Starting phenix.real_space_refine on Sat Feb 24 03:23:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8u_21578/02_2024/6w8u_21578.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8u_21578/02_2024/6w8u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8u_21578/02_2024/6w8u_21578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8u_21578/02_2024/6w8u_21578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8u_21578/02_2024/6w8u_21578.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8u_21578/02_2024/6w8u_21578.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A GLU 5": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "I GLU 5": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "M GLU 5": "OE1" <-> "OE2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O GLU 95": "OE1" <-> "OE2" Residue "P GLU 95": "OE1" <-> "OE2" Residue "Q GLU 5": "OE1" <-> "OE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "R GLU 5": "OE1" <-> "OE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "b GLU 5": "OE1" <-> "OE2" Residue "b GLU 95": "OE1" <-> "OE2" Residue "c GLU 5": "OE1" <-> "OE2" Residue "d GLU 5": "OE1" <-> "OE2" Residue "j GLU 5": "OE1" <-> "OE2" Residue "k GLU 5": "OE1" <-> "OE2" Residue "l GLU 5": "OE1" <-> "OE2" Residue "n GLU 5": "OE1" <-> "OE2" Residue "o GLU 5": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 22.16, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 15.21 Conformation dependent library (CDL) restraints added in 8.3 seconds 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: 4.94 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: 16.76 Time building geometry restraints manager: 16.62 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: 100.41 - 107.11: 993 107.11 - 113.82: 26275 113.82 - 120.52: 13918 120.52 - 127.22: 15763 127.22 - 133.93: 287 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 2.440 nonbonded pdb=" OG SER d 3 " pdb=" OE1 GLU f 5 " model vdw 2.064 2.440 nonbonded pdb=" OE1 GLU k 5 " pdb=" OG SER m 3 " model vdw 2.085 2.440 nonbonded pdb=" OG SER T 3 " pdb=" OE1 GLU V 5 " model vdw 2.086 2.440 nonbonded pdb=" OG SER D 3 " pdb=" OE1 GLU F 5 " model vdw 2.102 2.440 ... (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 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.900 Check model and map are aligned: 0.610 Set scattering table: 0.340 Process input model: 107.580 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.650 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.930 ------------------------------------------------------------------------------- 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 41656 Z= 0.280 Angle : 0.541 3.938 57236 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 : 10.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (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 TRP 0.016 0.003 TRP d 22 HIS 0.001 0.000 HIS k 130 PHE 0.008 0.002 PHE I 121 TYR 0.013 0.002 TYR K 25 ARG 0.003 0.000 ARG o 110 *********************** 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 fitting. rotamer outliers: 22 poor density : 817 time to evaluate : 4.628 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: 0.5679 time to fit residues: 753.6901 Evaluate side-chains 633 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 617 time to evaluate : 4.639 ------------------------------------------------------------------------------- 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 484 optimal weight: 9.9990 chunk 435 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 148 optimal weight: 0.0070 chunk 293 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 449 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 273 optimal weight: 0.4980 chunk 334 optimal weight: 8.9990 chunk 521 optimal weight: 2.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 ASN ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN l 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41656 Z= 0.171 Angle : 0.483 4.231 57236 Z= 0.275 Chirality : 0.049 0.197 7749 Planarity : 0.005 0.043 6970 Dihedral : 5.008 53.695 5963 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.57 % Allowed : 11.93 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.10), residues: 5658 helix: 1.51 (0.13), residues: 1271 sheet: -2.18 (0.09), residues: 2214 loop : -1.73 (0.11), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 22 HIS 0.000 0.000 HIS F 130 PHE 0.008 0.001 PHE Y 121 TYR 0.015 0.001 TYR S 92 ARG 0.002 0.000 ARG j 110 *********************** 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 874 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 757 time to evaluate : 4.288 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: 0.8957 (mmtt) cc_final: 0.8594 (mttm) REVERT: B 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8660 (mmtp) REVERT: C 34 GLN cc_start: 0.9217 (tp40) cc_final: 0.9002 (mm-40) REVERT: C 87 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8586 (mmtp) REVERT: D 34 GLN cc_start: 0.9295 (tp40) cc_final: 0.9003 (mm-40) REVERT: D 87 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8507 (mttm) REVERT: E 87 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8263 (mttp) REVERT: F 34 GLN cc_start: 0.9254 (tp40) cc_final: 0.9019 (mm-40) REVERT: F 87 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8571 (mttm) REVERT: F 121 PHE cc_start: 0.7615 (m-10) cc_final: 0.7364 (m-80) REVERT: G 87 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8437 (mmtm) REVERT: H 87 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8549 (mttm) REVERT: H 92 TYR cc_start: 0.9004 (m-80) cc_final: 0.8786 (m-80) REVERT: I 51 ASN cc_start: 0.8275 (m-40) cc_final: 0.8020 (m-40) REVERT: I 87 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8604 (mmtm) REVERT: I 121 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: J 87 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8475 (mttp) REVERT: K 34 GLN cc_start: 0.9186 (tp40) cc_final: 0.8654 (mm-40) REVERT: K 61 GLN cc_start: 0.8434 (tp40) cc_final: 0.8199 (mm-40) REVERT: K 87 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8478 (mmtm) REVERT: L 61 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: L 87 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8607 (mttm) REVERT: L 95 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7767 (mt-10) REVERT: L 121 PHE cc_start: 0.7564 (m-10) cc_final: 0.7314 (m-10) REVERT: L 137 LYS cc_start: 0.8817 (mttp) cc_final: 0.8483 (mttm) REVERT: M 87 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8629 (mttm) REVERT: N 87 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8628 (mttp) REVERT: O 34 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8669 (mm-40) REVERT: O 87 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8617 (mttm) REVERT: P 87 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8557 (mmtm) REVERT: Q 87 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8613 (mttm) REVERT: R 87 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8717 (mmtp) REVERT: S 87 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8576 (mmtm) REVERT: T 34 GLN cc_start: 0.9304 (tp40) cc_final: 0.9063 (mm-40) REVERT: T 61 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8166 (mm-40) REVERT: T 87 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8514 (mttm) REVERT: U 87 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8458 (mmtp) REVERT: V 87 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8609 (mmtp) REVERT: W 87 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8524 (mmtm) REVERT: X 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8457 (mmtm) REVERT: X 129 ASP cc_start: 0.8341 (p0) cc_final: 0.8129 (p0) REVERT: Y 87 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8679 (mttm) REVERT: Z 87 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8504 (mmtm) REVERT: a 87 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8659 (mttm) REVERT: b 22 TRP cc_start: 0.7848 (m100) cc_final: 0.7302 (m100) REVERT: b 37 LEU cc_start: 0.9229 (mt) cc_final: 0.9019 (mt) REVERT: b 87 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8631 (mttm) REVERT: b 113 LEU cc_start: 0.8874 (mt) cc_final: 0.8662 (mt) REVERT: c 87 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8604 (mttm) REVERT: d 34 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8838 (mm-40) REVERT: d 87 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8576 (mmtm) REVERT: e 87 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8535 (mttm) REVERT: e 95 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7642 (mt-10) REVERT: f 87 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8479 (mmtm) REVERT: g 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8640 (mmtp) REVERT: h 87 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8658 (mmtp) REVERT: h 92 TYR cc_start: 0.8940 (m-80) cc_final: 0.8723 (m-10) REVERT: i 87 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8575 (mttm) REVERT: i 92 TYR cc_start: 0.8912 (m-80) cc_final: 0.8550 (m-80) REVERT: j 87 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8629 (mttm) REVERT: k 87 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8558 (mttm) REVERT: l 87 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8531 (mttm) REVERT: m 87 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8566 (mmtm) REVERT: n 87 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8599 (mttm) REVERT: n 129 ASP cc_start: 0.8439 (p0) cc_final: 0.8044 (p0) REVERT: o 87 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8488 (mmtp) REVERT: o 129 ASP cc_start: 0.8321 (p0) cc_final: 0.7997 (p0) outliers start: 117 outliers final: 60 residues processed: 811 average time/residue: 0.5406 time to fit residues: 715.4103 Evaluate side-chains 709 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 646 time to evaluate : 4.465 ------------------------------------------------------------------------------- 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 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 G residue 49 ASP Chi-restraints excluded: chain H residue 13 VAL 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 J residue 49 ASP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 25 TYR Chi-restraints excluded: chain L residue 61 GLN 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 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 a residue 136 ASN 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 e residue 49 ASP Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 TYR 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 h residue 49 ASP Chi-restraints excluded: chain i residue 25 TYR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 433 optimal weight: 7.9990 chunk 354 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 522 optimal weight: 6.9990 chunk 564 optimal weight: 2.9990 chunk 465 optimal weight: 3.9990 chunk 517 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 418 optimal weight: 0.4980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 S 51 ASN W 51 ASN b 51 ASN e 51 ASN f 51 ASN g 51 ASN i 51 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 41656 Z= 0.250 Angle : 0.490 4.662 57236 Z= 0.276 Chirality : 0.048 0.199 7749 Planarity : 0.005 0.048 6970 Dihedral : 4.876 58.021 5959 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.50 % Allowed : 16.44 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.10), residues: 5658 helix: 1.89 (0.13), residues: 1271 sheet: -2.06 (0.10), residues: 2214 loop : -1.58 (0.11), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 22 HIS 0.001 0.000 HIS F 130 PHE 0.014 0.001 PHE K 121 TYR 0.017 0.001 TYR M 25 ARG 0.002 0.000 ARG o 110 *********************** 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 771 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 657 time to evaluate : 4.376 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: 0.8903 (mmtt) cc_final: 0.8564 (mttm) REVERT: B 37 LEU cc_start: 0.9318 (mt) cc_final: 0.9072 (mt) REVERT: B 87 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8640 (mmtp) REVERT: C 87 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8465 (mmtm) REVERT: D 25 TYR cc_start: 0.8700 (m-80) cc_final: 0.8496 (m-80) REVERT: D 34 GLN cc_start: 0.9297 (tp40) cc_final: 0.9052 (mm-40) REVERT: D 87 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8531 (mttm) REVERT: D 92 TYR cc_start: 0.8977 (m-80) cc_final: 0.8621 (m-10) REVERT: E 87 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8332 (mmtp) REVERT: F 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8594 (mttm) REVERT: G 87 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8473 (mmtm) REVERT: H 87 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8524 (mttm) REVERT: I 87 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8613 (mmtm) REVERT: I 121 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: J 87 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8515 (mmtm) REVERT: K 34 GLN cc_start: 0.9258 (tp40) cc_final: 0.9036 (mm-40) REVERT: K 87 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8502 (mmtm) REVERT: L 87 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8619 (mmtp) REVERT: L 137 LYS cc_start: 0.8812 (mttp) cc_final: 0.8596 (mttp) REVERT: M 87 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8595 (mttm) REVERT: N 87 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8589 (mttp) REVERT: O 87 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8610 (mttm) REVERT: P 87 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8565 (mmtm) REVERT: Q 87 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8608 (mttm) REVERT: R 87 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8730 (mmtp) REVERT: S 61 GLN cc_start: 0.8321 (tp40) cc_final: 0.8066 (mm-40) REVERT: S 87 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8620 (mmtm) REVERT: T 87 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8520 (mttm) REVERT: U 87 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8479 (mmtp) REVERT: V 87 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8630 (mmtp) REVERT: W 87 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8605 (mmtm) REVERT: X 87 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8492 (mmtm) REVERT: X 129 ASP cc_start: 0.8303 (p0) cc_final: 0.8095 (p0) REVERT: X 137 LYS cc_start: 0.8774 (mttp) cc_final: 0.8554 (mttm) REVERT: Y 37 LEU cc_start: 0.9152 (mt) cc_final: 0.8943 (mt) REVERT: Y 87 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8722 (mttm) REVERT: Z 87 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8567 (mmtp) REVERT: Z 137 LYS cc_start: 0.8945 (mttt) cc_final: 0.8659 (mttp) REVERT: a 87 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8673 (mttm) REVERT: b 22 TRP cc_start: 0.8099 (m100) cc_final: 0.7407 (m100) REVERT: b 87 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8585 (mttm) REVERT: c 87 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8592 (mttm) REVERT: d 87 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8613 (mmtm) REVERT: d 129 ASP cc_start: 0.8360 (p0) cc_final: 0.8103 (p0) REVERT: e 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8463 (mttp) REVERT: e 95 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7660 (mt-10) REVERT: f 87 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8520 (mmtm) REVERT: f 95 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7643 (mt-10) REVERT: g 87 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8659 (mmtp) REVERT: g 121 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7623 (m-10) REVERT: h 25 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: h 87 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8686 (mmtp) REVERT: h 95 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7702 (mp0) REVERT: i 87 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8577 (mttm) REVERT: i 92 TYR cc_start: 0.9022 (m-80) cc_final: 0.8635 (m-80) REVERT: k 41 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8379 (mttt) REVERT: k 87 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8540 (mttm) REVERT: l 25 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7499 (t80) REVERT: l 87 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8535 (mttm) REVERT: m 87 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8560 (mmtm) REVERT: n 87 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8601 (mttm) REVERT: n 129 ASP cc_start: 0.8458 (p0) cc_final: 0.8094 (p0) REVERT: o 87 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8521 (mmtm) REVERT: o 95 GLU cc_start: 0.7867 (mp0) cc_final: 0.7607 (mp0) REVERT: o 129 ASP cc_start: 0.8336 (p0) cc_final: 0.8043 (p0) outliers start: 114 outliers final: 83 residues processed: 718 average time/residue: 0.5853 time to fit residues: 674.6015 Evaluate side-chains 692 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 605 time to evaluate : 4.678 ------------------------------------------------------------------------------- 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 C residue 13 VAL Chi-restraints excluded: chain C residue 25 TYR Chi-restraints excluded: chain C residue 49 ASP 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 G residue 49 ASP Chi-restraints excluded: chain H residue 13 VAL 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 N residue 49 ASP Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain O residue 49 ASP 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 49 ASP 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 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 a residue 136 ASN 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 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 49 ASP 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 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 25 TYR Chi-restraints excluded: chain h residue 27 THR Chi-restraints excluded: chain h residue 49 ASP Chi-restraints excluded: chain i residue 25 TYR Chi-restraints excluded: chain i residue 49 ASP 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 6 ILE Chi-restraints excluded: chain j residue 13 VAL Chi-restraints excluded: chain k residue 118 ILE 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 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 49 ASP 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 515 optimal weight: 3.9990 chunk 392 optimal weight: 0.9980 chunk 271 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 249 optimal weight: 0.0670 chunk 350 optimal weight: 2.9990 chunk 524 optimal weight: 0.7980 chunk 554 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 496 optimal weight: 5.9990 chunk 149 optimal weight: 0.0870 overall best weight: 0.