdb=" O ILE c 71 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 90 through 96 removed outlier: 4.705A pdb=" N VAL d 52 " --> pdb=" O LEU d 96 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR d 53 " --> pdb=" O ILE d 44 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE d 44 " --> pdb=" O TYR d 53 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN d 55 " --> pdb=" O ALA d 42 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA d 42 " --> pdb=" O ASN d 55 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR d 57 " --> pdb=" O THR d 40 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N THR d 124 " --> pdb=" O THR d 40 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA d 42 " --> pdb=" O THR d 124 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL d 126 " --> pdb=" O ALA d 42 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE d 44 " --> pdb=" O VAL d 126 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 76 through 79 removed outlier: 6.984A pdb=" N VAL d 112 " --> pdb=" O SER d 69 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE d 71 " --> pdb=" O ARG d 110 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG d 110 " --> pdb=" O ILE d 71 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 90 through 96 removed outlier: 4.767A pdb=" N VAL e 52 " --> pdb=" O LEU e 96 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR e 53 " --> pdb=" O ILE e 44 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE e 44 " --> pdb=" O TYR e 53 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN e 55 " --> pdb=" O ALA e 42 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA e 42 " --> pdb=" O ASN e 55 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR e 57 " --> pdb=" O THR e 40 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N THR e 124 " --> pdb=" O THR e 40 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA e 42 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL e 126 " --> pdb=" O ALA e 42 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE e 44 " --> pdb=" O VAL e 126 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'e' and resid 76 through 79 removed outlier: 6.974A pdb=" N VAL e 112 " --> pdb=" O SER e 69 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE e 71 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG e 110 " --> pdb=" O ILE e 71 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'f' and resid 90 through 96 removed outlier: 4.740A pdb=" N VAL f 52 " --> pdb=" O LEU f 96 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR f 53 " --> pdb=" O ILE f 44 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE f 44 " --> pdb=" O TYR f 53 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN f 55 " --> pdb=" O ALA f 42 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA f 42 " --> pdb=" O ASN f 55 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR f 57 " --> pdb=" O THR f 40 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N THR f 124 " --> pdb=" O THR f 40 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA f 42 " --> pdb=" O THR f 124 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL f 126 " --> pdb=" O ALA f 42 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE f 44 " --> pdb=" O VAL f 126 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 76 through 79 removed outlier: 6.971A pdb=" N VAL f 112 " --> pdb=" O SER f 69 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE f 71 " --> pdb=" O ARG f 110 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG f 110 " --> pdb=" O ILE f 71 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'g' and resid 90 through 96 removed outlier: 4.712A pdb=" N VAL g 52 " --> pdb=" O LEU g 96 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR g 53 " --> pdb=" O ILE g 44 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE g 44 " --> pdb=" O TYR g 53 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN g 55 " --> pdb=" O ALA g 42 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA g 42 " --> pdb=" O ASN g 55 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR g 57 " --> pdb=" O THR g 40 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N THR g 124 " --> pdb=" O THR g 40 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA g 42 " --> pdb=" O THR g 124 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL g 126 " --> pdb=" O ALA g 42 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE g 44 " --> pdb=" O VAL g 126 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'g' and resid 76 through 79 removed outlier: 6.950A pdb=" N VAL g 112 " --> pdb=" O SER g 69 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE g 71 " --> pdb=" O ARG g 110 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG g 110 " --> pdb=" O ILE g 71 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 90 through 96 removed outlier: 4.736A pdb=" N VAL h 52 " --> pdb=" O LEU h 96 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR h 53 " --> pdb=" O ILE h 44 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE h 44 " --> pdb=" O TYR h 53 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN h 55 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA h 42 " --> pdb=" O ASN h 55 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR h 57 " --> pdb=" O THR h 40 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N THR h 124 " --> pdb=" O THR h 40 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA h 42 " --> pdb=" O THR h 124 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL h 126 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE h 44 " --> pdb=" O VAL h 126 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 76 through 79 removed outlier: 6.926A pdb=" N VAL h 112 " --> pdb=" O SER h 69 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE h 71 " --> pdb=" O ARG h 110 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG h 110 " --> pdb=" O ILE h 71 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'i' and resid 90 through 96 removed outlier: 4.656A pdb=" N VAL i 52 " --> pdb=" O LEU i 96 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR i 53 " --> pdb=" O ILE i 44 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE i 44 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN i 55 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA i 42 " --> pdb=" O ASN i 55 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR i 57 " --> pdb=" O THR i 40 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N THR i 124 " --> pdb=" O THR i 40 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA i 42 " --> pdb=" O THR i 124 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL i 126 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE i 44 " --> pdb=" O VAL i 126 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'i' and resid 76 through 79 removed outlier: 6.982A pdb=" N VAL i 112 " --> pdb=" O SER i 69 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE i 71 " --> pdb=" O ARG i 110 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG i 110 " --> pdb=" O ILE i 71 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'j' and resid 90 through 96 removed outlier: 3.542A pdb=" N LEU j 96 " --> pdb=" O VAL j 52 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL j 52 " --> pdb=" O LEU j 96 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR j 53 " --> pdb=" O ILE j 44 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE j 44 " --> pdb=" O TYR j 53 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN j 55 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA j 42 " --> pdb=" O ASN j 55 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR j 57 " --> pdb=" O THR j 40 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N THR j 124 " --> pdb=" O THR j 40 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA j 42 " --> pdb=" O THR j 124 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL j 126 " --> pdb=" O ALA j 42 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE j 44 " --> pdb=" O VAL j 126 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'j' and resid 76 through 79 removed outlier: 4.149A pdb=" N VAL j 66 " --> pdb=" O VAL j 86 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'j' and resid 76 through 79 removed outlier: 6.949A pdb=" N VAL j 112 " --> pdb=" O SER j 69 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE j 71 " --> pdb=" O ARG j 110 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG j 110 " --> pdb=" O ILE j 71 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'k' and resid 90 through 96 removed outlier: 4.597A pdb=" N VAL k 52 " --> pdb=" O LEU k 96 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR k 53 " --> pdb=" O ILE k 44 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE k 44 " --> pdb=" O TYR k 53 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN k 55 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA k 42 " --> pdb=" O ASN k 55 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR k 57 " --> pdb=" O THR k 40 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N THR k 124 " --> pdb=" O THR k 40 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA k 42 " --> pdb=" O THR k 124 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL k 126 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE k 44 " --> pdb=" O VAL k 126 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'k' and resid 76 through 79 removed outlier: 6.995A pdb=" N VAL k 112 " --> pdb=" O SER k 69 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE k 71 " --> pdb=" O ARG k 110 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG k 110 " --> pdb=" O ILE k 71 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'l' and resid 90 through 96 removed outlier: 4.657A pdb=" N VAL l 52 " --> pdb=" O LEU l 96 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR l 53 " --> pdb=" O ILE l 44 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE l 44 " --> pdb=" O TYR l 53 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN l 55 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA l 42 " --> pdb=" O ASN l 55 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR l 57 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N THR l 124 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA l 42 " --> pdb=" O THR l 124 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N VAL l 126 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE l 44 " --> pdb=" O VAL l 126 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'l' and resid 76 through 79 removed outlier: 6.935A pdb=" N VAL l 112 " --> pdb=" O SER l 69 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE l 71 " --> pdb=" O ARG l 110 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG l 110 " --> pdb=" O ILE l 71 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'm' and resid 90 through 96 removed outlier: 4.734A pdb=" N VAL m 52 " --> pdb=" O LEU m 96 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR m 53 " --> pdb=" O ILE m 44 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE m 44 " --> pdb=" O TYR m 53 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN m 55 " --> pdb=" O ALA m 42 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA m 42 " --> pdb=" O ASN m 55 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR m 57 " --> pdb=" O THR m 40 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N THR m 124 " --> pdb=" O THR m 40 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA m 42 " --> pdb=" O THR m 124 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL m 126 " --> pdb=" O ALA m 42 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE m 44 " --> pdb=" O VAL m 126 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'm' and resid 76 through 79 removed outlier: 6.981A pdb=" N VAL m 112 " --> pdb=" O SER m 69 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE m 71 " --> pdb=" O ARG m 110 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG m 110 " --> pdb=" O ILE m 71 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'n' and resid 90 through 96 removed outlier: 4.671A pdb=" N VAL n 52 " --> pdb=" O LEU n 96 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR n 53 " --> pdb=" O ILE n 44 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE n 44 " --> pdb=" O TYR n 53 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN n 55 " --> pdb=" O ALA n 42 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA n 42 " --> pdb=" O ASN n 55 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR n 57 " --> pdb=" O THR n 40 " (cutoff:3.500A) removed outlier: 10.954A pdb=" N THR n 124 " --> pdb=" O THR n 40 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA n 42 " --> pdb=" O THR n 124 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL n 126 " --> pdb=" O ALA n 42 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE n 44 " --> pdb=" O VAL n 126 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'n' and resid 76 through 79 removed outlier: 4.074A pdb=" N VAL n 66 " --> pdb=" O VAL n 86 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'n' and resid 76 through 79 removed outlier: 6.969A pdb=" N VAL n 112 " --> pdb=" O SER n 69 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE n 71 " --> pdb=" O ARG n 110 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG n 110 " --> pdb=" O ILE n 71 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'o' and resid 90 through 96 removed outlier: 4.722A pdb=" N VAL o 52 " --> pdb=" O LEU o 96 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR o 53 " --> pdb=" O ILE o 44 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE o 44 " --> pdb=" O TYR o 53 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN o 55 " --> pdb=" O ALA o 42 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA o 42 " --> pdb=" O ASN o 55 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR o 57 " --> pdb=" O THR o 40 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR o 124 " --> pdb=" O THR o 40 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA o 42 " --> pdb=" O THR o 124 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL o 126 " --> pdb=" O ALA o 42 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE o 44 " --> pdb=" O VAL o 126 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'o' and resid 76 through 79 removed outlier: 7.012A pdb=" N VAL o 112 " --> pdb=" O SER o 69 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE o 71 " --> pdb=" O ARG o 110 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG o 110 " --> pdb=" O ILE o 71 " (cutoff:3.500A) 1906 hydrogen bonds defined for protein. 5211 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: 8.97 Time building geometry restraints manager: 3.99 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: 12956 1.34 - 1.46: 7253 1.46 - 1.58: 21283 1.58 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 41656 Sorted by residual: bond pdb=" CB GLU W 5 " pdb=" CG GLU W 5 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" CB GLU Z 5 " pdb=" CG GLU Z 5 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CB GLU F 5 " pdb=" CG GLU F 5 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CB GLU I 5 " pdb=" CG GLU I 5 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CB GLU T 5 " pdb=" CG GLU T 5 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.63e+00 ... (remaining 41651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 51130 0.79 - 1.58: 4892 1.58 - 2.36: 741 2.36 - 3.15: 397 3.15 - 3.94: 76 Bond angle restraints: 57236 Sorted by residual: angle pdb=" C PHE D 121 " pdb=" CA PHE D 121 " pdb=" CB PHE D 121 " ideal model delta sigma weight residual 111.65 107.71 3.94 1.44e+00 4.82e-01 7.48e+00 angle pdb=" N VAL B 13 " pdb=" CA VAL B 13 " pdb=" CB VAL B 13 " ideal model delta sigma weight residual 110.55 107.43 3.12 1.17e+00 7.31e-01 7.13e+00 angle pdb=" N VAL N 13 " pdb=" CA VAL N 13 " pdb=" CB VAL N 13 " ideal model delta sigma weight residual 110.55 107.53 3.02 1.17e+00 7.31e-01 6.64e+00 angle pdb=" C ILE B 12 " pdb=" N VAL B 13 " pdb=" CA VAL B 13 " ideal model delta sigma weight residual 120.56 123.75 -3.19 1.26e+00 6.30e-01 6.40e+00 angle pdb=" C PHE A 121 " pdb=" CA PHE A 121 " pdb=" CB PHE A 121 " ideal model delta sigma weight residual 111.65 108.01 3.64 1.44e+00 4.82e-01 6.38e+00 ... (remaining 57231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 22928 17.37 - 34.73: 1558 34.73 - 52.10: 245 52.10 - 69.47: 50 69.47 - 86.84: 24 Dihedral angle restraints: 24805 sinusoidal: 8241 harmonic: 16564 Sorted by residual: dihedral pdb=" CA MET m 1 " pdb=" C MET m 1 " pdb=" N THR m 2 " pdb=" CA THR m 2 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE M 121 " pdb=" C PHE M 121 " pdb=" N THR M 122 " pdb=" CA THR M 122 " ideal model delta harmonic sigma weight residual 180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE D 121 " pdb=" C PHE D 121 " pdb=" N THR D 122 " pdb=" CA THR D 122 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 24802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4437 0.028 - 0.056: 1560 0.056 - 0.084: 893 0.084 - 0.112: 597 0.112 - 0.140: 262 Chirality restraints: 7749 Sorted by residual: chirality pdb=" CB THR U 122 " pdb=" CA THR U 122 " pdb=" OG1 THR U 122 " pdb=" CG2 THR U 122 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CB THR E 122 " pdb=" CA THR E 122 " pdb=" OG1 THR E 122 " pdb=" CG2 THR E 122 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CB THR W 122 " pdb=" CA THR W 122 " pdb=" OG1 THR W 122 " pdb=" CG2 THR W 122 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 7746 not shown) Planarity restraints: 6970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER h 119 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO h 120 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO h 120 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO h 120 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 119 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO M 120 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO M 120 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 120 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 119 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B 120 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.028 5.00e-02 4.00e+02 ... (remaining 6967 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 371 2.63 - 3.20: 37388 3.20 - 3.76: 59700 3.76 - 4.33: 80968 4.33 - 4.90: 137400 Nonbonded interactions: 315827 Sorted by model distance: nonbonded pdb=" OG SER X 3 " pdb=" OE1 GLU Z 5 " model vdw 2.062 3.040 nonbonded pdb=" OG SER d 3 " pdb=" OE1 GLU f 5 " model vdw 2.064 3.040 nonbonded pdb=" OE1 GLU k 5 " pdb=" OG SER m 3 " model vdw 2.085 3.040 nonbonded pdb=" OG SER T 3 " pdb=" OE1 GLU V 5 " model vdw 2.086 3.040 nonbonded pdb=" OG SER D 3 " pdb=" OE1 GLU F 5 " model vdw 2.102 3.040 ... (remaining 315822 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 34.610 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 41697 Z= 0.190 Angle : 0.541 3.938 57318 Z= 0.322 Chirality : 0.047 0.140 7749 Planarity : 0.005 0.052 6970 Dihedral : 12.248 86.835 14022 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.48 % Allowed : 5.67 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.73 (0.10), residues: 5658 helix: 0.16 (0.12), residues: 1271 sheet: -2.65 (0.09), residues: 2091 loop : -1.92 (0.11), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG o 110 TYR 0.013 0.002 TYR K 25 PHE 0.008 0.002 PHE I 121 TRP 0.016 0.003 TRP d 22 HIS 0.001 0.000 HIS k 130 Details of bonding type rmsd covalent geometry : bond 0.00417 (41656) covalent geometry : angle 0.54060 (57236) SS BOND : bond 0.00240 ( 41) SS BOND : angle 0.47430 ( 82) hydrogen bonds : bond 0.17102 ( 1886) hydrogen bonds : angle 8.27129 ( 5211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 817 time to evaluate : 1.489 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: A 87 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8586 (mttm) REVERT: B 34 GLN cc_start: 0.9289 (tp40) cc_final: 0.8944 (mm-40) REVERT: B 87 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8627 (mttm) REVERT: C 34 GLN cc_start: 0.9251 (tp40) cc_final: 0.9014 (mm-40) REVERT: C 61 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8100 (mm-40) REVERT: C 87 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8516 (mmtp) REVERT: D 34 GLN cc_start: 0.9382 (tp40) cc_final: 0.9087 (mm-40) REVERT: D 87 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8507 (mttm) REVERT: E 87 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8261 (mttp) REVERT: F 87 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8604 (mttm) REVERT: G 87 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8432 (mmtm) REVERT: G 137 LYS cc_start: 0.8837 (mttt) cc_final: 0.8630 (mttm) REVERT: H 87 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8543 (mttm) REVERT: H 92 TYR cc_start: 0.8991 (m-80) cc_final: 0.8711 (m-80) REVERT: I 87 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8641 (mttm) REVERT: I 121 PHE cc_start: 0.7400 (m-10) cc_final: 0.7099 (m-80) REVERT: I 137 LYS cc_start: 0.8803 (mttt) cc_final: 0.8583 (mttm) REVERT: J 87 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8434 (mttp) REVERT: K 34 GLN cc_start: 0.9293 (tp40) cc_final: 0.9056 (mm-40) REVERT: K 87 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8489 (mmtm) REVERT: K 121 PHE cc_start: 0.7687 (m-10) cc_final: 0.7319 (m-80) REVERT: L 87 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8593 (mttm) REVERT: M 34 GLN cc_start: 0.9316 (tp40) cc_final: 0.8989 (mm-40) REVERT: M 87 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8606 (mttm) REVERT: N 61 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8160 (mm-40) REVERT: N 87 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8708 (mttm) REVERT: O 61 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8199 (mm-40) REVERT: O 87 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8625 (mttm) REVERT: O 137 LYS cc_start: 0.9004 (mttt) cc_final: 0.8795 (mttp) REVERT: P 87 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8536 (mmtm) REVERT: P 95 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7626 (mt-10) REVERT: Q 87 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8633 (mttm) REVERT: R 87 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8680 (mttm) REVERT: S 34 GLN cc_start: 0.9247 (tp40) cc_final: 0.9020 (mm-40) REVERT: S 87 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8506 (mttp) REVERT: T 34 GLN cc_start: 0.9363 (tp40) cc_final: 0.9060 (mm-40) REVERT: T 87 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8524 (mttm) REVERT: T 137 LYS cc_start: 0.8994 (mttt) cc_final: 0.8716 (mttm) REVERT: U 34 GLN cc_start: 0.9347 (tp40) cc_final: 0.9019 (mm-40) REVERT: U 87 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8491 (mttm) REVERT: V 87 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8575 (mmtp) REVERT: V 137 LYS cc_start: 0.8907 (mttt) cc_final: 0.8653 (mttp) REVERT: W 87 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8515 (mmtm) REVERT: W 137 LYS cc_start: 0.8935 (mttt) cc_final: 0.8693 (mtpp) REVERT: X 87 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8586 (mmtp) REVERT: X 129 ASP cc_start: 0.8367 (p0) cc_final: 0.8162 (p0) REVERT: Y 87 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8668 (mttm) REVERT: Y 137 LYS cc_start: 0.8794 (mttt) cc_final: 0.8590 (mttm) REVERT: Z 87 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8527 (mmtp) REVERT: Z 95 GLU cc_start: 0.7813 (mp0) cc_final: 0.7510 (mp0) REVERT: Z 137 LYS cc_start: 0.8966 (mttt) cc_final: 