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN L 51 ASN N 51 ASN S 51 ASN ** U 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 ASN b 51 ASN f 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41656 Z= 0.190 Angle : 0.463 4.435 57236 Z= 0.263 Chirality : 0.048 0.214 7749 Planarity : 0.005 0.053 6970 Dihedral : 4.768 59.841 5958 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.15 % Allowed : 18.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 5658 helix: 2.13 (0.13), residues: 1271 sheet: -1.81 (0.10), residues: 2173 loop : -1.50 (0.11), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 22 HIS 0.000 0.000 HIS X 130 PHE 0.017 0.001 PHE F 121 TYR 0.016 0.001 TYR K 25 ARG 0.001 0.000 ARG o 110 *********************** 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 761 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 663 time to evaluate : 4.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8560 (mmtp) REVERT: B 37 LEU cc_start: 0.9315 (mt) cc_final: 0.9063 (mt) REVERT: B 87 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8635 (mmtp) REVERT: C 87 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8448 (mmtm) REVERT: D 34 GLN cc_start: 0.9275 (tp40) cc_final: 0.9039 (mm-40) REVERT: D 87 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8552 (mmtm) REVERT: E 87 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8330 (mmtp) REVERT: F 48 LYS cc_start: 0.9270 (mtmt) cc_final: 0.9040 (mtmm) REVERT: F 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8569 (mttm) REVERT: G 87 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8458 (mmtm) REVERT: H 87 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8569 (mttm) REVERT: I 87 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8603 (mmtm) REVERT: J 87 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8519 (mmtm) REVERT: K 87 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8525 (mmtm) REVERT: L 87 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8622 (mmtp) REVERT: M 87 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8593 (mttm) REVERT: N 41 LYS cc_start: 0.8805 (mttt) cc_final: 0.8522 (mttp) REVERT: N 87 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8729 (mmtm) REVERT: O 87 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8575 (mttm) REVERT: P 87 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8545 (mmtm) REVERT: Q 87 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8601 (mttm) REVERT: R 87 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8693 (mmtp) REVERT: S 61 GLN cc_start: 0.8259 (tp40) cc_final: 0.8046 (mm-40) REVERT: S 87 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8614 (mmtm) REVERT: S 129 ASP cc_start: 0.8390 (p0) cc_final: 0.8008 (p0) REVERT: T 87 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8529 (mttm) REVERT: T 95 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7501 (mt-10) REVERT: U 87 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8500 (mmtp) REVERT: V 87 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8629 (mmtp) REVERT: W 87 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8602 (mmtm) REVERT: X 43 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9010 (p) REVERT: X 87 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8443 (mmtm) REVERT: X 129 ASP cc_start: 0.8223 (p0) cc_final: 0.7970 (p0) REVERT: Y 37 LEU cc_start: 0.9159 (mt) cc_final: 0.8946 (mt) REVERT: Y 87 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8709 (mttm) REVERT: Z 87 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8553 (mmtp) REVERT: Z 137 LYS cc_start: 0.8897 (mttt) cc_final: 0.8676 (mttp) REVERT: a 87 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8645 (mttm) REVERT: b 87 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8575 (mttm) REVERT: c 87 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8599 (mttm) REVERT: d 87 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8685 (mmtm) REVERT: d 129 ASP cc_start: 0.8316 (p0) cc_final: 0.8063 (p0) REVERT: e 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8479 (mttp) REVERT: e 95 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7666 (mt-10) REVERT: f 87 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8520 (mmtm) REVERT: g 87 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8676 (mmtp) REVERT: g 121 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: h 25 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: h 87 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8675 (mmtp) REVERT: i 87 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8429 (mttm) REVERT: i 92 TYR cc_start: 0.9016 (m-80) cc_final: 0.8657 (m-80) REVERT: j 1 MET cc_start: 0.3990 (mtt) cc_final: 0.3683 (mtt) REVERT: k 41 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8344 (mttt) REVERT: k 87 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8534 (mttm) REVERT: l 25 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7394 (t80) REVERT: l 87 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8490 (mttm) REVERT: m 87 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8574 (mmtm) REVERT: n 87 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8594 (mttm) REVERT: n 129 ASP cc_start: 0.8409 (p0) cc_final: 0.8045 (p0) REVERT: o 87 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8529 (mmtm) REVERT: o 129 ASP cc_start: 0.8282 (p0) cc_final: 0.8000 (p0) outliers start: 98 outliers final: 74 residues processed: 722 average time/residue: 0.5567 time to fit residues: 652.0647 Evaluate side-chains 683 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 605 time to evaluate : 4.945 ------------------------------------------------------------------------------- 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 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 C 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 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 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 136 ASN 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 78 ILE 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 49 ASP 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 i residue 25 TYR 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 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 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 462 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 413 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 473 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 498 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 51 ASN C 33 GLN D 33 GLN E 33 GLN G 33 GLN I 33 GLN K 33 GLN M 33 GLN N 33 GLN N 51 ASN O 33 GLN Q 33 GLN R 33 GLN S 33 GLN W 51 ASN Y 33 GLN b 51 ASN c 33 GLN d 33 GLN f 51 ASN g 33 GLN i 33 GLN m 33 GLN o 33 GLN o 61 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 41656 Z= 0.452 Angle : 0.590 5.591 57236 Z= 0.327 Chirality : 0.050 0.260 7749 Planarity : 0.005 0.059 6970 Dihedral : 5.143 59.433 5958 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.12 % Allowed : 20.59 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.11), residues: 5658 helix: 1.88 (0.13), residues: 1271 sheet: -2.09 (0.10), residues: 2255 loop : -1.39 (0.12), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Z 22 HIS 0.001 0.000 HIS F 130 PHE 0.029 0.002 PHE F 121 TYR 0.018 0.002 TYR c 23 ARG 0.004 0.001 ARG o 110 *********************** 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 767 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 625 time to evaluate : 4.572 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 87 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8581 (mmtp) REVERT: B 37 LEU cc_start: 0.9371 (mt) cc_final: 0.9122 (mt) REVERT: B 87 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8668 (mmtp) REVERT: C 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8553 (mmtm) REVERT: D 34 GLN cc_start: 0.9369 (tp40) cc_final: 0.9152 (mm-40) REVERT: D 87 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8560 (mmtm) REVERT: E 87 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8323 (mmtp) REVERT: F 87 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8626 (mmtm) REVERT: G 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8628 (mmtm) REVERT: H 87 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8541 (mttm) REVERT: I 48 LYS cc_start: 0.9201 (ttpp) cc_final: 0.8968 (ttpp) REVERT: I 87 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8631 (mmtm) REVERT: I 121 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7285 (m-10) REVERT: J 87 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8571 (mmtm) REVERT: J 95 GLU cc_start: 0.8053 (mp0) cc_final: 0.7771 (mp0) REVERT: K 87 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8524 (mmtm) REVERT: L 87 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8630 (mmtp) REVERT: M 87 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8641 (mttm) REVERT: N 87 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8615 (mttp) REVERT: N 95 GLU cc_start: 0.8069 (mp0) cc_final: 0.7804 (mp0) REVERT: O 87 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8613 (mttm) REVERT: P 87 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8574 (mmtm) REVERT: Q 87 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8699 (mmtp) REVERT: R 87 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8789 (mmtp) REVERT: S 87 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8688 (mmtm) REVERT: S 129 ASP cc_start: 0.8474 (p0) cc_final: 0.8106 (p0) REVERT: T 87 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8568 (mttm) REVERT: U 87 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8504 (mmtp) REVERT: V 87 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8717 (mmtp) REVERT: W 87 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8663 (mmtm) REVERT: X 43 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9042 (p) REVERT: X 87 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8602 (mmtm) REVERT: X 129 ASP cc_start: 0.8302 (p0) cc_final: 0.8068 (p0) REVERT: Y 87 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8725 (mttm) REVERT: Z 87 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8566 (mmtp) REVERT: Z 137 LYS cc_start: 0.9013 (mttt) cc_final: 0.8733 (mttp) REVERT: a 87 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8672 (mttm) REVERT: b 87 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8556 (mttm) REVERT: c 87 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8669 (mttm) REVERT: d 87 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8714 (mmtm) REVERT: d 129 ASP cc_start: 0.8380 (p0) cc_final: 0.8112 (p0) REVERT: e 87 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8517 (mttp) REVERT: e 95 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7644 (mt-10) REVERT: f 87 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8668 (mmtm) REVERT: g 87 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8696 (mmtp) REVERT: g 121 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7525 (m-10) REVERT: h 87 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8727 (mmtp) REVERT: i 87 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8484 (mttm) REVERT: i 92 TYR cc_start: 0.9056 (m-80) cc_final: 0.8620 (m-80) REVERT: k 87 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8503 (mttm) REVERT: l 25 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7590 (t80) REVERT: l 87 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8558 (mttm) REVERT: m 87 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8649 (mmtm) REVERT: n 87 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8651 (mttm) REVERT: n 129 ASP cc_start: 0.8545 (p0) cc_final: 0.8192 (p0) REVERT: o 87 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8696 (mmtp) REVERT: o 129 ASP cc_start: 0.8392 (p0) cc_final: 0.8097 (p0) outliers start: 142 outliers final: 101 residues processed: 703 average time/residue: 0.5763 time to fit residues: 642.1731 Evaluate side-chains 679 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 574 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 25 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 49 ASP 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 G residue 49 ASP Chi-restraints excluded: chain H residue 13 VAL 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 I residue 121 PHE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 49 ASP 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 M residue 27 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 N residue 49 ASP Chi-restraints excluded: chain O residue 25 TYR Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 49 ASP Chi-restraints excluded: chain P residue 25 TYR Chi-restraints excluded: chain Q residue 25 TYR Chi-restraints excluded: chain Q residue 49 ASP Chi-restraints excluded: chain Q residue 121 PHE 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 49 ASP 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 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 25 TYR 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 49 ASP Chi-restraints excluded: chain a residue 95 GLU Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain a residue 136 ASN Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain e residue 25 TYR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 ASP 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 i residue 1 MET Chi-restraints excluded: chain i residue 27 THR Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 102 SER Chi-restraints excluded: chain i residue 118 ILE Chi-restraints excluded: chain j residue 1 MET 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 k residue 27 THR Chi-restraints excluded: chain k residue 49 ASP 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 13 VAL Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 49 ASP 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 49 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 186 optimal weight: 0.9990 chunk 499 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 555 optimal weight: 5.9990 chunk 461 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 291 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN D 33 GLN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN G 33 GLN I 33 GLN K 33 GLN M 33 GLN N 33 GLN O 33 GLN P 51 ASN R 33 GLN Y 33 GLN c 33 GLN d 33 GLN g 33 GLN i 33 GLN m 33 GLN m 61 GLN o 33 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41656 Z= 0.215 Angle : 0.506 9.904 57236 Z= 0.281 Chirality : 0.049 0.248 7749 Planarity : 0.004 0.047 6970 Dihedral : 4.603 59.605 5954 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.70 % Allowed : 21.60 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.11), residues: 5658 helix: 2.23 (0.13), residues: 1271 sheet: -1.74 (0.10), residues: 2173 loop : -1.36 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP d 22 HIS 0.000 0.000 HIS X 130 PHE 0.014 0.001 PHE W 121 TYR 0.014 0.001 TYR S 92 ARG 0.002 0.000 ARG E 110 *********************** 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 747 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 624 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8549 (mmtp) REVERT: B 37 LEU cc_start: 0.9359 (mt) cc_final: 0.9118 (mt) REVERT: B 87 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8694 (mmtp) REVERT: C 87 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8521 (mmtm) REVERT: D 34 GLN cc_start: 0.9299 (tp40) cc_final: 0.9039 (mm-40) REVERT: D 87 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8566 (mttm) REVERT: E 87 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8344 (mmtm) REVERT: F 87 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8628 (mmtm) REVERT: G 87 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8551 (mmtm) REVERT: H 87 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8548 (mmtm) REVERT: I 87 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8577 (mmtm) REVERT: I 121 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6973 (m-10) REVERT: J 87 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8547 (mmtm) REVERT: K 87 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8506 (mmtm) REVERT: L 87 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8650 (mmtp) REVERT: M 87 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8633 (mttm) REVERT: N 87 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8648 (mttp) REVERT: O 87 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8639 (mttm) REVERT: P 87 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8576 (mmtm) REVERT: Q 87 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8681 (mmtp) REVERT: R 87 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8802 (mmtp) REVERT: S 61 GLN cc_start: 0.8089 (tp40) cc_final: 0.7882 (mm-40) REVERT: S 87 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8674 (mmtm) REVERT: S 129 ASP cc_start: 0.8384 (p0) cc_final: 0.8034 (p0) REVERT: T 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8588 (mttm) REVERT: U 87 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8479 (mmtp) REVERT: V 87 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8712 (mmtp) REVERT: W 87 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8610 (mmtm) REVERT: X 43 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9046 (p) REVERT: X 87 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8583 (mmtm) REVERT: X 129 ASP cc_start: 0.8230 (p0) cc_final: 0.7967 (p0) REVERT: X 137 LYS cc_start: 0.8794 (mttp) cc_final: 0.8586 (mttm) REVERT: Y 87 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8731 (mttm) REVERT: Z 87 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8597 (mmtp) REVERT: Z 137 LYS cc_start: 0.8913 (mttt) cc_final: 0.8651 (mttp) REVERT: a 87 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8656 (mttm) REVERT: b 87 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8580 (mttm) REVERT: c 87 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8602 (mttm) REVERT: c 121 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: d 43 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8795 (p) REVERT: d 87 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8737 (mmtm) REVERT: d 129 ASP cc_start: 0.8320 (p0) cc_final: 0.8073 (p0) REVERT: e 87 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8531 (mttp) REVERT: f 87 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8743 (mmtm) REVERT: g 87 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8695 (mmtp) REVERT: g 121 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: h 87 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8723 (mmtp) REVERT: i 87 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8474 (mttm) REVERT: i 92 TYR cc_start: 0.9021 (m-80) cc_final: 0.8595 (m-80) REVERT: j 1 MET cc_start: 0.4853 (OUTLIER) cc_final: 0.4486 (mtt) REVERT: k 87 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8513 (mttm) REVERT: l 25 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7512 (t80) REVERT: l 43 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9054 (p) REVERT: l 87 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8535 (mttm) REVERT: m 87 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8609 (mmtm) REVERT: n 22 TRP cc_start: 0.8099 (m100) cc_final: 0.7656 (m100) REVERT: n 87 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8631 (mttm) REVERT: n 129 ASP cc_start: 0.8410 (p0) cc_final: 0.8012 (p0) REVERT: o 87 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8633 (mmtm) REVERT: o 129 ASP cc_start: 0.8258 (p0) cc_final: 0.7965 (p0) outliers start: 123 outliers final: 84 residues processed: 696 average time/residue: 0.5540 time to fit residues: 626.3101 Evaluate side-chains 681 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 589 time to evaluate : 4.413 ------------------------------------------------------------------------------- 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 13 VAL 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 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 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 J residue 49 ASP 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 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 49 ASP 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 14 LEU 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 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 a residue 136 ASN Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 25 TYR Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 121 PHE Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 25 TYR Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 25 TYR 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 2 THR Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL 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 1 MET 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 13 VAL 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 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 535 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 316 optimal weight: 0.9990 chunk 405 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 467 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 553 optimal weight: 0.0020 chunk 346 optimal weight: 6.9990 chunk 337 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN P 51 ASN S 51 ASN W 51 ASN m 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41656 Z= 0.198 Angle : 0.494 9.963 57236 Z= 0.272 Chirality : 0.048 0.252 7749 Planarity : 0.004 0.048 6970 Dihedral : 4.437 59.065 5954 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.46 % Allowed : 22.28 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.11), residues: 5658 helix: 2.25 (0.13), residues: 1271 sheet: -1.60 (0.11), residues: 2173 loop : -1.24 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP d 22 HIS 0.000 0.000 HIS d 130 PHE 0.011 0.001 PHE G 121 TYR 0.025 0.001 TYR H 53 ARG 0.001 0.000 ARG I 110 *********************** 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 762 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 650 time to evaluate : 4.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8541 (mmtp) REVERT: B 87 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8719 (mmtp) REVERT: C 22 TRP cc_start: 0.8196 (m100) cc_final: 0.7639 (m100) REVERT: C 87 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8511 (mmtm) REVERT: D 34 GLN cc_start: 0.9285 (tp40) cc_final: 0.9032 (mm-40) REVERT: D 87 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8580 (mmtm) REVERT: E 87 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8320 (mmtm) REVERT: F 87 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8599 (mmtm) REVERT: G 87 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8558 (mmtm) REVERT: H 87 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8535 (mmtm) REVERT: I 87 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8562 (mmtm) REVERT: I 121 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6915 (m-10) REVERT: J 87 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8542 (mmtm) REVERT: K 87 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8487 (mmtm) REVERT: L 87 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8656 (mmtp) REVERT: M 87 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8624 (mttm) REVERT: N 87 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8727 (mmtp) REVERT: O 87 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8616 (mttm) REVERT: P 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8561 (mmtm) REVERT: Q 87 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8683 (mmtp) REVERT: R 87 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8757 (mmtp) REVERT: S 37 LEU cc_start: 0.9406 (mt) cc_final: 0.9084 (mt) REVERT: S 61 GLN cc_start: 0.8069 (tp40) cc_final: 0.7748 (mt0) REVERT: S 87 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8657 (mmtm) REVERT: S 129 ASP cc_start: 0.8321 (p0) cc_final: 0.8003 (p0) REVERT: T 87 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8578 (mttm) REVERT: U 87 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8483 (mmtp) REVERT: V 87 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8696 (mmtp) REVERT: W 87 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8631 (mmtm) REVERT: X 43 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9025 (p) REVERT: X 87 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8568 (mmtm) REVERT: X 129 ASP cc_start: 0.8199 (p0) cc_final: 0.7900 (p0) REVERT: Y 48 LYS cc_start: 0.9296 (mtmt) cc_final: 0.9043 (mtmm) REVERT: Y 87 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8731 (mmtm) REVERT: Z 53 TYR cc_start: 0.9021 (p90) cc_final: 0.8792 (p90) REVERT: Z 87 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8555 (mmtp) REVERT: Z 137 LYS cc_start: 0.8878 (mttt) cc_final: 0.8622 (mttp) REVERT: a 87 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8630 (mttm) REVERT: b 87 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8547 (mttm) REVERT: c 87 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8514 (mttp) REVERT: d 43 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8798 (p) REVERT: d 87 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8747 (mmtm) REVERT: e 87 