0.8582 (mttp) REVERT: a 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8609 (mttp) REVERT: b 61 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8303 (mm-40) REVERT: b 87 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8582 (mttm) REVERT: c 87 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8575 (mttp) REVERT: d 87 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8535 (mmtp) REVERT: e 87 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8606 (mttm) REVERT: f 87 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8451 (mmtm) REVERT: g 87 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8614 (mmtp) REVERT: h 41 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8625 (mtmm) REVERT: h 61 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8627 (mm-40) REVERT: h 87 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8667 (mttm) REVERT: i 87 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8594 (mttm) REVERT: j 87 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8582 (mttm) REVERT: k 87 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8512 (mttm) REVERT: l 87 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8528 (mttm) REVERT: m 25 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: m 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8600 (mttm) REVERT: m 137 LYS cc_start: 0.8934 (mttt) cc_final: 0.8715 (mtpp) REVERT: n 61 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8663 (mm-40) REVERT: n 78 ILE cc_start: 0.8585 (mt) cc_final: 0.8318 (pt) REVERT: n 87 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8593 (mttm) REVERT: n 129 ASP cc_start: 0.8490 (p0) cc_final: 0.8128 (p0) REVERT: o 78 ILE cc_start: 0.8434 (mt) cc_final: 0.8127 (pt) REVERT: o 87 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8528 (mmtp) REVERT: o 129 ASP cc_start: 0.8335 (p0) cc_final: 0.8018 (p0) outliers start: 22 outliers final: 15 residues processed: 835 average time/residue: 0.2354 time to fit residues: 315.6626 Evaluate side-chains 633 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 617 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain m residue 25 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 394 optimal weight: 0.7980 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 0.3980 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN G 61 GLN I 61 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN P 61 GLN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN f 61 GLN l 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.092133 restraints weight = 62378.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.096535 restraints weight = 33988.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.099491 restraints weight = 21962.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101475 restraints weight = 15801.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102949 restraints weight = 12255.375| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41697 Z= 0.125 Angle : 0.499 4.507 57318 Z= 0.284 Chirality : 0.049 0.188 7749 Planarity : 0.004 0.041 6970 Dihedral : 5.077 55.269 5963 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.55 % Allowed : 12.13 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.10), residues: 5658 helix: 1.49 (0.12), residues: 1271 sheet: -2.18 (0.10), residues: 2214 loop : -1.59 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 110 TYR 0.014 0.001 TYR S 92 PHE 0.008 0.001 PHE Y 121 TRP 0.015 0.002 TRP d 22 HIS 0.002 0.000 HIS Y 130 Details of bonding type rmsd covalent geometry : bond 0.00271 (41656) covalent geometry : angle 0.49920 (57236) SS BOND : bond 0.00063 ( 41) SS BOND : angle 0.58174 ( 82) hydrogen bonds : bond 0.05058 ( 1886) hydrogen bonds : angle 5.51453 ( 5211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 769 time to evaluate : 1.504 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: A 72 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 87 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8593 (mttm) REVERT: B 72 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7728 (mt-10) REVERT: B 87 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8662 (mmtp) REVERT: C 34 GLN cc_start: 0.9173 (tp40) cc_final: 0.8955 (mm-40) REVERT: C 72 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 87 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8562 (mmtm) REVERT: D 34 GLN cc_start: 0.9281 (tp40) cc_final: 0.8998 (mm-40) REVERT: D 87 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8488 (mttm) REVERT: D 92 TYR cc_start: 0.8941 (m-80) cc_final: 0.8704 (m-10) REVERT: E 87 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8242 (mttp) REVERT: F 87 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8591 (mttm) REVERT: G 87 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8487 (mmtm) REVERT: H 87 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8576 (mttm) REVERT: I 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8618 (mmtm) REVERT: I 121 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: J 72 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7539 (mt-10) REVERT: J 87 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8444 (mttp) REVERT: K 34 GLN cc_start: 0.9180 (tp40) cc_final: 0.8642 (mm-40) REVERT: K 61 GLN cc_start: 0.8419 (tp40) cc_final: 0.8190 (mm-40) REVERT: K 87 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8522 (mmtm) REVERT: L 87 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8576 (mttm) REVERT: M 25 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: M 87 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8624 (mttm) REVERT: N 87 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8629 (mttp) REVERT: O 72 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7676 (mt-10) REVERT: O 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8619 (mttm) REVERT: P 72 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7333 (mt-10) REVERT: P 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8557 (mmtm) REVERT: Q 61 GLN cc_start: 0.8139 (tp40) cc_final: 0.7938 (mm-40) REVERT: Q 87 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8594 (mttm) REVERT: R 87 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8709 (mmtp) REVERT: S 87 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8607 (mmtm) REVERT: S 129 ASP cc_start: 0.8363 (p0) cc_final: 0.7984 (p0) REVERT: T 34 GLN cc_start: 0.9284 (tp40) cc_final: 0.9058 (mm-40) REVERT: T 87 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8513 (mttm) REVERT: U 87 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8460 (mmtp) REVERT: V 72 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7484 (mt-10) REVERT: V 87 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8684 (mmtp) REVERT: W 87 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8594 (mmtm) REVERT: X 87 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8526 (mmtm) REVERT: X 129 ASP cc_start: 0.8185 (p0) cc_final: 0.7952 (p0) REVERT: Y 87 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8691 (mttm) REVERT: Y 129 ASP cc_start: 0.8312 (p0) cc_final: 0.8075 (p0) REVERT: Z 87 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8635 (mmtm) REVERT: Z 95 GLU cc_start: 0.7747 (mp0) cc_final: 0.7409 (mp0) REVERT: Z 137 LYS cc_start: 0.8854 (mttt) cc_final: 0.8560 (mttp) REVERT: a 87 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8670 (mttm) REVERT: b 22 TRP cc_start: 0.7845 (m100) cc_final: 0.7315 (m100) REVERT: b 37 LEU cc_start: 0.9210 (mt) cc_final: 0.9008 (mt) REVERT: b 72 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7485 (mt-10) REVERT: b 87 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8620 (mttm) REVERT: b 113 LEU cc_start: 0.8848 (mt) cc_final: 0.8621 (mt) REVERT: c 87 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8622 (mttm) REVERT: d 87 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8671 (mmtm) REVERT: e 87 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8548 (mttm) REVERT: e 95 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7520 (mt-10) REVERT: f 72 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7353 (mt-10) REVERT: f 87 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8550 (mmtm) REVERT: g 87 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8740 (mmtp) REVERT: h 72 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7643 (mt-10) REVERT: h 87 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8646 (mmtp) REVERT: i 87 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8577 (mttm) REVERT: j 72 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7583 (mt-10) REVERT: j 87 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8578 (mttm) REVERT: k 87 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8572 (mttm) REVERT: l 87 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8483 (mttm) REVERT: m 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8586 (mmtm) REVERT: n 87 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8554 (mttm) REVERT: o 87 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8587 (mmtp) REVERT: o 129 ASP cc_start: 0.8325 (p0) cc_final: 0.8072 (p0) outliers start: 116 outliers final: 60 residues processed: 820 average time/residue: 0.2320 time to fit residues: 303.7952 Evaluate side-chains 701 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 639 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 121 PHE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain M residue 25 TYR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain P residue 91 GLU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 25 TYR Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain i residue 121 PHE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 37 LEU Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain o residue 91 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 87 optimal weight: 2.9990 chunk 564 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 412 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 485 optimal weight: 10.0000 chunk 553 optimal weight: 1.9990 chunk 573 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN B 51 ASN E 51 ASN H 51 ASN L 51 ASN N 51 ASN O 51 ASN S 51 ASN W 33 GLN W 51 ASN W 61 GLN b 51 ASN d 33 GLN e 51 ASN f 51 ASN g 51 ASN i 51 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.090453 restraints weight = 63311.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094655 restraints weight = 34247.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097462 restraints weight = 22103.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099346 restraints weight = 15895.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100675 restraints weight = 12377.307| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 41697 Z= 0.203 Angle : 0.531 4.835 57318 Z= 0.299 Chirality : 0.049 0.211 7749 Planarity : 0.005 0.064 6970 Dihedral : 5.069 59.541 5959 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.59 % Allowed : 16.83 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.10), residues: 5658 helix: 1.88 (0.13), residues: 1271 sheet: -2.30 (0.09), residues: 2173 loop : -1.25 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG o 110 TYR 0.014 0.002 TYR k 23 PHE 0.021 0.002 PHE F 121 TRP 0.012 0.002 TRP K 22 HIS 0.002 0.000 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00481 (41656) covalent geometry : angle 0.53095 (57236) SS BOND : bond 0.00236 ( 41) SS BOND : angle 0.55490 ( 82) hydrogen bonds : bond 0.05378 ( 1886) hydrogen bonds : angle 5.42579 ( 5211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 657 time to evaluate : 1.199 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: A 72 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 87 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8592 (mmtp) REVERT: B 37 LEU cc_start: 0.9283 (mt) cc_final: 0.9036 (mt) REVERT: B 87 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8681 (mmtp) REVERT: B 95 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 87 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8609 (mmtm) REVERT: D 72 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7555 (mt-10) REVERT: D 87 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8532 (mttm) REVERT: E 87 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8366 (mmtp) REVERT: F 87 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8609 (mttm) REVERT: G 87 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8527 (mmtm) REVERT: G 95 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7800 (mp0) REVERT: H 87 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8558 (mttm) REVERT: H 95 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7546 (mp0) REVERT: I 72 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7472 (mt-10) REVERT: I 87 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8637 (mmtm) REVERT: I 121 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.7015 (m-10) REVERT: J 72 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7725 (mt-10) REVERT: J 87 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8543 (mmtm) REVERT: K 34 GLN cc_start: 0.9264 (tp40) cc_final: 0.9053 (mm-40) REVERT: K 61 GLN cc_start: 0.8450 (tp40) cc_final: 0.8195 (mm-40) REVERT: K 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8580 (mmtm) REVERT: L 87 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8632 (mmtp) REVERT: M 87 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8628 (mttm) REVERT: N 87 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8619 (mttp) REVERT: N 95 GLU cc_start: 0.8026 (mp0) cc_final: 0.7815 (mp0) REVERT: O 72 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7789 (mt-10) REVERT: O 87 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8591 (mttm) REVERT: P 72 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7428 (mt-10) REVERT: P 87 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8574 (mmtm) REVERT: Q 61 GLN cc_start: 0.8227 (tp40) cc_final: 0.7980 (mm-40) REVERT: Q 87 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8613 (mttm) REVERT: R 72 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7534 (mt-10) REVERT: R 87 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8720 (mmtp) REVERT: S 87 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8628 (mmtm) REVERT: S 129 ASP cc_start: 0.8432 (p0) cc_final: 0.8062 (p0) REVERT: T 87 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8549 (mttm) REVERT: V 87 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8728 (mmtp) REVERT: W 87 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8681 (mmtm) REVERT: X 87 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8637 (mmtm) REVERT: X 110 ARG cc_start: 0.8878 (mtm180) cc_final: 0.8613 (mtm180) REVERT: X 129 ASP cc_start: 0.8232 (p0) cc_final: 0.7976 (p0) REVERT: X 137 LYS cc_start: 0.8767 (mttp) cc_final: 0.8551 (mttm) REVERT: Y 87 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8721 (mttm) REVERT: Y 129 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8061 (p0) REVERT: Y 137 LYS cc_start: 0.8791 (mttt) cc_final: 0.8590 (mttm) REVERT: Z 87 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8637 (mmtp) REVERT: Z 95 GLU cc_start: 0.7839 (mp0) cc_final: 0.7448 (mp0) REVERT: Z 137 LYS cc_start: 0.8966 (mttt) cc_final: 0.8626 (mttp) REVERT: a 72 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7223 (mt-10) REVERT: a 87 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8674 (mttm) REVERT: b 87 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8590 (mttm) REVERT: c 87 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8621 (mttm) REVERT: d 87 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8750 (mmtm) REVERT: e 72 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7709 (mt-10) REVERT: e 87 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8507 (mttp) REVERT: e 95 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7567 (mt-10) REVERT: f 72 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7547 (mt-10) REVERT: f 87 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8767 (mmtm) REVERT: g 87 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8732 (mmtp) REVERT: g 121 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: h 87 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8702 (mmtp) REVERT: i 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8580 (mttm) REVERT: i 92 TYR cc_start: 0.9003 (m-80) cc_final: 0.8643 (m-80) REVERT: k 87 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8567 (mttm) REVERT: l 25 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7531 (t80) REVERT: l 87 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8507 (mttm) REVERT: m 87 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8593 (mmtm) REVERT: m 137 LYS cc_start: 0.8916 (mttt) cc_final: 0.8685 (mtpp) REVERT: n 22 TRP cc_start: 0.8123 (m100) cc_final: 0.7534 (m100) REVERT: n 87 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8552 (mttm) REVERT: o 87 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8622 (mmtm) REVERT: o 129 ASP cc_start: 0.8417 (p0) cc_final: 0.8181 (p0) outliers start: 118 outliers final: 80 residues processed: 724 average time/residue: 0.2631 time to fit residues: 298.2042 Evaluate side-chains 660 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 576 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 121 PHE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 25 TYR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Y residue 129 ASP Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain i residue 121 PHE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 13 VAL Chi-restraints excluded: chain j residue 37 LEU Chi-restraints excluded: chain j residue 110 ARG Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain k residue 129 ASP Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 121 PHE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 96 LEU Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 205 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 475 optimal weight: 7.9990 chunk 507 optimal weight: 0.7980 chunk 408 optimal weight: 0.8980 chunk 353 optimal weight: 4.9990 chunk 558 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN H 51 ASN N 51 ASN P 51 ASN W 33 GLN b 51 ASN d 33 GLN e 33 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.091110 restraints weight = 58870.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.095247 restraints weight = 32244.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.098047 restraints weight = 20837.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099984 restraints weight = 14954.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101273 restraints weight = 11531.002| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41697 Z= 0.125 Angle : 0.484 8.748 57318 Z= 0.271 Chirality : 0.049 0.228 7749 Planarity : 0.005 0.055 6970 Dihedral : 4.828 59.946 5958 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.77 % Allowed : 18.15 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.11), residues: 5658 helix: 2.27 (0.13), residues: 1271 sheet: -1.87 (0.10), residues: 2214 loop : -1.36 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 110 TYR 0.016 0.001 TYR M 25 PHE 0.014 0.001 PHE F 121 TRP 0.016 0.002 TRP b 22 HIS 0.002 0.000 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00284 (41656) covalent geometry : angle 0.48389 (57236) SS BOND : bond 0.00101 ( 41) SS BOND : angle 0.41625 ( 82) hydrogen bonds : bond 0.04643 ( 1886) hydrogen bonds : angle 4.88738 ( 5211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 681 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7510 (mt-10) REVERT: A 87 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8583 (mmtp) REVERT: B 37 LEU cc_start: 0.9233 (mt) cc_final: 0.8962 (mt) REVERT: B 72 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7522 (mt-10) REVERT: B 87 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8685 (mmtp) REVERT: C 87 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8642 (mmtm) REVERT: D 72 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7473 (mt-10) REVERT: D 87 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8573 (mmtm) REVERT: E 87 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8351 (mmtm) REVERT: F 87 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8609 (mttm) REVERT: G 87 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8594 (mmtm) REVERT: H 87 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8541 (mttm) REVERT: I 87 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8608 (mmtm) REVERT: I 121 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: J 72 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7637 (mt-10) REVERT: J 87 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8526 (mmtm) REVERT: K 34 GLN cc_start: 0.9145 (tp40) cc_final: 0.8781 (mm-40) REVERT: K 87 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8570 (mmtm) REVERT: L 87 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8651 (mmtp) REVERT: M 72 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7391 (mt-10) REVERT: M 87 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8580 (mttm) REVERT: N 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8669 (mttm) REVERT: O 87 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8584 (mttm) REVERT: P 87 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8562 (mmtm) REVERT: Q 61 GLN cc_start: 0.8036 (tp40) cc_final: 0.7813 (mm-40) REVERT: Q 87 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8654 (mmtp) REVERT: R 87 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8698 (mmtp) REVERT: S 61 GLN cc_start: 0.8275 (tp40) cc_final: 0.8048 (mm-40) REVERT: S 78 ILE cc_start: 0.8544 (mt) cc_final: 0.8264 (tt) REVERT: S 87 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8614 (mmtm) REVERT: S 129 ASP cc_start: 0.8312 (p0) cc_final: 0.7995 (p0) REVERT: T 72 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7665 (mt-10) REVERT: T 87 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8547 (mttm) REVERT: V 87 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8764 (mmtp) REVERT: W 87 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8707 (mmtm) REVERT: X 43 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8992 (p) REVERT: X 72 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7156 (mt-10) REVERT: X 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8581 (mmtm) REVERT: X 129 ASP cc_start: 0.8213 (p0) cc_final: 0.7965 (p0) REVERT: X 137 LYS cc_start: 0.8682 (mttp) cc_final: 0.8466 (mttm) REVERT: Y 48 LYS cc_start: 0.9159 (mtmt) cc_final: 0.8956 (mtmm) REVERT: Y 87 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8710 (mttm) REVERT: Y 95 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7313 (mt-10) REVERT: Z 87 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8668 (mmtp) REVERT: Z 137 LYS cc_start: 0.8853 (mttt) cc_final: 0.8617 (mttp) REVERT: a 72 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7427 (mt-10) REVERT: a 87 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8682 (mttm) REVERT: b 22 TRP cc_start: 0.7964 (m100) cc_final: 0.7447 (m100) REVERT: b 87 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8551 (mttm) REVERT: c 87 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8654 (mttm) REVERT: d 87 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8778 (mmtm) REVERT: e 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8553 (mttp) REVERT: f 72 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7191 (mt-10) REVERT: f 87 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8749 (mmtm) REVERT: g 87 