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8519 (mttp) REVERT: f 87 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8712 (mmtm) REVERT: g 87 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8712 (mmtp) REVERT: g 121 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: h 87 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8749 (mmtp) REVERT: i 87 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8559 (mmtm) REVERT: i 92 TYR cc_start: 0.8988 (m-80) cc_final: 0.8497 (m-80) REVERT: j 1 MET cc_start: 0.4369 (OUTLIER) cc_final: 0.4041 (mtt) REVERT: k 87 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8546 (mmtm) REVERT: l 25 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7484 (t80) REVERT: l 43 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9041 (p) REVERT: l 87 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8512 (mttm) REVERT: l 92 TYR cc_start: 0.8967 (m-80) cc_final: 0.8704 (m-80) REVERT: m 87 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8610 (mmtm) REVERT: n 87 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8652 (mmtp) REVERT: n 129 ASP cc_start: 0.8385 (p0) cc_final: 0.7962 (p0) REVERT: o 1 MET cc_start: 0.3768 (mtp) cc_final: 0.3474 (mtp) REVERT: o 22 TRP cc_start: 0.8026 (m100) cc_final: 0.7577 (m100) REVERT: o 87 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8603 (mmtm) REVERT: o 129 ASP cc_start: 0.8213 (p0) cc_final: 0.7967 (p0) outliers start: 112 outliers final: 79 residues processed: 719 average time/residue: 0.5474 time to fit residues: 637.2865 Evaluate side-chains 688 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 602 time to evaluate : 4.585 ------------------------------------------------------------------------------- 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 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 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 121 PHE Chi-restraints excluded: chain H residue 13 VAL 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 J residue 66 VAL Chi-restraints excluded: chain L residue 13 VAL 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 U residue 13 VAL Chi-restraints excluded: chain U residue 49 ASP 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 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 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 136 ASN Chi-restraints excluded: chain b residue 13 VAL 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 d residue 43 THR Chi-restraints excluded: chain d residue 78 ILE 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 121 PHE Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 13 VAL 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 1 MET 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 l residue 13 VAL Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR 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 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 342 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 351 optimal weight: 5.9990 chunk 376 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 434 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 P 51 ASN S 51 ASN m 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41656 Z= 0.269 Angle : 0.527 9.468 57236 Z= 0.289 Chirality : 0.049 0.269 7749 Planarity : 0.004 0.050 6970 Dihedral : 4.496 59.232 5954 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.88 % Allowed : 22.81 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.11), residues: 5658 helix: 2.21 (0.13), residues: 1271 sheet: -1.61 (0.11), residues: 2173 loop : -1.16 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 22 HIS 0.001 0.000 HIS d 130 PHE 0.019 0.002 PHE D 121 TYR 0.041 0.001 TYR G 53 ARG 0.002 0.001 ARG o 110 *********************** 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 729 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 598 time to evaluate : 4.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8568 (mmtp) REVERT: B 87 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8749 (mmtp) REVERT: C 87 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8554 (mmtm) REVERT: D 34 GLN cc_start: 0.9319 (tp40) cc_final: 0.9043 (mm-40) REVERT: D 87 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8596 (mmtm) REVERT: E 25 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7211 (t80) REVERT: E 87 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8377 (mmtm) REVERT: F 87 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8575 (mmtm) REVERT: G 87 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8612 (mmtm) REVERT: H 87 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8540 (mmtm) REVERT: I 48 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8958 (ttpp) REVERT: I 87 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8568 (mmtm) REVERT: I 121 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: J 87 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8537 (mmtp) REVERT: K 87 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8483 (mmtm) REVERT: L 87 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8670 (mmtp) REVERT: M 87 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8629 (mttm) REVERT: N 87 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8730 (mmtp) REVERT: O 87 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8617 (mttm) REVERT: P 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8569 (mmtm) REVERT: Q 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8725 (mmtp) REVERT: R 87 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8822 (mmtp) REVERT: S 61 GLN cc_start: 0.8114 (tp40) cc_final: 0.7911 (mm-40) REVERT: S 87 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8653 (mmtm) REVERT: S 129 ASP cc_start: 0.8337 (p0) cc_final: 0.8002 (p0) REVERT: T 43 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.9031 (p) REVERT: T 87 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8570 (mttm) REVERT: U 87 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8485 (mmtp) REVERT: V 87 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8684 (mmtp) REVERT: V 129 ASP cc_start: 0.8306 (p0) cc_final: 0.8055 (p0) REVERT: W 87 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8607 (mmtm) REVERT: X 43 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9018 (p) REVERT: X 87 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8579 (mmtm) REVERT: X 129 ASP cc_start: 0.8228 (p0) cc_final: 0.7935 (p0) REVERT: Y 87 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8655 (mttm) REVERT: Z 87 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8562 (mmtp) REVERT: Z 137 LYS cc_start: 0.8923 (mttt) cc_final: 0.8653 (mttp) REVERT: a 87 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8658 (mttm) REVERT: b 87 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8549 (mttm) REVERT: c 25 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: c 87 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8720 (mmtp) REVERT: c 121 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7854 (m-10) REVERT: d 43 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8796 (p) REVERT: d 87 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8727 (mmtm) REVERT: e 87 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8532 (mttp) REVERT: f 87 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8564 (mmtm) REVERT: g 87 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8725 (mmtp) REVERT: g 121 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: h 87 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8747 (mmtp) REVERT: i 55 ASN cc_start: 0.6943 (t0) cc_final: 0.6634 (t0) REVERT: i 87 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8574 (mmtm) REVERT: i 92 TYR cc_start: 0.8927 (m-80) cc_final: 0.8637 (m-80) REVERT: j 1 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.4367 (mtt) REVERT: k 87 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8526 (mmtm) REVERT: l 25 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7516 (t80) REVERT: l 43 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9031 (p) REVERT: l 87 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8531 (mttm) REVERT: m 87 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8623 (mmtm) REVERT: n 22 TRP cc_start: 0.8030 (m100) cc_final: 0.7663 (m100) REVERT: n 87 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8652 (mmtp) REVERT: n 129 ASP cc_start: 0.8421 (p0) cc_final: 0.8007 (p0) REVERT: o 22 TRP cc_start: 0.8076 (m100) cc_final: 0.7630 (m100) REVERT: o 87 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8610 (mmtm) REVERT: o 129 ASP cc_start: 0.8206 (p0) cc_final: 0.7954 (p0) outliers start: 131 outliers final: 100 residues processed: 676 average time/residue: 0.5702 time to fit residues: 618.3798 Evaluate side-chains 700 