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8716 (mmtp) REVERT: g 121 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: h 25 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: h 87 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8657 (mmtp) REVERT: i 87 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8604 (mmtp) REVERT: k 41 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8532 (mttt) REVERT: k 87 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8559 (mttm) REVERT: l 25 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7417 (t80) REVERT: l 87 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8483 (mttm) REVERT: m 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8605 (mmtm) REVERT: n 87 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8541 (mmtm) REVERT: o 87 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8635 (mmtm) outliers start: 126 outliers final: 79 residues processed: 753 average time/residue: 0.2424 time to fit residues: 290.4203 Evaluate side-chains 675 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 591 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain I residue 121 PHE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 25 TYR Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain f residue 2 THR Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 25 TYR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain i residue 121 PHE Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain k residue 129 ASP Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 379 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 549 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 414 optimal weight: 8.9990 chunk 423 optimal weight: 2.9990 chunk 468 optimal weight: 5.9990 chunk 315 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 417 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 51 ASN ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN P 51 ASN b 51 ASN d 33 GLN o 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095156 restraints weight = 57430.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099365 restraints weight = 31198.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102076 restraints weight = 20070.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104049 restraints weight = 14478.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105403 restraints weight = 11169.122| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41697 Z= 0.128 Angle : 0.484 6.999 57318 Z= 0.271 Chirality : 0.049 0.223 7749 Planarity : 0.005 0.091 6970 Dihedral : 4.722 59.830 5958 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.61 % Allowed : 20.17 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.11), residues: 5658 helix: 2.33 (0.13), residues: 1271 sheet: -1.74 (0.10), residues: 2214 loop : -1.26 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 110 TYR 0.010 0.001 TYR U 23 PHE 0.017 0.001 PHE K 121 TRP 0.014 0.002 TRP d 22 HIS 0.002 0.000 HIS d 130 Details of bonding type rmsd covalent geometry : bond 0.00295 (41656) covalent geometry : angle 0.48379 (57236) SS BOND : bond 0.00100 ( 41) SS BOND : angle 0.41161 ( 82) hydrogen bonds : bond 0.04563 ( 1886) hydrogen bonds : angle 4.77115 ( 5211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 634 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7534 (mt-10) REVERT: A 87 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8580 (mmtp) REVERT: B 87 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8707 (mmtp) REVERT: C 72 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7476 (pt0) REVERT: C 87 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8611 (mmtm) REVERT: D 87 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8599 (mmtm) REVERT: E 87 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8328 (mmtm) REVERT: F 72 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7166 (mt-10) REVERT: F 87 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8623 (mttm) REVERT: G 87 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8588 (mmtm) REVERT: H 87 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8583 (mmtm) REVERT: I 87 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8590 (mmtm) REVERT: J 72 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7683 (mt-10) REVERT: J 87 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8510 (mmtp) REVERT: K 34 GLN cc_start: 0.9162 (tp40) cc_final: 0.8924 (mm-40) REVERT: K 87 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8575 (mmtm) REVERT: L 87 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8634 (mmtp) REVERT: M 87 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8614 (mttm) REVERT: N 87 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8717 (mmtp) REVERT: O 72 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7204 (mt-10) REVERT: O 87 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8560 (mttm) REVERT: P 87 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8537 (mmtm) REVERT: Q 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8659 (mmtp) REVERT: R 87 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8720 (mmtp) REVERT: S 61 GLN cc_start: 0.8234 (tp40) cc_final: 0.8027 (mm-40) REVERT: S 87 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8604 (mmtm) REVERT: S 129 ASP cc_start: 0.8194 (p0) cc_final: 0.7925 (p0) REVERT: T 87 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8545 (mttm) REVERT: V 87 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8778 (mmtp) REVERT: W 87 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8702 (mmtm) REVERT: X 43 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.8975 (p) REVERT: X 87 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8572 (mmtm) REVERT: X 129 ASP cc_start: 0.8130 (p0) cc_final: 0.7900 (p0) REVERT: Y 87 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8663 (mttm) REVERT: Z 33 GLN cc_start: 0.8478 (mt0) cc_final: 0.8194 (mt0) REVERT: Z 87 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8649 (mmtm) REVERT: Z 95 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7387 (mp0) REVERT: Z 137 LYS cc_start: 0.8777 (mttt) cc_final: 0.8556 (mttp) REVERT: a 72 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7312 (mt-10) REVERT: a 87 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8697 (mttm) REVERT: b 22 TRP cc_start: 0.7931 (m100) cc_final: 0.7355 (m100) REVERT: b 87 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8543 (mttm) REVERT: c 87 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8657 (mttm) REVERT: d 87 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8793 (mmtm) REVERT: e 72 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7610 (mt-10) REVERT: e 87 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8532 (mttp) REVERT: f 72 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7493 (mt-10) REVERT: f 87 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8748 (mmtm) REVERT: g 87 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8649 (mmtp) REVERT: g 121 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: h 25 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: h 87 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8649 (mmtp) REVERT: i 87 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8612 (mmtm) REVERT: k 41 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8536 (mttt) REVERT: k 87 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8528 (mttm) REVERT: l 25 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7459 (t80) REVERT: l 43 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9026 (p) REVERT: l 87 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8465 (mttm) REVERT: m 87 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8598 (mmtm) REVERT: n 87 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8555 (mmtm) REVERT: o 87 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8665 (mmtm) outliers start: 119 outliers final: 80 residues processed: 700 average time/residue: 0.2396 time to fit residues: 267.7378 Evaluate side-chains 668 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 583 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 25 TYR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 102 SER Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain i residue 121 PHE Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain k residue 129 ASP Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 121 PHE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 208 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 540 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 374 optimal weight: 0.9990 chunk 511 optimal weight: 7.9990 chunk 560 optimal weight: 2.9990 chunk 441 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 573 optimal weight: 0.0770 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 33 GLN b 51 ASN d 33 GLN f 33 GLN o 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094234 restraints weight = 57812.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098389 restraints weight = 31417.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101165 restraints weight = 20226.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103030 restraints weight = 14516.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104380 restraints weight = 11266.358| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41697 Z= 0.143 Angle : 0.495 6.141 57318 Z= 0.277 Chirality : 0.049 0.259 7749 Planarity : 0.005 0.083 6970 Dihedral : 4.686 58.916 5958 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.79 % Allowed : 20.79 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.11), residues: 5658 helix: 2.36 (0.13), residues: 1271 sheet: -1.66 (0.10), residues: 2214 loop : -1.18 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 110 TYR 0.013 0.001 TYR M 25 PHE 0.021 0.002 PHE K 121 TRP 0.014 0.002 TRP C 22 HIS 0.002 0.000 HIS Y 130 Details of bonding type rmsd covalent geometry : bond 0.00334 (41656) covalent geometry : angle 0.49524 (57236) SS BOND : bond 0.00138 ( 41) SS BOND : angle 0.41267 ( 82) hydrogen bonds : bond 0.04622 ( 1886) hydrogen bonds : angle 4.75774 ( 5211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 626 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 87 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8577 (mmtp) REVERT: B 87 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8709 (mmtp) REVERT: C 87 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8752 (mmtp) REVERT: D 87 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8588 (mmtm) REVERT: E 87 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8309 (mmtm) REVERT: F 87 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8632 (mmtm) REVERT: G 87 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8595 (mmtm) REVERT: G 110 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8400 (mtm180) REVERT: G 121 PHE cc_start: 0.7184 (m-80) cc_final: 0.6881 (m-80) REVERT: H 87 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8579 (mmtm) REVERT: I 87 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8572 (mmtm) REVERT: J 72 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7655 (mt-10) REVERT: J 87 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8522 (mmtp) REVERT: K 34 GLN cc_start: 0.9195 (tp40) cc_final: 0.8978 (mm-40) REVERT: K 72 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7712 (mt-10) REVERT: K 87 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8572 (mmtm) REVERT: L 87 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8646 (mmtp) REVERT: M 87 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8595 (mttm) REVERT: N 87 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8731 (mmtp) REVERT: O 87 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8566 (mttm) REVERT: P 87 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8540 (mmtm) REVERT: Q 87 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8665 (mmtp) REVERT: R 87 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8739 (mmtp) REVERT: S 61 GLN cc_start: 0.8225 (tp40) cc_final: 0.7998 (mm-40) REVERT: S 87 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8623 (mmtm) REVERT: S 129 ASP cc_start: 0.8194 (p0) cc_final: 0.7961 (p0) REVERT: T 87 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8513 (mttm) REVERT: V 87 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8762 (mmtm) REVERT: W 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8695 (mmtm) REVERT: X 43 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8976 (p) REVERT: X 87 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8631 (mmtm) REVERT: X 129 ASP cc_start: 0.8207 (p0) cc_final: 0.7966 (p0) REVERT: Y 87 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8663 (mmtp) REVERT: Z 87 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8644 (mmtp) REVERT: Z 95 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7330 (mp0) REVERT: Z 137 LYS cc_start: 0.8807 (mttt) cc_final: 0.8564 (mttp) REVERT: a 72 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7303 (mt-10) REVERT: a 87 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8734 (mttm) REVERT: b 22 TRP cc_start: 0.8029 (m100) cc_final: 0.7422 (m100) REVERT: b 87 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8567 (mttm) REVERT: c 4 LEU cc_start: 0.8124 (mm) cc_final: 0.7849 (mm) REVERT: c 87 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8725 (mmtp) REVERT: d 43 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8832 (p) REVERT: d 87 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8811 (mmtm) REVERT: e 87 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8533 (mttp) REVERT: f 72 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7553 (mt-10) REVERT: f 87 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8756 (mmtm) REVERT: g 87 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8669 (mmtp) REVERT: g 121 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: h 72 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6711 (pt0) REVERT: h 87 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8678 (mmtp) REVERT: h 110 ARG cc_start: 0.8646 (mtm180) cc_final: 0.8429 (mtm180) REVERT: i 87 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8618 (mmtm) REVERT: k 41 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8569 (mttt) REVERT: k 87 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8515 (mttm) REVERT: l 25 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7511 (t80) REVERT: l 43 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8974 (p) REVERT: l 87 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8481 (mttm) REVERT: m 87 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8601 (mmtm) REVERT: n 87 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8546 (mmtp) REVERT: o 87 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8694 (mmtm) outliers start: 127 outliers final: 88 residues processed: 704 average time/residue: 0.2494 time to fit residues: 280.0193 Evaluate side-chains 672 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 579 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 121 PHE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain W residue 121 PHE Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 102 SER Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain i residue 121 PHE Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 121 PHE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 374 optimal weight: 4.9990 chunk 439 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 549 optimal weight: 6.9990 chunk 432 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 291 optimal weight: 6.9990 chunk 442 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 485 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN Q 33 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 33 GLN i 33 GLN o 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085099 restraints weight = 60266.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088845 restraints weight = 33236.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.091374 restraints weight = 21733.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093050 restraints weight = 15873.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094281 restraints weight = 12564.525| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 41697 Z= 0.333 Angle : 0.658 9.348 57318 Z= 0.363 Chirality : 0.052 0.296 7749 Planarity : 0.006 0.089 6970 Dihedral : 5.231 58.319 5958 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.25 % Allowed : 21.71 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.11), residues: 5658 helix: 1.90 (0.13), residues: 1271 sheet: -2.02 (0.10), residues: 2173 loop : -1.02 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG R 110 TYR 0.045 0.002 TYR Z 53 PHE 0.030 0.002 PHE G 121 TRP 0.018 0.002 TRP m 22 HIS 0.002 0.001 HIS d 130 Details of bonding type rmsd covalent geometry : bond 0.00802 (41656) covalent geometry : angle 0.65786 (57236) SS BOND : bond 0.00398 ( 41) SS BOND : angle 0.53164 ( 82) hydrogen bonds : bond 0.05861 ( 1886) hydrogen bonds : angle 5.46440 ( 5211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 625 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.9158 (p90) cc_final: 0.8909 (p90) REVERT: A 72 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 87 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8631 (mmtp) REVERT: B 87 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8713 (mttp) REVERT: C 87 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8637 (mmtm) REVERT: D 87 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8653 (mmtm) REVERT: E 87 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8427 (mmtm) REVERT: F 87 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8662 (mmtm) REVERT: G 87 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8675 (mmtm) REVERT: H 87 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8632 (mmtm) REVERT: H 92 TYR cc_start: 0.9090 (m-80) cc_final: 0.8844 (m-80) REVERT: I 48 LYS cc_start: 0.9090 (ttpp) cc_final: 0.8844 (ttpp) REVERT: I 87 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8584 (mmtm) REVERT: J 87 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8605 (mmtp) REVERT: J 95 GLU cc_start: 0.7949 (mp0) cc_final: 0.7666 (mp0) REVERT: K 87 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8641 (mmtm) REVERT: L 87 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8694 (mmtp) REVERT: M 87 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8659 (mttm) REVERT: N 87 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8765 (mmtp) REVERT: N 135 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7907 (mm-30) REVERT: O 87 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8623 (mttm) REVERT: P 87 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8626 (mmtm) REVERT: Q 87 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8736 (mmtp) REVERT: R 87 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8819 (mmtp) REVERT: S 87 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8719 (mmtm) REVERT: S 129 ASP cc_start: 0.8321 (p0) cc_final: 0.7991 (p0) REVERT: T 87 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8606 (mttm) REVERT: V 87 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8768 (mmtm) REVERT: W 53 TYR cc_start: 0.9153 (p90) cc_final: 0.8869 (p90) REVERT: W 87 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8692 (mmtm) REVERT: W 95 GLU cc_start: 0.7849 (mp0) cc_final: 0.7479 (mp0) REVERT: X 43 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9043 (p) REVERT: X 87 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8712 (mttm) REVERT: X 129 ASP cc_start: 0.8199 (p0) cc_final: 0.7995 (p0) REVERT: Y 87 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8748 (mmtm) REVERT: Z 87 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8730 (mmtm) REVERT: Z 137 LYS cc_start: 0.8999 (mttt) cc_final: 0.8713 (mttp) REVERT: a 87 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8756 (mttm) REVERT: b 87 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8599 (mttm) REVERT: c 87 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8779 (mmtp) REVERT: d 43 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8860 (p) REVERT: d 87 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8802 (mmtm) REVERT: e 87 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8625 (mttp) REVERT: f 87 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8809 (mmtp) REVERT: g 87 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8762 (mmtp) REVERT: g 121 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: h 87 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8701 (mmtp) REVERT: i 87 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8653 (mmtm) REVERT: k 87 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8566 (mttm) REVERT: k 95 GLU cc_start: 0.7834 (mp0) cc_final: 0.7594 (mp0) REVERT: l 25 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7623 (t80) REVERT: l 87 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8564 (mttm) REVERT: l 92 TYR cc_start: 0.9057 (m-80) cc_final: 0.8845 (m-80) REVERT: m 87 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8688 (mmtm) REVERT: m 137 LYS cc_start: 0.8956 (mttt) cc_final: 0.8746 (mtpp) REVERT: n 87 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8576 (mmtp) REVERT: o 87 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8727 (mmtp) outliers start: 148 outliers final: 101 residues processed: 717 average time/residue: 0.2514 time to fit residues: 287.6086 Evaluate side-chains 674 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 569 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain Q residue 129 ASP Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 121 PHE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain V residue 91 GLU Chi-restraints excluded: chain V residue 121 PHE Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain W residue 121 PHE Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Y residue 121 PHE Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 121 PHE Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 96 LEU Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 13 VAL Chi-restraints excluded: chain j residue 37 LEU Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain k residue 6 ILE Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 91 GLU Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain k residue 129 ASP Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 121 PHE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 467 optimal weight: 2.9990 chunk 363 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 chunk 555 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 338 optimal weight: 0.7980 chunk 500 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN I 33 GLN P 51 ASN Q 33 GLN U 33 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN i 33 GLN m 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094341 restraints weight = 57686.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098492 restraints weight = 31312.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101170 restraints weight = 20105.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103108 restraints weight = 14467.