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 589 time to evaluate : 4.569 ------------------------------------------------------------------------------- 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 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 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 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 J residue 66 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain L residue 1 MET 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 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 T residue 43 THR Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 14 LEU 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 1 MET 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 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 49 ASP Chi-restraints excluded: chain Z residue 121 PHE Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain a residue 136 ASN Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 25 TYR Chi-restraints excluded: chain c residue 121 PHE 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 78 ILE 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 2 THR 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 j residue 1 MET 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 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 13 VAL Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR 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 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 503 optimal weight: 5.9990 chunk 530 optimal weight: 0.7980 chunk 483 optimal weight: 10.0000 chunk 515 optimal weight: 2.9990 chunk 529 optimal weight: 5.9990 chunk 310 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 404 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 465 optimal weight: 0.9980 chunk 487 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 51 ASN S 33 GLN m 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41656 Z= 0.193 Angle : 0.504 8.623 57236 Z= 0.276 Chirality : 0.049 0.289 7749 Planarity : 0.004 0.048 6970 Dihedral : 4.312 59.301 5954 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.31 % Allowed : 23.64 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 5658 helix: 2.36 (0.13), residues: 1271 sheet: -1.49 (0.11), residues: 2173 loop : -1.09 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP d 22 HIS 0.001 0.000 HIS Z 130 PHE 0.016 0.001 PHE G 121 TYR 0.047 0.001 TYR Z 53 ARG 0.001 0.000 ARG O 110 *********************** 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 756 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 651 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8587 (mmtp) REVERT: B 87 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8667 (mmtp) REVERT: C 37 LEU cc_start: 0.9355 (mt) cc_final: 0.9025 (mt) REVERT: C 87 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8552 (mmtm) REVERT: D 34 GLN cc_start: 0.9287 (tp40) cc_final: 0.9034 (mm-40) REVERT: D 87 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8585 (mmtm) REVERT: D 95 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: E 87 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8373 (mmtm) REVERT: F 87 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8578 (mttm) REVERT: G 87 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8556 (mmtm) REVERT: H 87 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8516 (mmtm) REVERT: H 137 LYS cc_start: 0.8887 (mttm) cc_final: 0.8635 (mttm) REVERT: I 87 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8561 (mmtm) REVERT: I 121 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6937 (m-10) REVERT: J 87 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8516 (mmtp) REVERT: K 87 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8486 (mmtm) REVERT: L 22 TRP cc_start: 0.8244 (m100) cc_final: 0.7658 (m100) REVERT: L 87 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8652 (mmtp) REVERT: M 87 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8653 (mttm) REVERT: N 87 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8733 (mmtp) REVERT: O 87 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8596 (mttm) REVERT: P 87 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8555 (mmtm) REVERT: Q 87 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8729 (mmtp) REVERT: R 87 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8781 (mmtp) REVERT: S 37 LEU cc_start: 0.9410 (mt) cc_final: 0.9109 (mt) REVERT: S 61 GLN cc_start: 0.8061 (tp40) cc_final: 0.7831 (mt0) REVERT: S 87 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8636 (mmtm) REVERT: S 129 ASP cc_start: 0.8331 (p0) cc_final: 0.8052 (p0) REVERT: T 43 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.9001 (p) REVERT: T 87 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8574 (mttm) REVERT: U 87 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8450 (mmtp) REVERT: V 87 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8668 (mmtp) REVERT: W 87 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8610 (mmtm) REVERT: X 43 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9012 (p) REVERT: X 87 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8564 (mmtm) REVERT: X 129 ASP cc_start: 0.8152 (p0) cc_final: 0.7860 (p0) REVERT: Y 48 LYS cc_start: 0.9316 (mtmt) cc_final: 0.9075 (mtmm) REVERT: Y 87 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8580 (mmtp) REVERT: Z 87 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8564 (mmtm) REVERT: Z 95 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7522 (mp0) REVERT: Z 137 LYS cc_start: 0.8847 (mttt) cc_final: 0.8497 (mttp) REVERT: a 87 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8657 (mttm) REVERT: b 87 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8552 (mttm) REVERT: c 87 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8635 (mmtm) REVERT: d 43 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8748 (p) REVERT: d 87 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8770 (mmtm) REVERT: e 87 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8537 (mttp) REVERT: f 87 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8545 (mmtm) REVERT: g 87 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8679 (mmtp) REVERT: g 121 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: h 87 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8760 (mmtp) REVERT: i 87 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8545 (mmtm) REVERT: i 92 TYR cc_start: 0.8841 (m-80) cc_final: 0.8472 (m-80) REVERT: k 87 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8508 (mmtm) REVERT: l 25 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7432 (t80) REVERT: l 43 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.9021 (p) REVERT: l 87 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8535 (mttm) REVERT: m 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8643 (mmtm) REVERT: n 87 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8651 (mmtp) REVERT: n 129 ASP cc_start: 0.8434 (p0) cc_final: 0.8063 (p0) REVERT: o 87 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8601 (mmtm) REVERT: o 129 ASP cc_start: 0.8165 (p0) cc_final: 0.7941 (p0) outliers start: 105 outliers final: 83 residues processed: 714 average time/residue: 0.5324 time to fit residues: 615.9254 Evaluate side-chains 703 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 612 time to evaluate : 4.508 ------------------------------------------------------------------------------- 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 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 95 GLU 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 121 PHE Chi-restraints excluded: chain H residue 13 VAL 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 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 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 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 R residue 13 VAL Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 121 PHE Chi-restraints excluded: chain T residue 43 THR 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 14 LEU 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 25 TYR 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 c residue 4 LEU 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 43 THR Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain e residue 13 VAL 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 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 121 PHE Chi-restraints excluded: chain h residue 13 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 102 SER 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 k residue 118 ILE 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 43 THR 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 o residue 121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 513 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 545 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 378 optimal weight: 1.9990 chunk 571 optimal weight: 8.9990 chunk 526 optimal weight: 0.8980 chunk 455 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 351 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 ASN e 55 ASN f 55 ASN m 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41656 Z= 0.213 Angle : 0.510 8.064 57236 Z= 0.280 Chirality : 0.048 0.267 7749 Planarity : 0.004 0.048 6970 Dihedral : 4.303 58.883 5954 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.15 % Allowed : 24.30 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5658 helix: 2.34 (0.13), residues: 1271 sheet: -1.46 (0.11), residues: 2173 loop : -1.00 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 22 HIS 0.001 0.000 HIS V 130 PHE 0.014 0.001 PHE G 121 TYR 0.040 0.001 TYR Z 53 ARG 0.001 0.000 ARG I 110 ********************** 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 702 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 604 time to evaluate : 4.