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104446 restraints weight = 11177.858| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41697 Z= 0.136 Angle : 0.535 10.452 57318 Z= 0.294 Chirality : 0.051 0.281 7749 Planarity : 0.005 0.096 6970 Dihedral : 4.714 54.270 5958 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.72 % Allowed : 23.31 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.11), residues: 5658 helix: 2.39 (0.13), residues: 1271 sheet: -1.67 (0.10), residues: 2214 loop : -1.18 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 110 TYR 0.034 0.001 TYR Z 53 PHE 0.016 0.001 PHE H 121 TRP 0.022 0.003 TRP C 22 HIS 0.003 0.000 HIS K 130 Details of bonding type rmsd covalent geometry : bond 0.00317 (41656) covalent geometry : angle 0.53465 (57236) SS BOND : bond 0.00109 ( 41) SS BOND : angle 0.50770 ( 82) hydrogen bonds : bond 0.04777 ( 1886) hydrogen bonds : angle 4.77564 ( 5211) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 649 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 87 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8626 (mmtp) REVERT: B 37 LEU cc_start: 0.9099 (mt) cc_final: 0.8711 (mt) REVERT: B 87 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8826 (mmtp) REVERT: C 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8616 (mmtm) REVERT: D 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8625 (mmtm) REVERT: E 87 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8395 (mmtm) REVERT: F 87 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8676 (mmtm) REVERT: G 87 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8676 (mmtm) REVERT: G 110 ARG cc_start: 0.8804 (mtm180) cc_final: 0.8435 (mtm180) REVERT: G 121 PHE cc_start: 0.7212 (m-80) cc_final: 0.6972 (m-80) REVERT: H 87 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8606 (mmtm) REVERT: H 95 GLU cc_start: 0.7742 (mp0) cc_final: 0.7296 (mp0) REVERT: I 87 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8550 (mmtm) REVERT: J 72 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7448 (mt-10) REVERT: J 87 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8574 (mmtp) REVERT: K 87 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8603 (mmtm) REVERT: L 87 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8716 (mmtp) REVERT: M 87 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8646 (mttm) REVERT: N 87 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8750 (mmtp) REVERT: O 87 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8639 (mttm) REVERT: P 87 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8598 (mmtm) REVERT: Q 87 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8703 (mmtp) REVERT: R 72 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7256 (pt0) REVERT: R 87 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8809 (mmtp) REVERT: S 87 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8686 (mmtm) REVERT: T 87 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8578 (mttm) REVERT: V 87 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8763 (mmtm) REVERT: W 87 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8648 (mmtm) REVERT: W 110 ARG cc_start: 0.9010 (mtm180) cc_final: 0.8798 (mtm180) REVERT: X 43 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9023 (p) REVERT: X 87 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8673 (mmtm) REVERT: X 129 ASP cc_start: 0.8160 (p0) cc_final: 0.7944 (p0) REVERT: Y 87 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8745 (mmtm) REVERT: Z 87 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8755 (mmtm) REVERT: Z 129 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8031 (p0) REVERT: Z 137 LYS cc_start: 0.8843 (mttt) cc_final: 0.8587 (mttp) REVERT: a 87 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8722 (mttm) REVERT: b 22 TRP cc_start: 0.8223 (m100) cc_final: 0.7597 (m100) REVERT: b 87 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8619 (mttm) REVERT: c 87 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8762 (mmtp) REVERT: d 43 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8822 (p) REVERT: d 87 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8785 (mmtm) REVERT: e 87 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8570 (mttp) REVERT: f 87 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8807 (mmtp) REVERT: g 87 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8761 (mmtp) REVERT: g 121 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: h 72 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6868 (pt0) REVERT: h 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8696 (mmtp) REVERT: i 87 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8656 (mmtm) REVERT: k 87 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8595 (mmtm) REVERT: l 25 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7589 (t80) REVERT: l 43 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8988 (p) REVERT: l 87 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8539 (mttm) REVERT: m 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8632 (mmtm) REVERT: n 22 TRP cc_start: 0.8098 (m100) cc_final: 0.7710 (m100) REVERT: n 87 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8538 (mmtp) REVERT: o 22 TRP cc_start: 0.8059 (m100) cc_final: 0.7679 (m100) REVERT: o 87 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8732 (mmtp) outliers start: 124 outliers final: 93 residues processed: 728 average time/residue: 0.2526 time to fit residues: 291.9501 Evaluate side-chains 691 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 592 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain Q residue 129 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 121 PHE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain W residue 121 PHE Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain Z residue 129 ASP Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 37 LEU Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 129 ASP Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain k residue 129 ASP Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 121 PHE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 25 TYR Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 125 optimal weight: 7.9990 chunk 422 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 chunk 548 optimal weight: 0.8980 chunk 361 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 453 optimal weight: 0.6980 chunk 417 optimal weight: 0.9990 chunk 330 optimal weight: 4.9990 chunk 486 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN Q 33 GLN b 51 ASN d 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096479 restraints weight = 57193.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100653 restraints weight = 30995.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103465 restraints weight = 19922.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105364 restraints weight = 14237.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106662 restraints weight = 10980.217| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41697 Z= 0.130 Angle : 0.531 9.189 57318 Z= 0.291 Chirality : 0.050 0.279 7749 Planarity : 0.005 0.048 6970 Dihedral : 4.545 54.313 5958 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.55 % Allowed : 23.29 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.11), residues: 5658 helix: 2.36 (0.13), residues: 1271 sheet: -1.58 (0.10), residues: 2173 loop : -1.18 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 110 TYR 0.041 0.001 TYR O 53 PHE 0.016 0.001 PHE H 121 TRP 0.021 0.003 TRP C 22 HIS 0.001 0.000 HIS K 130 Details of bonding type rmsd covalent geometry : bond 0.00305 (41656) covalent geometry : angle 0.53072 (57236) SS BOND : bond 0.00095 ( 41) SS BOND : angle 0.44315 ( 82) hydrogen bonds : bond 0.04602 ( 1886) hydrogen bonds : angle 4.68588 ( 5211) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 638 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7573 (mt-10) REVERT: A 87 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8584 (mmtp) REVERT: B 87 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8815 (mmtp) REVERT: C 37 LEU cc_start: 0.9301 (mt) cc_final: 0.8946 (mt) REVERT: C 87 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8729 (mmtp) REVERT: D 87 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8619 (mmtm) REVERT: E 25 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7318 (t80) REVERT: E 87 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8403 (mmtm) REVERT: F 87 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8659 (mmtm) REVERT: G 87 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8672 (mmtm) REVERT: G 110 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8425 (mtm180) REVERT: G 121 PHE cc_start: 0.7170 (m-80) cc_final: 0.6892 (m-80) REVERT: H 87 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8590 (mmtm) REVERT: I 87 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8540 (mmtm) REVERT: J 72 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7441 (mt-10) REVERT: J 87 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8578 (mmtp) REVERT: K 87 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8591 (mmtm) REVERT: L 87 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8725 (mmtp) REVERT: M 72 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7614 (pt0) REVERT: M 87 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8638 (mttm) REVERT: N 87 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8748 (mmtp) REVERT: O 87 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8614 (mttm) REVERT: P 87 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8576 (mmtm) REVERT: Q 87 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8664 (mmtp) REVERT: R 87 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8759 (mmtp) REVERT: S 87 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8674 (mmtm) REVERT: T 72 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7351 (pt0) REVERT: T 87 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8561 (mttm) REVERT: T 110 ARG cc_start: 0.8878 (ptm-80) cc_final: 0.8242 (ptm-80) REVERT: V 87 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8752 (mmtm) REVERT: W 87 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8676 (mmtm) REVERT: X 43 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9023 (p) REVERT: X 87 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8627 (mmtm) REVERT: X 129 ASP cc_start: 0.8154 (p0) cc_final: 0.7912 (p0) REVERT: Y 87 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8685 (mmtm) REVERT: Z 87 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8723 (mmtm) REVERT: Z 137 LYS cc_start: 0.8762 (mttt) cc_final: 0.8545 (mttp) REVERT: a 87 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8699 (mttm) REVERT: b 22 TRP cc_start: 0.8135 (m100) cc_final: 0.7468 (m100) REVERT: b 87 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8600 (mttm) REVERT: b 92 TYR cc_start: 0.8899 (m-80) cc_final: 0.8663 (m-80) REVERT: c 87 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8744 (mmtp) REVERT: d 43 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8825 (p) REVERT: d 87 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8799 (mmtm) REVERT: e 72 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7332 (mt-10) REVERT: e 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8533 (mttp) REVERT: f 87 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8769 (mmtp) REVERT: f 95 GLU cc_start: 0.7746 (mp0) cc_final: 0.7396 (mp0) REVERT: g 87 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8714 (mmtp) REVERT: g 121 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: h 72 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7267 (pt0) REVERT: h 87 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8695 (mmtp) REVERT: i 87 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8671 (mmtm) REVERT: k 87 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8571 (mmtm) REVERT: l 25 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7448 (t80) REVERT: l 43 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8958 (p) REVERT: l 71 ILE cc_start: 0.9013 (mt) cc_final: 0.8810 (mm) REVERT: l 87 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8516 (mttm) REVERT: m 87 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8629 (mmtm) REVERT: n 22 TRP cc_start: 0.8015 (m100) cc_final: 0.7710 (m100) REVERT: n 87 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8554 (mmtp) REVERT: o 22 TRP cc_start: 0.7992 (m100) cc_final: 0.7672 (m100) REVERT: o 87 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8678 (mmtm) outliers start: 116 outliers final: 90 residues processed: 708 average time/residue: 0.2572 time to fit residues: 292.3716 Evaluate side-chains 697 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 601 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 121 PHE Chi-restraints excluded: chain S residue 129 ASP Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain V residue 121 PHE Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain W residue 121 PHE Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain i residue 121 PHE Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 37 LEU Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 129 ASP Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 121 PHE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 25 TYR Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 90 optimal weight: 0.0770 chunk 510 optimal weight: 3.9990 chunk 217 optimal weight: 0.0980 chunk 550 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 417 optimal weight: 8.9990 chunk 505 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 531 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 GLN L 55 ASN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN e 33 GLN i 33 GLN m 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097781 restraints weight = 56993.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101983 restraints weight = 30963.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104819 restraints weight = 19886.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106708 restraints weight = 14186.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108002 restraints weight = 10948.425| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41697 Z= 0.130 Angle : 0.530 9.224 57318 Z= 0.292 Chirality : 0.050 0.284 7749 Planarity : 0.004 0.059 6970 Dihedral : 4.451 53.894 5958 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.61 % Allowed : 23.40 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.11), residues: 5658 helix: 2.40 (0.13), residues: 1271 sheet: -1.50 (0.11), residues: 2173 loop : -1.12 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 110 TYR 0.033 0.001 TYR O 53 PHE 0.015 0.001 PHE H 121 TRP 0.021 0.003 TRP C 22 HIS 0.002 0.000 HIS e 130 Details of bonding type rmsd covalent geometry : bond 0.00303 (41656) covalent geometry : angle 0.53006 (57236) SS BOND : bond 0.00092 ( 41) SS BOND : angle 0.40934 ( 82) hydrogen bonds : bond 0.04515 ( 1886) hydrogen bonds : angle 4.61421 ( 5211) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11316 Ramachandran restraints generated. 5658 Oldfield, 0 Emsley, 5658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 635 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.9008 (p90) cc_final: 0.8786 (p90) REVERT: A 72 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 87 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8616 (mmtp) REVERT: B 37 LEU cc_start: 0.9108 (mt) cc_final: 0.8700 (mt) REVERT: B 87 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8817 (mmtp) REVERT: C 22 TRP cc_start: 0.8129 (m100) cc_final: 0.7612 (m100) REVERT: C 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8714 (mmtp) REVERT: D 72 GLU cc_start: 0.7184 (pt0) cc_final: 0.6983 (pt0) REVERT: D 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8619 (mmtm) REVERT: E 25 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7348 (t80) REVERT: E 87 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8361 (mmtm) REVERT: F 87 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8649 (mmtm) REVERT: G 87 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8666 (mmtm) REVERT: G 110 ARG cc_start: 0.8866 (mtm180) cc_final: 0.8362 (mtp180) REVERT: G 121 PHE cc_start: 0.7100 (m-80) cc_final: 0.6844 (m-80) REVERT: H 87 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8588 (mmtm) REVERT: I 87 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8539 (mmtm) REVERT: J 72 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7422 (mt-10) REVERT: J 87 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8571 (mmtm) REVERT: K 87 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8584 (mmtm) REVERT: L 87 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8679 (mmtp) REVERT: M 72 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7521 (pt0) REVERT: M 87 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8618 (mttm) REVERT: N 87 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8798 (mmtp) REVERT: O 87 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8594 (mttm) REVERT: P 87 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8565 (mmtm) REVERT: P 95 GLU cc_start: 0.7899 (mp0) cc_final: 0.7401 (mp0) REVERT: Q 87 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8680 (mmtp) REVERT: R 87 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8761 (mmtp) REVERT: S 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8670 (mmtm) REVERT: T 87 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8561 (mttm) REVERT: V 87 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8714 (mmtm) REVERT: W 87 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8669 (mmtm) REVERT: X 43 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9038 (p) REVERT: X 87 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8630 (mmtm) REVERT: X 129 ASP cc_start: 0.8151 (p0) cc_final: 0.7897 (p0) REVERT: Y 1 MET cc_start: 0.3738 (ptt) cc_final: 0.3485 (ptt) REVERT: Y 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8682 (mmtm) REVERT: Z 87 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8642 (mmtp) REVERT: a 1 MET cc_start: 0.4098 (ptt) cc_final: 0.3747 (ptt) REVERT: a 87 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8726 (mttm) REVERT: b 22 TRP cc_start: 0.7991 (m100) cc_final: 0.7446 (m100) REVERT: b 87 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8582 (mttm) REVERT: c 72 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7148 (pt0) REVERT: c 87 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8696 (mmtm) REVERT: d 43 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8824 (p) REVERT: d 87 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8812 (mmtm) REVERT: e 87 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8538 (mttp) REVERT: f 43 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8920 (p) REVERT: f 87 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8567 (mmtm) REVERT: g 87 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8706 (mmtp) REVERT: g 121 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: h 72 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7127 (pt0) REVERT: i 87 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8652 (mmtm) REVERT: k 87 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8561 (mmtm) REVERT: l 43 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8967 (p) REVERT: l 61 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8062 (mt0) REVERT: l 71 ILE cc_start: 0.8969 (mt) cc_final: 0.8745 (mm) REVERT: l 87 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8510 (mttm) REVERT: m 87 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8628 (mmtm) REVERT: n 87 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8565 (mmtp) REVERT: o 87 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8674 (mmtm) outliers start: 119 outliers final: 98 residues processed: 708 average time/residue: 0.2364 time to fit residues: 268.8688 Evaluate side-chains 701 residues out of total 4551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 597 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 25 TYR Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain F residue 25 TYR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 TYR Chi-restraints excluded: chain H residue 121 PHE Chi-restraints excluded: chain I residue 25 TYR Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 121 PHE Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 25 TYR Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain O residue 110 ARG Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 121 PHE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 129 ASP Chi-restraints excluded: chain T residue 13 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 25 TYR Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 TYR Chi-restraints excluded: chain W residue 121 PHE Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 25 TYR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 TYR Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 110 ARG Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR Chi-restraints excluded: chain f residue 27 THR Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 102 SER Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 25 TYR Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain i residue 121 PHE Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 37 LEU Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 107 LEU Chi-restraints excluded: chain k residue 27 THR Chi-restraints excluded: chain k residue 91 GLU Chi-restraints excluded: chain k residue 118 ILE Chi-restraints excluded: chain k residue 121 PHE Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 118 ILE Chi-restraints excluded: chain m residue 121 PHE Chi-restraints excluded: chain n residue 6 ILE Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 25 TYR Chi-restraints excluded: chain n residue 129 ASP Chi-restraints excluded: chain o residue 118 ILE Chi-restraints excluded: chain o residue 121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 462 optimal weight: 6.9990 chunk 505 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 503 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 268 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 GLN G 33 GLN J 33 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN f 55 ASN i 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094756 restraints weight = 57894.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098870 restraints weight = 31183.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101610 restraints weight = 19970.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103401 restraints weight = 14284.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104771 restraints weight = 11107.659| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41697 Z= 0.163 Angle : 0.552 8.599 57318 Z= 0.304 Chirality : 0.050 0.278 7749 Planarity : 0.005 0.048 6970 Dihedral : 4.526 53.423 5958 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.55 % Allowed : 23.71 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.11), residues: 5658 helix: 2.36 (0.13), residues: 1271 sheet: -1.53 (0.10), residues: 2173 loop : -1.11 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 110 TYR 0.033 0.001 TYR O 53 PHE 0.015 0.002 PHE G 121 TRP 0.018 0.002 TRP C 22 HIS 0.002 0.000 HIS o 130 Details of bonding type rmsd covalent geometry : bond 0.00387 (41656) covalent geometry : angle 0.55266 (57236) SS BOND : bond 0.00158 ( 41) SS BOND : angle 0.40813 ( 82) hydrogen bonds : bond 0.04740 ( 1886) hydrogen bonds : angle 4.79106 ( 5211) =============================================================================== Job complete usr+sys time: 6075.46 seconds wall clock time: 106 minutes 13.12 seconds (6373.12 seconds total)