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8633 (mmtp) REVERT: B 87 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8732 (mmtp) REVERT: C 87 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8548 (mmtm) REVERT: D 34 GLN cc_start: 0.9302 (tp40) cc_final: 0.9051 (mm-40) REVERT: D 87 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8585 (mmtm) REVERT: D 95 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: E 87 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8371 (mmtm) REVERT: F 87 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8553 (mttm) REVERT: G 87 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8586 (mmtm) REVERT: H 87 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8524 (mmtm) REVERT: H 137 LYS cc_start: 0.8888 (mttm) cc_final: 0.8624 (mttm) REVERT: I 87 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8562 (mmtm) REVERT: I 121 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: J 87 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8527 (mmtp) REVERT: K 87 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8476 (mmtm) REVERT: L 87 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8648 (mmtp) REVERT: M 87 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8649 (mttm) REVERT: N 87 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8713 (mmtp) REVERT: O 87 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8592 (mttm) REVERT: P 87 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8557 (mmtm) REVERT: Q 87 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8767 (mmtp) REVERT: R 87 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8772 (mmtp) REVERT: S 37 LEU cc_start: 0.9411 (mt) cc_final: 0.9136 (mt) REVERT: S 61 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: S 87 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8649 (mmtm) REVERT: S 129 ASP cc_start: 0.8294 (p0) cc_final: 0.8028 (p0) REVERT: T 43 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8992 (p) REVERT: T 87 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8571 (mttm) REVERT: U 87 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8428 (mmtp) REVERT: V 87 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8675 (mmtp) REVERT: W 87 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8583 (mmtm) REVERT: X 43 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9005 (p) REVERT: X 87 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8553 (mmtm) REVERT: X 129 ASP cc_start: 0.8166 (p0) cc_final: 0.7872 (p0) REVERT: Y 48 LYS cc_start: 0.9317 (mtmt) cc_final: 0.9078 (mtmm) REVERT: Y 87 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8587 (mmtm) REVERT: Y 112 VAL cc_start: 0.9148 (t) cc_final: 0.8893 (m) REVERT: Z 87 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8565 (mmtm) REVERT: Z 95 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7458 (mp0) REVERT: Z 137 LYS cc_start: 0.8863 (mttt) cc_final: 0.8503 (mttp) REVERT: a 87 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8676 (mttm) REVERT: b 87 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8551 (mttm) REVERT: c 87 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8651 (mmtm) REVERT: d 43 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8770 (p) REVERT: d 87 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8733 (mmtm) REVERT: e 87 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8536 (mttp) REVERT: f 87 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8531 (mmtm) REVERT: f 95 GLU cc_start: 0.7817 (mp0) cc_final: 0.7511 (mp0) REVERT: g 87 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8688 (mmtp) REVERT: g 121 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7621 (m-80) REVERT: h 87 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8774 (mmtp) REVERT: i 87 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8572 (mmtm) REVERT: k 87 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8507 (mmtm) REVERT: l 25 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7466 (t80) REVERT: l 43 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9039 (p) REVERT: l 87 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8538 (mttm) REVERT: m 87 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8645 (mmtm) REVERT: n 87 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8618 (mmtp) REVERT: n 129 ASP cc_start: 0.8445 (p0) cc_final: 0.8079 (p0) REVERT: o 87 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8611 (mmtm) outliers start: 98 outliers final: 83 residues processed: 663 average time/residue: 0.5413 time to fit residues: 577.7724 Evaluate side-chains 685 residues out of total 4551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 593 time to evaluate : 4.519 ------------------------------------------------------------------------------- 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 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 95 GLU 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 121 PHE Chi-restraints excluded: chain H residue 13 VAL 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 J residue 66 VAL Chi-restraints excluded: chain K residue 121 PHE Chi-restraints excluded: chain L residue 13 VAL 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 61 GLN Chi-restraints excluded: chain T residue 43 THR 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 14 LEU 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 25 TYR 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 b residue 13 VAL Chi-restraints excluded: chain c residue 4 LEU 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 43 THR Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain e residue 13 VAL 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 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 13 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 102 SER 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 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 13 VAL Chi-restraints excluded: chain l residue 25 TYR Chi-restraints excluded: chain l residue 43 THR 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 o residue 121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 279 optimal weight: 0.5980 chunk 361 optimal weight: 9.9990 chunk 485 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 419 optimal weight: 0.3980 chunk 67 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 456 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 468 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN N 51 ASN P 51 ASN Q 33 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 ASN b 51 ASN m 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100348 restraints weight = 57067.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104633 restraints weight = 30672.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107436 restraints weight = 19513.457| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41656 Z= 0.181 Angle : 0.501 8.532 57236 Z= 0.274 Chirality : 0.048 0.237 7749 Planarity : 0.004 0.048 6970 Dihedral : 4.187 59.082 5954 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.00 % Allowed : 24.59 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 5658 helix: 2.44 (0.13), residues: 1271 sheet: -1.37 (0.11), residues: 2173 loop : -0.94 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP d 22 HIS 0.002 0.000 HIS o 130 PHE 0.014 0.001 PHE G 121 TYR 0.037 0.001 TYR h 53 ARG 0.001 0.000 ARG T 110 =============================================================================== Job complete usr+sys time: 10160.66 seconds wall clock time: 184 minutes 30.28 seconds (11070.28 seconds total)